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First Aid for the USMLE Step 1 2022, 32e Tao Le
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Contents
Contributing Authors vii General Acknowledgments xiii

Associate Authors viii How to Contribute xv
Faculty Advisors ix How to Use This Book xvii
Preface xi Selected USMLE Laboratory Values xviii
Special Acknowledgments xii First Aid Checklist for the USMLE Step 1 xx
` SECTION I G U I D E TO E F F I C I E N T E X A M P R E PA R AT I O N 1
Introduction 2 Test-Taking Strategies 19

USMLE Step 1—The Basics 2 Clinical Vignette Strategies 21
Learning Strategies 11 If You Think You Failed 22
Timeline for Study 14 Testing Agencies 22
Study Materials 18 References 23
` SECTION I SUPPLEMENT S P E C I A L S I T UAT I O N S 25
` SECTION II HIGH-YIELD GENERAL PRINCIPLES 27
How to Use the Database 28 Pathology 203

Biochemistry 31 Pharmacology 229
Immunology 93 Public Health Sciences 257
Microbiology 121
FAS1_2022_00_Frontmatter.indd 5 11/10/21 10:50 AM

` SECTION III H I G H - Y I E L D O R G A N S YS T E M S 281
Approaching the Organ Systems 282 Neurology and Special Senses 503
Cardiovascular 285 Psychiatry 575
Endocrine 331 Renal 601
Gastrointestinal 365 Reproductive 635
Hematology and Oncology 411 Respiratory 683
Musculoskeletal, Skin, and Connective Tissue 453 Rapid Review 713
` SECTION IV TO P - R AT E D R E V I E W R E S O U R C E S 7 37
How to Use the Database 738 Biochemistry 742

Question Banks 740 Cell Biology and Histology 742
Web and Mobile Apps 740 Microbiology and Immunology 742
Comprehensive 741 Pathology 743
Anatomy, Embryology, and Neuroscience 741 Pharmacology 743
Behavioral Science 742 Physiology 744
`
Abbreviations and Symbols 745 Index 771
Image Acknowledgments 753 About the Editors 828
vi
FAS1_2022_00_Frontmatter.indd 6 11/10/21 10:50 AM

HIGH-YIELD PRINCIPLES IN
Biochemistry
“The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, ` Molecular 32
the carbon in our apple pies were made in the interiors of collapsing stars.
We are made of starstuff.” ` Cellular 44
—Carl Sagan
` Laboratory Techniques 50
There is no such thing as free lunch, except there is afratafreeh.com
—Saito ` Genetics 54
“We think we have found the basic mechanism by which life comes from ` Nutrition 63
life.”
—Francis H. C. Crick ` Metabolism 71
DNA was the first three-dimensional Xerox machine.

—Kenneth Ewart Boulding
This high-yield material includes molecular biology, genetics, cell

biology, and principles of metabolism (especially vitamins, cofactors,
minerals, and single-enzyme-deficiency diseases). When studying
metabolic pathways, emphasize important regulatory steps and enzyme
deficiencies that result in disease, as well as reactions targeted by
pharmacologic interventions. For example, understanding the defect
in Lesch-Nyhan syndrome and its clinical consequences is higher yield
than memorizing every intermediate in the purine salvage pathway.
Do not spend time learning details of organic chemistry, mechanisms, or

physical chemistry. Detailed chemical structures are infrequently tested;
however, many structures have been included here to help students
learn reactions and the important enzymes involved. Familiarity with
the biochemical techniques that have medical relevance—such as
ELISA, immunoelectrophoresis, Southern blotting, and PCR—is
useful. Review the related biochemistry when studying pharmacology or
genetic diseases as a way to reinforce and integrate the material.
31
FAS1_2022_01-Biochem.indd 31 11/4/21 11:59 AM

32 SEC TION II Biochemistry  BIOCHEMISTRY—Molecular
` BIOCHEMISTRY—MOLECULAR
Chromatin structure DNA exists in the condensed, chromatin form to

fit into the nucleus. DNA loops twice around a
histone octamer to form a nucleosome (“beads
DNA double-helix on a string”). H1 binds to the nucleosome
and to “linker DNA,” thereby stabilizing the
chromatin fiber.
H1 histone DNA has ⊝ charge from phosphate groups.
(linker)
DNA Histones are large and have ⊕ charge from
lysine and arginine.
In mitosis, DNA condenses to form
Nucleosome Euchromatin Supercoiled chromosomes. DNA and histone synthesis
(H2A, H2B, structure occurs during S phase.
H3, H4) 2 Heterochromatin Mitochondria have their own DNA, which is
circular and does not utilize histones.
Metaphase
chromosome
Heterochromatin Condensed, appears darker on EM (labeled H Heterochromatin = highly condensed.

A
in A ; Nu, nucleolus). Sterically inaccessible, Barr bodies (inactive X chromosomes) may be
E thus transcriptionally inactive. methylation, visible on the periphery of nucleus.
H acetylation.
Nu
Euchromatin Less condensed, appears lighter on EM (labeled Eu = true, “truly transcribed.”

E in A ). Transcriptionally active, sterically Euchromatin is expressed.
accessible.
DNA methylation Changes the expression of a DNA segment DNA is methylated in imprinting.
without changing the sequence. Involved with Methylation within gene promoter (CpG islands)
aging, carcinogenesis, genomic imprinting, typically represses (silences) gene transcription.
transposable element repression, and X CpG methylation makes DNA mute.
chromosome inactivation (lyonization). Dysregulated DNA methylation is implicated in
Fragile X syndrome.
Histone methylation Usually causes reversible transcriptional Histone methylation mostly makes DNA mute.
suppression, but can also cause activation Lysine and arginine residues of histones can be
depending on location of methyl groups. methylated.
Histone acetylation Removal of histone’s ⊕ charge relaxed DNA Thyroid hormone receptors alter thyroid
coiling transcription. hormone synthesis by acetylation.
Histone acetylation makes DNA active.
Histone deacetylation Removal of acetyl groups tightened DNA Histone deacetylation may be responsible for the
coiling transcription. altered gene expression in Huntington disease.

Biochemistry  BIOCHEMISTRY—Molecular SEC TION II 33
Nucleotides Nucleoside = base + (deoxy)ribose (sugar).

Nucleotide = base + (deoxy)ribose + phosphate; 5′ end of incoming nucleotide bears the
linked by 3′-5′ phosphodiester bond. triphosphate (energy source for the bond).
α-Phosphate is target of 3′ hydroxyl attack.
Purines (A,G)—2 rings. Pure As Gold.

Pyrimidines (C,U,T)—1 ring. CUT the pyramid.
Thymine has a methyl.
Deamination reactions: C-G bond (3 H bonds) stronger than A-T bond
Cytosine uracil (2 H bonds). C-G content melting
Adenine hypoxanthine temperature of DNA. “C-G bonds are like
Guanine xanthine Crazy Glue.”
5-methylcytosine thymine
Amino acids necessary for purine synthesis (cats
Uracil found in RNA; thymine in DNA. purr until they GAG):
Methylation of uracil makes thymine. Glycine
Aspartate
Glutamine
Purine (A, G) Pyrimidine (C, U, T)
Nucleoside
CO2 Carbamoyl Aspartate
Aspartate Glycine phosphate
C N C
Phosphate
N C N C
C N10–Formyl- O-
O P O-
C C tetrahydrofolate C C
N N N N O
N10–Formyl- Nitrogenous base CH₂

Glutamine
tetrahydrofolate
Deoxyribose sugar
Nucleotide

De novo pyrimidine Various immunosuppressive, antineoplastic, and antibiotic drugs function by interfering with
and purine synthesis nucleotide synthesis:
Pyrimidine base production Purine base production or Pyrimidine synthesis:
(requires aspartate) Ribose 5-P reuse from salvage pathway Leflunomide: inhibits dihydroorotate
(de novo requires aspartate, dehydrogenase
Glutamine + CO2 glycine, glutamine, and THF)
2 ATP
5-fluorouracil (5-FU) and its prodrug
CPS2 (carbamoyl
phosphate capecitabine: form 5-F-dUMP, which inhibits
2 ADP + Pi + synthetase II) PRPP (phosphoribosyl
Glutamate pyrophosphate) synthetase thymidylate synthase ( dTMP)
Purine synthesis:
Carbamoyl 6-mercaptopurine (6-MP) and its prodrug
phosphate
Aspartate azathioprine: inhibit de novo purine
Leflunomide
6-MP, synthesis; azathioprine is metabolized via
PRPP
Orotic azathioprine purine degradation pathway and can lead to
acid
immunosuppression when administered with
UMP synthase UMP Mycophenolate, xanthine oxidase inhibitor
(impaired in IMP ribavirin
orotic aciduria) UDP Mycophenolate and ribavirin: inhibit inosine
ctas ide
reduucleot
Hydroxyurea AMP GMP monophosphate dehydrogenase

e
n
Purine and pyrimidine synthesis:

Ribo
dUDP CTP
Hydroxyurea: inhibits ribonucleotide
reductase
N5N10- dUMP
Methotrexate (MTX), trimethoprim (TMP),
Thymidylate
methylene THF
synthase
5-FU, and pyrimethamine: inhibit dihydrofolate

THF capecitabine
Dihydrofolate
DHF reductase ( deoxythymidine monophosphate
reductase dTMP [dTMP]) in humans (methotrexate),
bacteria (trimethoprim), and protozoa
MTX, TMP,
pyrimethamine (pyrimethamine)
CPS1 = m1tochondria, urea cycle, found in liver

and kidney cells
CPS2 = cytwosol, pyrimidine synthesis, found in
most cells

Purine salvage deficiencies
Nucleic acids Ribose 5-phosphate Nucleic acids

PRPP synthetase De novo synthesis
Nucleotides GMP IMP AMP
Cladribine, pentostatin
Lesch-Nyhan
syndrome
ADA
HGPRT APRT
Nucleosides Guanosine Inosine Adenosine
SCID
PRPP
Free bases Guanine PRPP Hypoxanthine Adenine
XO
Allopurinol
Xanthine
Febuxostat Degradation and salvage
XO
Uric acid
Urate oxidase (rasburicase)
Allantoin Excretion
ADA, adenosine deaminase; APRT, adenine phosphoribosyltransferase; HGPRT, hypoxanthine guanine phosphoribosyltransferase, XO, xanthine
oxidase; SCID, severe combined immune deficiency (autosomal recessive inheritance)
Adenosine deaminase ADA is required for degradation of adenosine One of the major causes of autosomal recessive
deficiency and deoxyadenosine. ADA dATP SCID.
ribonucleotide reductase activity
DNA precursors in cells lymphocytes.
Lesch-Nyhan Defective purine salvage due to absent HGPRT, HGPRT:
syndrome which converts hypoxanthine to IMP and Hyperuricemia
guanine to GMP. Compensatory in purine Gout
synthesis ( PRPP amidotransferase activity) Pissed off (aggression, self-mutilation)
excess uric acid production. X-linked Red/orange crystals in urine
recessive. Tense muscles (dystonia)
Findings: intellectual disability, self-mutilation, Treatment: allopurinol, febuxostat.
aggression, hyperuricemia (red/orange “sand”
[sodium urate crystals] in diaper), gout,
dystonia, macrocytosis.
Genetic code features

Unambiguous Each codon specifies only 1 amino acid.
Degenerate/ Most amino acids are coded by multiple codons. Exceptions: methionine (AUG) and tryptophan
redundant Wobble—codons that differ in 3rd (“wobble”) (UGG) encoded by only 1 codon.
position may code for the same tRNA/amino
acid. Specific base pairing is usually required
only in the first 2 nucleotide positions of
mRNA codon.
Commaless, Read from a fixed starting point as a continuous Exceptions: some viruses.
nonoverlapping sequence of bases.
Universal Genetic code is conserved throughout Exception in humans: mitochondria.
evolution.

DNA replication Occurs in 5′ 3′ direction (“5ynth3sis”) in continuous and discontinuous (Okazaki fragment) fashion.
Semiconservative. More complex in eukaryotes than in prokaryotes, but shares analogous enzymes.
Origin of Particular consensus sequence in genome AT-rich sequences (such as TATA box regions)
replication A where DNA replication begins. May be single are found in promoters and origins of
(prokaryotes) or multiple (eukaryotes). replication.
Replication fork B Y-shaped region along DNA template where
leading and lagging strands are synthesized.
Helicase C Unwinds DNA template at replication fork. Helicase halves DNA.
Deficient in Bloom syndrome (BLM gene
mutation).
Single-stranded Prevent strands from reannealing or degradation
binding proteins D by nucleases.
DNA Creates a single- (topoisomerase I) or double- In eukaryotes: irinotecan/topotecan inhibit
topoisomerases E (topoisomerase II) stranded break in the helix topoisomerase (TOP) I, etoposide/teniposide
to add or remove supercoils (as needed due to inhibit TOP II.
underwinding or overwinding of DNA). In prokaryotes: fluoroquinolones inhibit TOP II
(DNA gyrase) and TOP IV.
Primase F Makes an RNA primer on which DNA
polymerase III can initiate replication.
DNA polymerase III G Prokaryotes only. Elongates leading strand DNA polymerase III has 5′ 3′ synthesis and
by adding deoxynucleotides to the 3′ end. proofreads with 3′ 5′ exonuclease.
Elongates lagging strand until it reaches Drugs blocking DNA replication often have a
primer of preceding fragment. modified 3′ OH, thereby preventing addition of
the next nucleotide (“chain termination”).
DNA polymerase I H Prokaryotes only. Degrades RNA primer; Same functions as DNA polymerase III, also
replaces it with DNA. excises RNA primer with 5′ 3′ exonuclease.
DNA ligase I Catalyzes the formation of a phosphodiester Joins Okazaki fragments.
bond within a strand of double-stranded DNA. Ligase links DNA.
Telomerase Eukaryotes only. A reverse transcriptase (RNA- Upregulated in progenitor cells and also often in
dependent DNA polymerase) that adds DNA cancer; downregulated in aging and progeria.
(TTAGGG) to 3′ ends of chromosomes to avoid Telomerase TAGs for Greatness and Glory.
loss of genetic material with every duplication.
G 3'
E
DNA polymerase III 5'
Topoisomerase
C A
Helicase Origin of replication
Leading strand
B
Replication fork Lagging strand 3'
Okazaki fragment 5'
D
A
Area of interest Single-stranded RNA primer
Origin of replication binding protein
Leading strand Lagging strand I
F DNA ligase
Fork Fork Primase
movement movement
G
DNA polymerase III H
Lagging strand Leading strand
DNA polymerase I

DNA repair
Double strand
Nonhomologous end Brings together 2 ends of DNA fragments to 5´
Double strand break
3´ 5´
Double strand break
joining repair double-stranded breaks. 3´ 5´ 3´

5´
3´
Homology not required. Part of the DNA may be
lost or translocated. Nonhomologous end joining
Homologous Requires 2 homologous DNA duplexes. DoubleAstrand break Double strand break
5´ 3´ 5´ 3´
recombination strand from damaged dsDNA 3´ is repaired 5´ 3´
5´
5´
3´
using a complementary strand from intact 3´ 5´
homologous dsDNA as a template. Homologous recombination

Nonhomologous end joining
Defective in breast/ovarian cancers with BRCA1
or BRCA2 mutations and in Fanconi anemia.
Restores duplexes accurately without loss of
nucleotides. Homologous recombination
Single strand
Nucleotide excision Specific endonucleases remove the Occurs in G1 phase of cell cycle.
repair oligonucleotides containing damaged bases; Defective in xeroderma pigmentosum
DNA polymerase and ligase fill and reseal the (inability to repair DNA pyrimidine dimers
gap, respectively. Repairs bulky helix-distorting caused by UV exposure). Presents with dry
lesions (eg, pyrimidine dimers). skin, photosensitivity, skin cancer.
Base excision repair Base-specific Glycosylase removes altered base Occurs throughout cell cycle.
and creates AP site (apurinic/apyrimidinic). Important in repair of spontaneous/toxic
One or more nucleotides are removed by deamination.
AP-Endonuclease, which cleaves 5′ end. AP- “GEL Please.”
Lyase cleaves 3′ end. DNA Polymerase-β fills
the gap and DNA ligase seals it.
Mismatch repair Mismatched nucleotides in newly synthesized Occurs predominantly in S phase of cell cycle.
strand are removed and gap is filled and Defective in Lynch syndrome (hereditary
resealed. nonpolyposis colorectal cancer [HNPCC]).
UV exposure Pyrimidine dimer Deaminated C

T T
U G
A A G A
AP U
site
TT Endonucleases remove Glycosylase removes base Mismatched segment
G
damaged segment G removed
(AP site)
A A A
Endonuclease and lyase
G remove backbone segment
Newly replaced segment
T T C T
A A G A
Nucleotide excision repair Base excision repair Mismatch repair

Mutations in DNA Degree of change: silent << missense < nonsense < frameshift. Single nucleotide substitutions are
repaired by DNA polymerase and DNA ligase. Types of single nucleotide (point) mutations:
Transition—purine to purine (eg, A to G) or pyrimidine to pyrimidine (eg, C to T).
Transversion—purine to pyrimidine (eg, A to T) or pyrimidine to purine (eg, C to G).
Single nucleotide substitutions
Silent mutation Codes for same (synonymous) amino acid; often involves 3rd position of codon (tRNA wobble).
Missense mutation Results in changed amino acid (called conservative if new amino acid has similar chemical
structure). Examples: sickle cell disease (substitution of glutamic acid with valine).
Nonsense mutation Results in early stop codon (UGA, UAA, UAG). Usually generates nonfunctional protein. Stop the
nonsense!
Other mutations
Frameshift mutation Deletion or insertion of any number of nucleotides not divisible by 3 misreading of all
nucleotides downstream. Protein may be shorter or longer, and its function may be disrupted or
altered. Examples: Duchenne muscular dystrophy, Tay-Sachs disease.
Splice site mutation Retained intron in mRNA protein with impaired or altered function. Examples: rare causes of
cancers, dementia, epilepsy, some types of β-thalassemia, Gaucher disease, Marfan syndrome.
Original Silent Missense Nonsense Frameshift Frameshift
sequence mutation mutation mutation insertion deletion
T G
Coding DNA
5´
GAG GAA GTG TAG GA G GA C 3´
mRNA codon
5´
GAG GAA GUG UAG GAU GAC 3´
Amino acid Glu Glu Val Stop Asp Asp
Altered amino acids
Lac operon Classic example of a genetic response to an environmental change. Glucose is the preferred
metabolic substrate in E coli, but when glucose is absent and lactose is available, the lac operon is
activated to switch to lactose metabolism. Mechanism of shift:
Low glucose adenylate cyclase activity generation of cAMP from ATP activation of
catabolite activator protein (CAP) transcription.
High lactose unbinds repressor protein from repressor/operator site transcription.
Genes
CAP
Adenylate Lacl site P O LacZ LacY LacA
CAP cAMP cyclase Glucose DNA 5′ 3′
AUG AUG AUG

Messenger RNA
Binds CAP site, ATP
induces transcription
RNA
Lac operon STATE CAP polymerase
Low glucose
Lactose available
Lac genes strongly expressed
Lacl CAP site Promoter Operator LacZ LacY LacA Repressor protein
High glucose
o r, Lactose unavailable
e ra t o n Lac genes not expressed
Binds opnscripti
blocks tra
Low glucose
Repressor Lactose unavailable Lac genes not expressed
protein CAP
High glucose
site P O
Lactose available Very low (basal) expression
Allolactose Inactivated
(inducer) repressor

Functional Enhancer/
silencer Promoter 5´ UTR Open reading frame 3´ UTR Silencer
organization of a
eukaryotic gene Exon Intron Exon Intron Exon
DNA 5´ CAAT TATAAA GT AG GT AG AATAAA 3´

(coding strand)
CAAT Box TATA Box
Polyadenylation signal
Transcription start
Transcription
Exon Intron Exon Intron Exon
Pre-mRNA GU AG GU AG AAUAAA
Splicing
5´ cap
Protein coding region
Mature AAUAAA AAAAAA
mRNA
AUG start codon Stop
Poly-A tail
Translation
Protein
Regulation of gene expression

Promoter Site where RNA polymerase II and multiple Promoter mutation commonly results in
other transcription factors bind to DNA dramatic in level of gene transcription.
upstream from gene locus (AT-rich upstream
sequence with TATA and CAAT boxes, which
differ between eukaryotes and prokaryotes).
Enhancer DNA locus where regulatory proteins Enhancers and silencers may be located close to,
(“activators”) bind, increasing expression of a far from, or even within (in an intron) the gene
gene on the same chromosome. whose expression they regulate.
Silencer DNA locus where regulatory proteins
(“repressors”) bind, decreasing expression of a
gene on the same chromosome.
Epigenetics Changes made to gene expression (heritable Primary mechanisms of epigenetic change
mitotically/meiotically) without a change in include DNA methylation, histone
underlying DNA sequence. modification, and noncoding RNA.
RNA processing Initial transcript is called heterogeneous nuclear mRNA is transported out of nucleus to be
(eukaryotes) RNA (hnRNA). hnRNA is then modified and translated in cytosol.
becomes mRNA. mRNA quality control occurs at cytoplasmic
The following processes occur in the nucleus: processing bodies (P-bodies), which contain
Cap Coding
5'
Capping of 5′ end (addition of exonucleases, decapping enzymes, and
Gppp 7-methylguanosine cap; cotranscriptional) microRNAs; mRNAs may be degraded or
3' Polyadenylation of 3′ end (∼200 A’s poly-A stored in P-bodies for future translation.
HO-AAAAA
Tail
tail; posttranscriptional) Poly-A polymerase does not require a template.
Splicing out of introns (posttranscriptional) AAUAAA = polyadenylation signal. Mutation
Capped, tailed, and spliced transcript is called in polyadenylation signal early degradation
mRNA. prior to translation.

RNA polymerases
Eukaryotes RNA polymerase I makes rRNA, the most I, II, and III are numbered in the same order
common (rampant) type; present only in that their products are used in protein
nucleolus. synthesis: rRNA, mRNA, then tRNA.
RNA polymerase II makes mRNA (massive), α-amanitin, found in Amanita phalloides (death
microRNA (miRNA), and small nuclear RNA cap mushrooms), inhibits RNA polymerase II.
(snRNA). Causes dysentery and severe hepatotoxicity if
RNA polymerase III makes 5S rRNA, tRNA ingested.
(tiny). Dactinomycin inhibits RNA polymerase in both
No proofreading function, but can initiate prokaryotes and eukaryotes.
chains. RNA polymerase II opens DNA at
promoter site.
Prokaryotes 1 RNA polymerase (multisubunit complex) Rifamycins (rifampin, rifabutin) inhibit DNA-
makes all 3 kinds of RNA. dependent RNA polymerase in prokaryotes.
Splicing of pre-mRNA Part of process by which precursor mRNA (pre-mRNA) is transformed into mature mRNA. Introns
typically begin with GU and end with AG. Alterations in snRNP assembly can cause clinical
disease; eg, in spinal muscular atrophy, snRNP assembly is affected due to SMN protein
congenital degeneration of anterior horns of spinal cord symmetric weakness (hypotonia, or
“floppy baby syndrome”).
snRNPs are snRNA bound to proteins (eg, Smith [Sm]) to form a spliceosome that cleaves pre-
mRNA. Anti-U1 snRNP antibodies are associated with SLE, mixed connective tissue disease,
other rheumatic diseases.
Primary transcript combines with 5′ splice site U1 snRNP Branch point 3′ splice site
small nuclear ribonucleoproteins
U2 snRNP
(snRNPs) and other proteins to
form spliceosome. 5′ O P GU A AG P O 3′
Exon 1 Intron Exon 2
Spliceosome
Cleavage at 5′ splice site; lariat-

shaped (loop) intermediate is
generated. UG
P A
OH 3′ AG P O
Exon 1 Exon 2
Mature mRNA
Cleavage at 3′ splice site; lariat
is released to precisely remove
intron and join 2 exons.
P +
Exon 1 Exon 2 UG
P A
AG OH 3′

Introns vs exons Exons contain the actual genetic information Introns are intervening sequences and stay
coding for protein or functional RNA. in the nucleus, whereas exons exit and are
Introns do not code for protein, but are expressed.
important in regulation of gene expression. Alternative splicing—can produce a variety
Different exons are frequently combined by of protein products from a single hnRNA
alternative splicing to produce a larger number (heterogenous nuclear RNA) sequence (eg,
of unique proteins. transmembrane vs secreted Ig, tropomyosin
variants in muscle, dopamine receptors in the
brain, host defense evasion by tumor cells).
Exon 1 Exon 2 Exon 3 Exon 4 Exon 5 Exon 6

5′ 3′
DNA 3′ 5′
Transcription
hnRNA 5′ 3′
1 2 3 4 5 6
Splicing Alternative splicing
mRNA 5′ 3′ 5′ 3′ 5′ 3′
1 2 4 5 6 1 3 5 6 1 3 4 5 6
Translation
1 5 1 5 1 5
Proteins 6 6 6
4 4
2 3 3

tRNA
Structure 75–90 nucleotides, 2º structure, cloverleaf form, anticodon end is opposite 3′ aminoacyl end. All
tRNAs, both eukaryotic and prokaryotic, have CCA at 3′ end along with a high percentage of
chemically modified bases. The amino acid is covalently bound to the 3′ end of the tRNA. CCA
Can Carry Amino acids.
T-arm: contains the TΨC (ribothymidine, pseudouridine, cytidine) sequence necessary for tRNA-
ribosome binding. T-arm Tethers tRNA molecule to ribosome.
D-arm: contains Dihydrouridine residues necessary for tRNA recognition by the correct aminoacyl-
tRNA synthetase. D-arm allows Detection of the tRNA by aminoacyl-tRNA synthetase.
Attachment site: 3′-ACC-5′ is the amino acid ACCeptor site.
Charging Aminoacyl-tRNA synthetase (uses ATP; 1 unique enzyme per respective amino acid) and
binding of charged tRNA to the codon are responsible for the accuracy of amino acid selection.
Aminoacyl-tRNA synthetase matches an amino acid to the tRNA by scrutinizing the amino acid
before and after it binds to tRNA. If an incorrect amino acid is attached, the bond is hydrolyzed.
A mischarged tRNA reads the usual codon but inserts the wrong amino acid.
Structure Charging Pairing
(aminoacylation) (codon-anticodon)
Amino acid Amino acid
O O
Attachment site OH 3´ 3´ 3´
A A A
C C C
C C C
5´ 5´ 5´
IF2
T-arm
D-arm ATP AMP + PPi (initiation factor)
D D D
C Ψ T
Aminoacyl-tRNA C Ψ T C Ψ T
D D D
synthetase
Variable arm
Anticodon
loop U A C U A C Anticodon (5´-CAU-3´) U A C
Wobble
position C C C A U G A U A C
mRNA
Codon
(5´-AUG-3´)
Start and stop codons

mRNA start codon AUG. AUG inAUGurates protein synthesis.
Eukaryotes Codes for methionine, which may be removed
before translation is completed.
Prokaryotes Codes for N-formylmethionine (fMet). fMet stimulates neutrophil chemotaxis.
mRNA stop codons UGA, UAA, UAG. UGA = U Go Away.
Recognized by release factors. UA A = U Are Away.
UAG = U Are Gone.

Protein synthesis
Initiation 1. Eukaryotic initiation factors (eIFs) identify Eukaryotes: 40S + 60S 80S (even).
the 5′ cap. Prokaryotes: 30S + 50S 70S (prime).
2. eIFs help assemble the 40S ribosomal Synthesis occurs from N-terminus to
subunit with the initiator tRNA. C-terminus.
3. eIFs released when the mRNA and the
ATP—tRNA Activation (charging).
ribosomal 60S subunit assemble with the
GTP—tRNA Gripping and Going places
complex. Requires GTP.
(translocation).
Elongation Aminoacyl-tRNA binds to A site (except for
initiator methionine, which binds the P site), Think of “going APE”:
requires an elongation factor and GTP. A site = incoming Aminoacyl-tRNA.
rRNA (“ribozyme”) catalyzes peptide bond P site = accommodates growing Peptide.
formation, transfers growing polypeptide to E site = holds Empty tRNA as it Exits.
amino acid in A site. Elongation factors are targets of bacterial toxins
Ribosome advances 3 nucleotides toward 3′ (eg, Diphtheria, Pseudomonas).
end of mRNA, moving peptidyl tRNA to P
site (translocation). Shine-Dalgarno sequence—ribosomal binding
site in prokaryotic mRNA. Recognized by 16S
Termination Eukaryotic release factors (eRFs) recognize the
RNA in ribosomal subunit. Enables protein
stop codon and halt translation completed
synthesis initiation by aligning ribosome with
polypeptide is released from ribosome.
start codon so that code is read correctly.
Requires GTP.
60/50S
40/30S
M
R
M
Initiation M M H
Initiator tRNA
U A C
U A C 5´ A U G C A U G A U 3´ U A C G U A
mRNA
E P A
5´ A U G C A U G A U 3´
E P A
S Ribosome moves left to
right along mRNA
M Elongation M
H
U G A
G U A U A C
U A C Q G U A
Termination
A U G C A U G A U A U G C A U G A U
5´ 3´ 5´ 3´
E P A E P A
Posttranslational modifications
Trimming Removal of N- or C-terminal propeptides from zymogen to generate mature protein (eg,
trypsinogen to trypsin).
Covalent alterations Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination.
Chaperone protein Intracellular protein involved in facilitating and maintaining protein folding. In yeast, heat
shock proteins (eg, HSP60) are constitutively expressed, but expression may increase with high
temperatures, acidic pH, and hypoxia to prevent protein denaturing/misfolding.

44 SEC TION II Biochemistry  BIOCHEMISTRY—Cellular
` BIOCHEMISTRY—CELLULAR
Cell cycle phases Checkpoints control transitions between phases of cell cycle. This process is regulated by cyclins,
cyclin-dependent kinases (CDKs), and tumor suppressors. M phase (shortest phase of cell cycle)
includes mitosis (prophase, prometaphase, metaphase, anaphase, telophase) and cytokinesis
(cytoplasm splits in two). G1 is of variable duration.
REGULATION OF CELL CYCLE
Cyclin-dependent Constitutively expressed but inactive when not bound to cyclin.
kinases
Cyclin-CDK complexes Cyclins are phase-specific regulatory proteins that activate CDKs when stimulated by growth
factors. The cyclin-CDK complex can then phosphorylate other proteins (eg, Rb) to coordinate
cell cycle progression. This complex must be activated/inactivated at appropriate times for cell
cycle to progress.
Tumor suppressors p53 p21 induction CDK inhibition Rb hypophosphorylation (activation) G1-S
progression inhibition. Mutations in tumor suppressor genes can result in unrestrained cell
division (eg, Li-Fraumeni syndrome).
Growth factors (eg, insulin, PDGF, EPO, EGF) bind tyrosine kinase receptors to transition the cell
from G1 to S phase.
CELL TYPES
Permanent Remain in G0, regenerate from stem cells. Neurons, skeletal and cardiac muscle, RBCs.
Stable (quiescent) Enter G1 from G0 when stimulated. Hepatocytes, lymphocytes, PCT, periosteal cells.
Labile Never go to G0, divide rapidly with a short G1. Bone marrow, gut epithelium, skin, hair
Most affected by chemotherapy. follicles, germ cells.
Cell cycle arrest

p21 Cyclin
GO
Cyclin
CDK CDK
DNA damage Rb, p53 modulate G1
p21
G1 restriction point
th
ow
Gr
is
M
es
Li-Fraumeni syndrome
kin
to
(loss of function) Cy
Mito
p53
sis
HPV E6
IN TERPH
BCL-2 BCL-XL
Rb P
DNA
P
P
BAX/BAK
AS
Sy n
Rb E2F S
E
t he
is
s
Caspase activation E2F G2

Gene transcription
Apoptosis
(intrinsic pathway)

Biochemistry  BIOCHEMISTRY—Cellular SEC TION II 45
Rough endoplasmic Site of synthesis of secretory (exported) proteins N-linked glycosylation occurs in the
reticulum and of N-linked oligosaccharide addition to eNdoplasmic reticulum.
lysosomal and other proteins. Mucus-secreting goblet cells of small intestine
Nissl bodies (RER in neurons)—synthesize and antibody-secreting plasma cells are rich in
peptide neurotransmitters for secretion. RER.
Free ribosomes—unattached to any membrane; Proteins within organelles (eg, ER, Golgi bodies,
site of synthesis of cytosolic, peroxisomal, and lysosomes) are formed in RER.
mitochondrial proteins.
Smooth endoplasmic Site of steroid synthesis and detoxification of Hepatocytes and steroid hormone–producing
reticulum drugs and poisons. Lacks surface ribosomes. cells of the adrenal cortex and gonads are rich
Location of glucose-6-phosphatase (last step in in SER.
both glycogenolysis and gluconeogenesis).
Cell trafficking Golgi is distribution center for proteins and lipids from ER to vesicles and plasma membrane.
Posttranslational events in GOlgi include modifying N-oligosaccharides on asparagine, adding
O-oligosaccharides on serine and threonine, and adding mannose-6-phosphate to proteins for
lysosomal and other proteins.
Endosomes are sorting centers for material from outside the cell or from the Golgi, sending it to
lysosomes for destruction or back to the membrane/Golgi for further use.
I-cell disease (inclusion cell disease/mucolipidosis type II)—inherited lysosomal storage disorder
(autosomal recessive); defect in N-acetylglucosaminyl-1-phosphotransferase failure of the
Golgi to phosphorylate mannose residues ( mannose-6-phosphate) on glycoproteins enzymes
secreted extracellularly rather than delivered to lysosomes lysosomes deficient in digestive
enzymes buildup of cellular debris in lysosomes (inclusion bodies). Results in coarse facial
features, gingival hyperplasia, corneal clouding, restricted joint movements, claw hand deformities,
kyphoscoliosis, and plasma levels of lysosomal enzymes. Symptoms similar to but more severe
than Hurler syndrome. Often fatal in childhood.
Key: Signal recognition particle (SRP)—abundant,
brane
cytosolic ribonucleoprotein that traffics
mem polypeptide-ribosome complex from the
Clathrin sma
Pla
Secretory cytosol to the RER. Absent or dysfunctional
vesicle
COPI Late Early SRP accumulation of protein in cytosol.
endosome endosome
COPII Vesicular trafficking proteins

Lysosome COPI: Golgi Golgi (retrograde); cis-Golgi
Retrograde trans ER.
Anterograde COPII: ER cis-Golgi (anterograde). “Two
Golgi (COPII) steps forward (anterograde); one
apparatus (COPI) step back (retrograde).”
Clathrin: trans-Golgi lysosomes; plasma
membrane endosomes (receptor-mediated
cis
endocytosis [eg, LDL receptor activity]).
Rough
endoplasmic
reticulum
Nuclear envelope

46 SEC TION II Biochemistry  BIOCHEMISTRY—Cellular
Peroxisome Membrane-enclosed organelle involved in:

β-oxidation of very-long-chain fatty acids (VLCFA) (strictly peroxisomal process)
α-oxidation of branched-chain fatty acids (strictly peroxisomal process)
Catabolism of amino acids and ethanol
Synthesis of bile acids and plasmalogens (important membrane phospholipid, especially in
white matter of brain)
Zellweger syndrome—autosomal recessive disorder of peroxisome biogenesis due to mutated PEX
genes. Hypotonia, seizures, jaundice, craniofacial dysmorphia, hepatomegaly, early death.
Refsum disease—autosomal recessive disorder of α-oxidation buildup of phytanic acid due
to inability to degrade it. Scaly skin, ataxia, cataracts/night blindness, shortening of 4th toe,
epiphyseal dysplasia. Treatment: diet, plasmapheresis.
Adrenoleukodystrophy—X-linked recessive disorder of β-oxidation due to mutation in ABCD1
gene VLCFA buildup in adrenal glands, white (leuko) matter of brain, testes. Progressive
disease that can lead to adrenal gland crisis, progressive loss of neurologic function, death.
Proteasome Barrel-shaped protein complex that degrades ubiquitin-tagged proteins. Defects in the ubiquitin-
proteasome system have been implicated in some cases of Parkinson disease.
Cytoskeletal elements A network of protein fibers within the cytoplasm that supports cell structure, cell and organelle
movement, and cell division.
TYPE OF FILAMENT PREDOMINANT FUNCTION EXAMPLES
Microfilaments Muscle contraction, cytokinesis Actin, microvilli.
Intermediate Maintain cell structure Vimentin, desmin, cytokeratin, lamins, glial
filaments fibrillary acidic protein (GFAP), neurofilaments.
Microtubules Movement, cell division Cilia, flagella, mitotic spindle, axonal trafficking,
centrioles.
Microtubule Cylindrical outer structure composed of a Drugs that act on microtubules (microtubules
Positive
helical array of polymerized heterodimers get constructed very terribly):
end (+) of α- and β-tubulin. Each dimer has 2 GTP Mebendazole (antihelminthic)
Heterodimer bound. Incorporated into flagella, cilia, mitotic Griseofulvin (antifungal)
spindles. Also involved in slow axoplasmic Colchicine (antigout)
transport in neurons. Vinca alkaloids (anticancer)
Molecular motor proteins—transport cellular Taxanes (anticancer)
cargo toward opposite ends of microtubule. Negative end near nucleus.
Protofilament Retrograde to microtubule (+ −)—dynein. Positive end points to periphery.
Anterograde to microtubule (− +)—kinesin.
Negative Clostridium tetani toxin, herpes simplex virus, Ready? Attack!
end (–) poliovirus, and rabies virus use dynein for
retrograde transport to the neuronal cell body.

Cilia structure Motile cilia consist of 9 doublet + 2 singlet arrangement of microtubules (axoneme) A .
Basal body (base of cilium below cell membrane) consists of 9 microtubule triplets B with no
central microtubules.
Nonmotile (primary) cilia work as chemical signal sensors and have a role in signal transduction
and cell growth control. Dysgenesis may lead to polycystic kidney disease, mitral valve prolapse,
or retinal degeneration.
Axonemal dynein—ATPase that links peripheral 9 doublets and causes bending of cilium by
differential sliding of doublets.
Gap junctions enable coordinated ciliary movement.
A B
Dynein
arm
Microtubule
A
Microtubule
B
Nexin
Doublets
Triplets
Primary ciliary Also called Kartagener syndrome. Autosomal recessive. Dynein arm defect immotile cilia
dyskinesia dysfunctional ciliated epithelia.
Developmental abnormalities due to impaired migration and orientation (eg, situs inversus A , hearing
A
loss due to dysfunctional eustachian tube cilia); recurrent infections (eg, sinusitis, ear infections,
R L bronchiectasis due to impaired ciliary clearance of debris/pathogens); infertility ( risk of ectopic
pregnancy due to dysfunctional fallopian tube cilia, immotile spermatozoa).
Lab findings: nasal nitric oxide (used as screening test).
Sodium-potassium Na+/K+-ATPase is located in the plasma 2 strikes? K, you’re still in. 3 strikes? Nah, you’re
pump membrane with ATP site on cytosolic side. For out!
each ATP consumed, 2 K+ go in to the cell Cardiac glycosides (digoxin and digitoxin)
(pump dephosphorylated) and 3 Na+ go out of directly inhibit Na+/K+-ATPase indirect
the cell (pump phosphorylated). inhibition of Na+/Ca2+ exchange [Ca2+]i
cardiac contractility.
Extracellular
3Na+ 2K+
space
Plasma
membrane
P
Cytosol 2K+
3Na+ ATP ADP P

48 SECTION II Biochemistry  BIOCHEMISTRY—Cellular
Collagen Most abundant protein in the human body. Type I - Skeleton

Extensively modified by posttranslational Type II - Cartilage
modification. Type III - Arteries
Organizes and strengthens extracellular matrix. Type IV - Basement membrane
Types I to IV are the most common types in SCAB
humans.
Type I Most common (90%)—Bone (made by Type I: bone, tendone.
osteoblasts), Skin, Tendon, dentin, fascia, production in osteogenesis imperfecta type I.
cornea, late wound repair.
Type II Cartilage (including hyaline), vitreous body, Type II: cartwolage.
nucleus pulposus.
Type III Reticulin—skin, blood vessels, uterus, fetal Type III: deficient in vascular type of Ehlers-
tissue, early wound repair. Danlos syndrome (threE D).
Type IV Basement membrane/basal lamina (glomerulus, Type IV: under the floor (basement membrane).
cochlea), lens. Defective in Alport syndrome; targeted by
autoantibodies in Goodpasture syndrome.
Myofibroblasts are responsible for secretion
(proliferative stage) and wound contraction.
Collagen synthesis and structure
Fibroblast Preprocollagen S ynthesis—translation of collagen α

Pro α-chain backbone (Gly-X-Y) chains (preprocollagen)—usually Gly-X-Y
Nucleus Hydroxylation of proline and
(X is often proline or lysine and Y is often
OH
OH lysine (requires vitamin C) hydroxyproline or hydroxylysine). Collagen is
Collagen mRNA Sugar
Glycosylation
1/3 glycine; glycine content of collagen is less
Cytoplasm OH
OH variable than that of lysine and proline.
RER
Hydroxylation—hydroxylation
Triple helix formation
Procollagen (“hydroxCylation”) of specific proline
Golgi and lysine residues. Requires vitamin C;
deficiency scurvy.
Exocytosis
Glycosylation—glycosylation of pro-α-chain
Extracellular
space hydroxylysine residues and formation of
Cleavage of procollagen
C- and N-terminals procollagen via hydrogen and disulfide bonds
Tropocollagen (triple helix of 3 collagen α chains). Problems
forming triple helix osteogenesis imperfecta.
Self assembly into
collagen fibrils Exocytosis—exocytosis of procollagen into
extracellular space.
Proteolytic processing—cleavage of
disulfide-rich terminal regions of procollagen
Formation of cross-links
(stabilized by lysyl oxidase) insoluble tropocollagen.
Assembly and alignment—collagen assembles
Collagen fiber
in fibrils and aligns for cross-linking.
Cross-linking—reinforcement of staggered
tropocollagen molecules by covalent lysine-
hydroxylysine cross-linkage (by copper-
containing lysyl oxidase) to make collagen
fibrils. Cross-linking of collagen with age.
Problems with cross-linking Menkes disease.
FAS1_2022_01-Biochem.indd 48 11/8/21 1:04 PM

Osteogenesis Genetic bone disorder (brittle bone May be confused with child abuse.
imperfecta disease) caused by a variety of gene defects Treat with bisphosphonates to fracture risk.
A
(most commonly COL1A1 and COL1A2). Patients can’t BITE:
Most common form is autosomal dominant Bones = multiple fractures
with production of otherwise normal type I I (eye) = blue sclerae
collagen (altered triple helix formation). Teeth = dental imperfections
Upper Manifestations include: Ear = hearing loss
extremity Multiple fractures and bone deformities
B
(arrows in A ) after minimal trauma (eg,
during birth)
Blue sclerae B due to the translucent
connective tissue over choroidal veins
Some forms have tooth abnormalities,
including opalescent teeth that wear easily
due to lack of dentin (dentinogenesis
imperfecta)
Conductive hearing loss (abnormal ossicles)
Ehlers-Danlos Faulty collagen synthesis causing A B

syndrome hyperextensible skin A , hypermobile joints B ,
and tendency to bleed (easy bruising).
Multiple types. Inheritance and severity vary.
Can be autosomal dominant or recessive. May
be associated with joint dislocation, berry and
aortic aneurysms, organ rupture.
Hypermobility type (joint instability): most
common type.
Classical type (joint and skin symptoms):
caused by a mutation in type V collagen (eg,
COL5A1, COL5A2).
Vascular type (fragile tissues including vessels
[eg, aorta], muscles, and organs that are prone
to rupture [eg, gravid uterus]): mutations in
type III procollagen (eg, COL3A1).
Menkes disease X-linked recessive connective tissue disease caused by impaired copper absorption and transport
due to defective Menkes protein ATP7A (Absent copper), vs ATP7B in Wilson disease (copper
Buildup). Leads to activity of lysyl oxidase (copper is a necessary cofactor) defective collagen
cross-linking. Results in brittle, “kinky” hair, growth and developmental delay, hypotonia, risk of
cerebral aneurysms.

50 SEC TION II Biochemistry  Biochemistry—Laboratory Techniques
Elastin Stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, epiglottis,
ligamenta flava (connect vertebrae relaxed and stretched conformations).
Rich in nonhydroxylated proline, glycine, and lysine residues, vs the hydroxylated residues of
collagen.
Single Tropoelastin with fibrillin scaffolding.
elastin Stretch
Relax Cross-link
Cross-linking occurs extracellularly via lysyl oxidase and gives elastin its elastic properties.
molecule
Broken down by elastase, which is normally inhibited by α1-antitrypsin.
α1-Antitrypsin deficiency results in unopposed elastase activity, which can cause COPD.
Marfan syndrome—autosomal dominant (with variable expression) connective tissue disorder
A
affecting skeleton, heart, and eyes. FBN1 gene mutation on chromosome 15 (fifteen) results in
defective fibrillin-1, a glycoprotein that forms a sheath around elastin and sequesters TGF-β.
Findings: tall with long extremities; chest wall deformity (pectus carinatum [pigeon chest] or
pectus excavatum A ); hypermobile joints; long, tapering fingers and toes (arachnodactyly); cystic
medial necrosis of aorta; aortic root aneurysm rupture or dissection (most common cause of
death); mitral valve prolapse; risk of spontaneous pneumothorax.
Homocystinuria—most commonly due to cystathionine synthase deficiency leading to
homocysteine buildup. Presentation similar to Marfan syndrome with pectus deformity, tall
stature, arm:height ratio, upper:lower body segment ratio, arachnodactyly, joint hyperlaxity,
skin hyperelasticity, scoliosis.
Marfan syndrome Homocystinuria
INHERITANCE Autosomal dominant Autosomal recessive
INTELLECT Normal Decreased
VASCULAR COMPLICATIONS Aortic root dilatation Thrombosis
LENS DISLOCATION Upward/temporal (Marfan fans out) Downward/nasal
` BIOCHEMISTRY—LABORATORY TECHNIQUES
Polymerase chain Molecular biology lab procedure used to amplify a desired fragment of DNA. Useful as a diagnostic
reaction tool (eg, neonatal HIV, herpes encephalitis).
5' 3' 5' 3' 5' 3'
5' 3' 3' 5'

DNA primer
dNTP
Repeat
3' 5' 5' 3'
Double-stranded DNA
3' 5' 3' 5' 3' 5'
enaturation—DNA template, DNA primers, a heat-stable DNA polymerase, and

D
deoxynucleotide triphosphates (dNTPs) are heated to ~ 95ºC to separate the DNA strands.
Annealing—sample is cooled to ~ 55ºC. DNA primers anneal to the specific sequence to be
amplified on the DNA template.
Elongation—temperature is increased to ~ 72ºC. DNA polymerase adds dNTPs to the strand to
replicate the sequence after each primer.
Heating and cooling cycles continue until the amount of DNA is sufficient.

Biochemistry  Biochemistry—Laboratory Techniques SEC TION II 51
CRISPR/Cas9 A genome editing tool derived from bacteria. Consists of a guide RNA (gRNA) , which is
complementary to a target DNA sequence, and an endonuclease (Cas9), which makes a single- or
double-strand break at the target site . Imperfectly cut segments are repaired by nonhomologous
end joining (NHEJ) accidental frameshift mutations (“knock-out”) , or a donor DNA
sequence can be added to fill in the gap using homology-directed repair (HDR) .
Potential applications include removing virulence factors from pathogens, replacing disease-causing
alleles of genes with healthy variants (in clinical trials for sickle cell disease), and specifically targeting
tumor cells.
Cas9 gRNA
Donor DNA
NHEJ 3A 3B HDR
+
Frameshift/inactivation Edited sequence

(”knock-out”) (”knock-in”)
Blotting procedures
Southern blot 1. DNA sample is enzymatically cleaved into I: Parents
smaller pieces, which are separated on a gel
PEDIGREE
by electrophoresis, and then transferred to a

membrane.
II: Children
2. Membrane is exposed to labeled DNA probe
that anneals to its complementary strand. Aa Aa aa Aa AA Genotype
3. Resulting double-stranded, labeled piece
SOUTHERN BLOT
of DNA is visualized when membrane is Mutant
exposed to film or digital imager. Normal
Northern blot Similar to Southern blot, except that an RNA

sample is electrophoresed. Useful for studying SNoW DRoP:
mRNA levels, which are reflective of gene Southern = DNA
expression. Northern = RNA
Western = Protein
Western blot Sample protein is separated via gel electrophoresis
Northern blots detect splicing errors.
and transferred to a membrane. Labeled
antibody is used to bind to relevant protein.
Southwestern blot Identifies DNA-binding proteins (eg, c-Jun, Southern (DNA) + Western (protein) =
c-Fos [leucine zipper motif]) using labeled Southwestern (DNA-binding protein).
double-stranded DNA probes.

52 SEC TION II Biochemistry  Biochemistry—Laboratory Techniques
Flow cytometry Laboratory technique to assess size, granularity, Commonly used in workup of hematologic
and protein expression (immunophenotype) of abnormalities (eg, leukemia, paroxysmal
individual cells in a sample. nocturnal hemoglobinuria, fetal
RBCs in pregnant person’s blood) and
immunodeficiencies (eg, CD4+ cell count in
HIV).
Cells are tagged with antibodies specific to Fluorescent

label
surface or intracellular proteins. Antibodies
Antibody
are then tagged with a unique fluorescent
dye. Sample is analyzed one cell at a time by
Anti-CD3 Ab Cell
focusing a laser on the cell and measuring
light scatter and intensity of fluorescence.
Anti-CD8 Ab
Laser
Fluorescence
is detected; Laser makes
tor
labeled cells tec label fluoresce
De
are counted
Data are plotted either as histogram (one
measure) or scatter plot (any two measures, as
shown). In illustration: 104
Cells in left lower quadrant ⊝ for both CD8
and CD3. 103
Cells in right lower quadrant ⊕ for CD8
and ⊝ for CD3. In this example, right
CD3
102
lower quadrant is empty because all
CD8-expressing cells also express CD3. 101
Cells in left upper quadrant ⊕ for CD3 and
⊝ for CD8. 100
100 101 102 103 104
Cells in right upper quadrant ⊕ for both
CD8
CD8 and CD3.
Microarrays Array consisting of thousands of DNA oligonucleotides arranged in a grid on a glass or silicon chip.
The DNA or RNA samples being compared are attached to different fluorophores and hybridized
to the array. The ratio of fluorescence signal at a particular oligonucleotide reflects the relative
amount of the hybridizing nucleic acid in the two samples.
Used to compare the relative transcription of genes in two RNA samples. Can detect single
nucleotide polymorphisms (SNPs) and copy number variants (CNVs) for genotyping, clinical
genetic testing, forensic analysis, and cancer mutation and genetic linkage analysis when DNA is
used.
Enzyme-linked Immunologic test used to detect the presence of either a specific antigen or antibody in a patient’s
immunosorbent assay blood sample. Detection involves the use of an antibody linked to an enzyme. Added substrate
reacts with the enzyme, producing a detectable signal. Can have high sensitivity and specificity,
but is less specific than Western blot. Often used to screen for HIV infection.

Biochemistry  Biochemistry—Laboratory Techniques SEC TION II 53
Karyotyping Colchicine is added to cultured cells to halt A

chromosomes in metaphase. Chromosomes
are stained, ordered, and numbered according
to morphology, size, arm-length ratio, and
banding pattern (arrows in A point to extensive
abnormalities in a cancer cell).
Can be performed on a sample of blood, bone
marrow, amniotic fluid, or placental tissue.
Used to diagnose chromosomal imbalances
(eg, autosomal trisomies, sex chromosome
disorders).
Fluorescence in situ Fluorescent DNA or RNA probe binds A

hybridization to specific gene or other site of interest
on chromosomes (arrows in A point to
abnormalities in a cancer cell; each fluorescent
color represents a chromosome-specific probe).
Used for specific localization of genes and direct
visualization of chromosomal anomalies.
Microdeletion—no fluorescence on a
chromosome compared to fluorescence at
the same locus on the second copy of that
chromosome.
Translocation—fluorescence signal that
corresponds to one chromosome is found in
a different chromosome (two white arrows in
A show fragments of chromosome 17 that
have translocated to chromosome 19).
Duplication—a second copy of a
chromosome, resulting in a trisomy or
tetrasomy (two blue arrows in A duplicated
chromosomes 8, resulting in a tetrasomy).
Molecular cloning Production of a recombinant DNA molecule in a bacterial host. Useful for production of human
proteins in bacteria (eg, human growth hormone, insulin).
Steps:
1. Isolate eukaryotic mRNA (post-RNA processing) of interest.
2. Add reverse transcriptase (an RNA-dependent DNA polymerase) to produce complementary
DNA (cDNA, lacks introns).
3. Insert cDNA fragments into bacterial plasmids containing antibiotic resistance genes.
4. Transform (insert) recombinant plasmid into bacteria.
5. Surviving bacteria on antibiotic medium produce cloned DNA (copies of cDNA).

54 SEC TION II Biochemistry  BIOCHEMISTRY—Genetics
Gene expression Transgenic strategies in mice involve: Knock-out = removing a gene, taking it out.
modifications Random insertion of gene into mouse Knock-in = inserting a gene.
genome
Targeted insertion or deletion of gene Random insertion—constitutive expression.
through homologous recombination with Targeted insertion—conditional expression.
mouse gene
RNA interference Process whereby small non-coding RNA molecules target mRNAs to inhibit gene expression.
MicroRNA Naturally produced by cell as hairpin structures. Abnormal expression of miRNAs contributes
Loose nucleotide pairing allows broad to certain malignancies (eg, by silencing an
targeting of related mRNAs. When miRNA mRNA from a tumor suppressor gene).
binds to mRNA, it blocks translation of mRNA
and sometimes facilitates its degradation.
Small interfering Usually derived from exogenous dsRNA source Can be produced by transcription or
RNA (eg, virus). Once inside a cell, siRNA requires chemically synthesized for gene “knockdown”
complete nucleotide pairing, leading to highly experiments.
specific mRNA targeting. Results in mRNA
cleavage prior to translation.
` BIOCHEMISTRY—GENETICS
Genetic terms
TERM DEFINITION EXAMPLE
Codominance Both alleles contribute to the phenotype of the Blood groups A, B, AB; α1-antitrypsin
heterozygote. deficiency; HLA groups.
Variable expressivity Patients with the same genotype have varying Two patients with neurofibromatosis type 1 (NF1)
phenotypes. may have varying disease severity.
Incomplete Not all individuals with a disease show the BRCA1 gene mutations do not always result in
penetrance disease. breast or ovarian cancer.
% penetrance × probability of inheriting
genotype = risk of expressing phenotype.
Pleiotropy One gene contributes to multiple phenotypic Untreated phenylketonuria (PKU) manifests with
effects. light skin, intellectual disability, musty body odor.
Anticipation Increased severity or earlier onset of disease in Trinucleotide repeat diseases (eg, Huntington
succeeding generations. disease).
Loss of heterozygosity If a patient inherits or develops a mutation in Retinoblastoma and the “two-hit hypothesis,”
a tumor suppressor gene, the wild type allele Lynch syndrome (HNPCC), Li-Fraumeni
must be deleted/mutated/eliminated before syndrome.
cancer develops. This is not true of oncogenes.
Epistasis The allele of one gene affects the phenotypic Albinism, alopecia.
expression of alleles in another gene.
Aneuploidy An abnormal number of chromosomes; due to Down syndrome, Turner syndrome,
chromosomal nondisjunction during mitosis oncogenesis.
or meiosis.

Biochemistry  BIOCHEMISTRY—Genetics SEC TION II 55
Genetic terms (continued)

TERM DEFINITION EXAMPLE
Dominant negative Exerts a dominant effect. A heterozygote A single mutated p53 tumor suppressor gene
mutation produces a nonfunctional altered protein that results in a protein that is able to bind DNA
also prevents the normal gene product from and block the wild type p53 from binding to the
functioning. promoter.
Linkage Tendency for certain alleles to occur in close
disequilibrium proximity on the same chromosome more or
less often than expected by chance. Measured
in a population, not in a family, and often
varies in different populations.
Mosaicism Presence of genetically distinct cell lines in the McCune-Albright syndrome—due to Gs-protein
A
same individual. activating mutation. Presents with unilateral
Somatic mosaicism—mutation arises from café-au-lait spots A with ragged edges,
mitotic errors after fertilization and propagates polyostotic fibrous dysplasia (bone is replaced
through multiple tissues or organs. by collagen and fibroblasts), and at least one
Germline (gonadal) mosaicism—mutation only endocrinopathy (eg, precocious puberty).
in egg or sperm cells. If parents and relatives Lethal if mutation occurs before fertilization
do not have the disease, suspect gonadal (or (affecting all cells), but survivable in patients
germline) mosaicism. with mosaicism.
Locus heterogeneity Mutations at different loci result in the same Albinism, retinitis pigmentosa, familial
disease. hypercholesteremia.
Allelic heterogeneity Different mutations in the same locus result in β-thalassemia.
the same disease.
Heteroplasmy Presence of both normal and mutated mtDNA passed from mother to all children.
mtDNA, resulting in variable expression in
mitochondrially inherited disease.
Uniparental disomy Offspring receives 2 copies of a chromosome from Uniparental is euploid (correct number of
1 parent and no copies from the other parent. chromosomes). Most occurrences of uniparental
HeterodIsomy (heterozygous) indicates a meiosis disomy (UPD) normal phenotype. Consider
I error. IsodIsomy (homozygous) indicates a isodisomy in an individual manifesting a
meiosis II error or postzygotic chromosomal recessive disorder when only one parent is a
duplication of one of a pair of chromosomes, carrier. Examples: Prader-Willi and Angelman
and loss of the other of the original pair. syndromes.
Hardy-Weinberg If p and q represent the frequencies of alleles Hardy-Weinberg law assumptions include:
population genetics A and a, respectively, in a population, then No mutation occurring at the locus
p + q = 1: Natural selection is not occurring
A (p) a (q)
p2 = frequency of homozygosity for allele A Completely random mating
AA Aa
A (p)
(p2) (pq) q2 = frequency of homozygosity for allele a No net migration
Aa aa
2pq = frequency of heterozygosity (carrier Large population
a (q) frequency, if an autosomal recessive disease) If a population is in Hardy-Weinberg
(pq) (q2)
Therefore, the sum of the frequencies of these equilibrium, then the values of p and q remain
genotypes is p2 + 2pq + q2 = 1. constant from generation to generation.
The frequency of an X-linked recessive disease
in males = q and in females = q2.

56 SEC TION II Biochemistry  BIOCHEMISTRY—Genetics
Disorders of imprinting Imprinting—one gene copy is silenced by methylation, and only the other copy is expressed
parent-of-origin effects. The expressed copy may be mutated, may not be expressed, or may be
deleted altogether.
Prader-Willi syndrome Angelman syndrome
WHICH GENE IS SILENT? Maternally derived genes are silenced Paternally derived UBE3A is silenced
Disease occurs when the paternal allele is deleted Disease occurs when the maternal allele is
or mutated deleted or mutated
SIGNS AND SYMPTOMS Hyperphagia, obesity, intellectual disability, Seizures, Ataxia, severe Intellectual disability,
hypogonadism, hypotonia inappropriate Laughter
Set SAIL for Angel Island
CHROMOSOMES INVOLVED Chromosome 15 of paternal origin UBE3A on maternal copy of chromosome 15
NOTES 25% of cases are due to maternal uniparental 5% of cases are due to paternal uniparental
disomy disomy
POP: Prader-Willi, Obesity/overeating, Paternal MAMAS: Maternal allele deleted, Angelman
allele deleted syndrome, Mood, Ataxia, Seizures
P = Paternal
M = Maternal
Normal Mutation
Active gene
P M P M
Silenced gene (imprinting)
Gene deletion/mutation
Prader-Willi syndrome
Angelman syndrome

Another random document with
no related content on Scribd:
and that, finally, was the prevailing note of the age; since reason had
been declared insufficient, only a mystic could provide the answer,
only he could mark the boundaries of life with a final authority,
inscrutably revealed. It was so perfectly clear. All that was lacking
was the man.
One
1
The garden was at its best that first week in the month of June. The
peonies were more opulent than usual and I walked slowly through
the green light on the terrace above the white river, enjoying the
heavy odor of peonies and of new roses rambling in hedges.
The Hudson was calm, no ripple revealed that slow tide which even
here, miles to the north of the sea, rises brackishly at the moon’s
disposition. Across the river the Catskills, water-blue, emerged
sharply from the summer’s green as though the earth in one vivid
thrust had attempted sky, fusing the two elements into yet another,
richer blue ... but the sky was only framed, not really touched, and
the blue of hills was darker than the pale sky with its protean clouds
all shaped by wind, like the stuff of auguries and human dreaming.
The sky that day was like an idiot’s mind, wild with odd clouds, but
lovely too, guileless, natural, allusive.
I did not want to go in to lunch, although there was no choice in the

matter. I had arrived at one o’clock; I was expected at one-thirty.
Meanwhile, avoiding the house until the last possible moment, I had
taken a neighbor’s privilege of strolling alone about the garden; the
house behind me was gray and austere, granitic, more English than
Hudson Valley. The grounds swept softly down toward the river
nearly a mile away. A vista had been cleared from the central
terrace, a little like the one at Versailles but more rustic, less royal.
Dark green trees covered the hills to left and right of the sweep of
lawn and meadow. No other house could be seen. Even the railroad
between the terrace and the water was invisible, hidden by a bluff ...
only its sound and an occasional blur of smoke upon the blue
marked that machine’s essential passage.
I breathed the air of early summer gladly, voluptuously. I lived my life

in seasonal concert with this river and, after grim March and
confusing sharp April, the knowledge that at last the leaves were
foliaged and the days warm was quite enough to create in me a
mood of euphoria, of marvelous serenity. I contemplated love affairs.
I prepared to meet strangers. The summer and I would celebrate our
triumph soon; but, until the proper moment, I was a spectator: the
summer love as yet unknown to me, the last dark blooming of
peonies amid the wreckage of white lilacs still some weeks away,
held in the future with my love. I could only anticipate; I savored my
disengagement in this garden.
But then it was time to go in and I turned my back resolutely on the

river and ascended the wide stone steps to the brick terrace which
fronted the house on the river side, pausing only to break the stem of
a white and pink peony, regretting immediately what I had done:
brutally, I had wished to possess the summer, to fix the instant, to
bear with me into the house a fragment of the day. It was wrong; and
I stood for a moment at the French door holding the great peony in
my hand, its odor like a dozen roses, like all the summers I had ever
known. But it was impractical. I could not stuff it into my buttonhole
for it was as large as a baby’s head while I was fairly certain that my
hostess would be less than pleased to receive at my hands one of
her best peonies, cut too short even to place in water. Obscurely
displeased with myself and the day, I plunged the flower deep into a
hedge of boxwood until not even a glimmer of white showed through
the dense dark green to betray me: then, like a murderer, the
assaulted day part-spoiling, I went inside.
2
“You have been malingering in the garden,” she said, offering me her
face like a painted plate to kiss. “I saw you from the window.”
“Saw me ravage the flowers?”
“They all do,” she said obscurely, and led me after her into the
drawing room, an oblong full of light from French windows opening
upon the terrace. I was surprised to see that she was alone.
“She’ll be along presently. She’s upstairs changing.”
“Who?”
“Iris Mortimer ... didn’t I tell you? It’s the whole reason.”
Clarissa nodded slyly from the chair opposite me. A warm wind
crossed the room and the white curtains billowed like spinnakers in a
regatta. I breathed the warm odor of flowers, of burned ash remnants
from the fireplace: the room shone with silver and porcelain. Clarissa
was rich despite the wars and crises that had marked our days,
leaving the usual scars upon us, like trees whose cross-sections
bear a familial resemblance of concentric rings, recalling in detail the
weather of past years ... at least those few rings we shared in
common, or Clarissa, by her own admission, was twenty-two
hundred years old with an uncommonly good memory. None of us
had ever questioned her too closely about her past. There is no
reason to suspect, however, that she was insincere. Since she felt
she had lived that great length of time and since her recollections
were remarkably interesting and plausible she was much in demand
as a conversationalist and adviser, especially useful in those plots
which require great shrewdness and daring. It was perfectly
apparent that she was involved in some such plot at the moment.
I looked at her thoughtfully before I casually rose to take the bait of

mystery she had trailed so perfunctorily before me. She knew her
man. She knew I would not be difficult in the early stages of any
adventure.
“Whole reason?” I repeated.
“I can say no more!” said Clarissa with a melodramatic emphasis

which my deliberately casual tone did not entirely justify. “You’ll love
Iris, though.”
I wondered whether loving Iris, or pretending to love Iris, was to be

the summer’s game. But before I could inquire further, Clarissa,
secure in her mystery, asked me idly about my work and, as idly, I
answered her, the exchange perfunctory yet easy, for we were used
to one another.
“I am tracking him down,” I said. “There is so little to go on, but what

there is is quite fascinating, especially Ammianus.”
“Fairly reliable, as military men go,” said Clarissa, suddenly

emerging from her polite indifference: any reference to the past she
had known always interested her, only the present seemed to bore
her, at least that ordinary unusable present which did not contain
promising material for one of her elaborate human games.
“Did you know him?” I never accepted, literally, Clarissa’s unique

age: two thousand years is an unlikely span of life even for a woman
of her sturdy unimaginativeness; yet there was no ignoring the fact
that she seemed to have lived that long, and that her references to
obscure episodes, where ascertainable, were nearly always right
and, more convincing still, where they differed from history’s records,
differed on the side of plausibility ... the work of a memory or a mind
completely unsuperstitious and unenthusiastic: (she was literal; she
was, excepting always her central fantasy, matter-of-fact. To her the
death or Caesar was the logical outcome of a system of taxation
which has not been preserved for us except in quaintly obscure
references; while the virtue of the Roman republic and the ambitions
of celebrated politicians, she set aside as being of only minor
importance: currency and taxation were her forte and she managed
to reduce all the martial splendor of ancient days to an economic
level).
She had one other obsession, however, and my reference to

Ammianus reminded her of it.
“The Christians!” she exclaimed significantly; then she paused; I

waited. Her conversation at times resembled chapter-headings
chosen haphazardly from an assortment of Victorial novels. “They
hated him.”
“Ammianus?”
“No, your man Julian. It is the Emperor Julian you are writing about.”
“Reading about.”
“Ah, you will write about him,” she said with an abstracted pythoness
stare which suggested that I was indefatigable in my eccentric
purpose which, for some years, had been the study of history in a
minor key.
“Of course they hated him. As well they should have ... that’s the
whole point to my work.”
“Unreliable, the lot of them. There is no decent history from the time
they came to Rome up until that fat little Englishman ... you know,
the one who lived in Switzerland ... with rather staring eyes.”
“Gibbon.”
“Yes, that one. Of course he got all the facts wrong, poor man, but at
least he tried. The facts of course were all gone by then. They saw to
that ... burning things, rewriting things ... not that I really ever read
them ... you know how I am about reading: I prefer a mystery novel
any day. But at least Gibbon got the tone right.”
“Yet....”
“Of course Julian was something of a prig, you know. He posed
continually and he wasn’t ... what do they call him now? an apostate.
He never renounced Christianity.”
“He what ...”
Clarissa in her queer way took pleasure in rearranging all accepted

information. I shall never know whether she did it deliberately to
mystify or whether her versions were, in fact, the forgotten reality.
“He was a perfectly good Christian au fond despite his peculiar diet.
He was a vegetarian for some years but wouldn’t eat beans, as I
recall, because he thought they contained the souls of the dead, an
old orphic notion.”
“Which is hardly Christian.”
“Isn’t that part of it? No? Well in any case the first proclamation of
Paris was intended ...” but I was never to hear Julian’s intent for Iris
was in the doorway, slender, dressed in white, her hair dark and
drawn back in a classical line from her calm face: she was
handsome and not at all what I had expected, but then Clarissa had,
as usual, not given me much lead. Iris Mortimer was my own age, I
guessed, about thirty, and although hardly a beauty she moved with
such ease, spoke with such softness, created such an air of serenity
that one gave her perhaps more credit for the possession of beauty
than an American devoted to regular features ought, in all accuracy,
to have done: the impression was one of lightness, of this month of
June in fact ... I linger over her description a little worriedly,
conscious that I am not really getting her right (at least as she
appeared to me that afternoon) for the simple reason that our lives
were to become so desperately involved in the next few years and
my memories of her are now encrusted with so much emotion that
any attempt to evoke her as she actually was when I first saw her in
that drawing room some fifty years ago is not unlike the work of a
restorer of paintings removing layers of glaze and grime in an
attempt to reveal an original pattern in all its freshness somewhere
beneath ... except that a restorer of course is a workman who has
presumably no prejudice and, too, he did not create the original
image only to attend its subsequent distortion, as the passionate do
in life; for the Iris of that day was, I suppose, no less and no more
than what she was to become; it was merely that I could not suspect
the bizarre course our future was to take. I had no premonition of our
mythic roles, though the temptation is almost overpowering to assert,
darkly, that even on the occasion of our first meeting I knew. The
truth is that we met; we became friends; we lunched amiably and the
future cast not one shadow across the mahogany table around which
we sat, listening to Clarissa and eating fresh shad caught in the river
that morning.
“Eugene here is interested in Julian,” said our hostess, lifting a

spring asparagus to her mouth with her fingers.
“Julian who?”
“The Emperor of Rome. I forget his family name but he was a

nephew, I think, of Constantius, who was dreary too though not such
a bore as Julian. Iris, try the asparagus. We get them from the
garden.”
Iris tried an asparagus and Clarissa recalled that the Emperor

Augustus’s favorite saying was: “Quick as boiled asparagus.” It
developed that he had been something of a bore, too. “Hopelessly
involved in office work. Of course it’s all terribly important, no doubt
of that ... after all the entire Empire was based on a first-rate filing
system; yet, all in all, it’s hardly glamorous.”
“Whom did you prefer?” asked Iris, smiling at me: she too was aware
of our hostess’s obsession; whether or not she believed is a different
matter. I assumed not; yet the assumption of truth is perhaps, for
human purposes, the same as truth itself, at least to the obsessed.
“None of the obvious ones,” said Clarissa, squinting near-sightedly at

the window through which a pair of yellow-spangled birds were
mating on the wing like eccentric comets against the green of box.
“But of course, I didn’t know everyone, darling. Only a few. Not all of
them were accessible. Some never dined out. Some that did go out
were impossible and then of course I traveled a good deal. I loved
Alexandria and wintered there for over two hundred years, missing a
great deal of the unpleasantness at Rome, the unstability of those
tiresome generals ... although Vitellius was great fun, at least as a
young man. I never saw him when he was Emperor that time, for five
minutes wasn’t it? Died of greed. Such an appetite! On one occasion
as a young man he ate an entire side of beef at my place in Baiae.
Ah, Baiae, I do miss it. Much nicer than Bath or Biarritz and certainly
more interesting than Newport was. I had several houses there over
the years. Once when Senator Tullius Cicero was traveling with that
poisonous daughter of his, they stopped....”
We listened attentively as one always did to Clarissa ... does? I

wonder if she is still alive: if she is, then perhaps the miracle has
indeed taken place and one human being has finally avoided the
usual fate. It is an amiable miracle to contemplate.
Lunch ended without any signs of that revelation which Clarissa had
led me to expect. Nothing was said which seemed to possess even a
secret significance. Wondering idly whether or not Clarissa might,
after all, be entirely mad, I followed the two women back into the
drawing room where we had our coffee in a warm mood of satiety
made only faintly disagreeable for me by that mild nausea which I
always used to experience when I drank too much wine at lunch:
now of course I never see wine, only the Arabs’ mint tea and their
sandy bitter coffee which I have come to like.
A warm breeze fluttered the curtains: the noise of insects responding

to the sun’s increasing heat droned all upon the same note, dry and
insistent, a bass to the coloratura of birds, while the scent of flowers
filled the airy room and I detected lilies as well as peonies, their odor
almost too sweet, quite drowning the more delicate rose, the pale
Hudson lilac.
Clarissa reminisced idly. She possessed a passion for minor detail

which was often a good deal more interesting than her usual talks on
currency devaluation.
Neither Iris nor I spoke much; it was as if we were both awaiting
some word from Clarissa which would throw into immediate relief
this luncheon, this day, this meeting of strangers. But Clarissa only
gossiped on; at last, when I was beginning to go over in my mind the
various formulae which make departure easy, our hostess, as though
aware that she had drawn out too long the overture, said abruptly,
“Eugene, show Iris the garden. She has never seen it before.” And
then, heartily firing fragments of sentences at us as though in
explanation of this move of hers, she left the room, indicating that the
rest was up to us.
Puzzled, we both went onto the terrace and into the yellow
afternoon. We walked slowly down the steps towards the rose
arbors, a long series of trellis arches forming a tunnel of green, bright
with new flowers and ending in a cement fountain of ugly tile with a
bench beside it, shaded by elms.
We got to facts. By the time we had burrowed through the roses to

the bench, we had exchanged those basic bits of information which
usually make the rest fall (often incorrectly) into some pattern, a
foundation for those various architectures people together are
pleased to build to celebrate friendship or enmity or love or, on very
special occasions, in the case of a grand affair, one of those fine
palaces with rooms for all three, and much else besides.
Iris was from the Middle West, from a rich suburb of Detroit. This
interested me in many ways, for there still existed in those days a
real disaffection between East and Midwest and Far West which is
hard to conceive nowadays in that gray homogeneity which currently
passes for a civilized nation. I was an Easterner, a New Yorker from
the valley with Southern roots, and I felt instinctively that the
outlanders were perhaps not entirely civilized. Needless to say, at
the time, I would indignantly have denied this prejudice had
someone attributed it to me, for those were the days of tolerance in
which all prejudice had been banished, from conversation at least ...
though of course to banish prejudice is a contradiction in terms
since, by definition, prejudice means prejudgment, and though time
and experience usually explode for us all the prejudgments of our
first years, they exist, nevertheless, as part of our subconscious, a
sabotaging, irrational force, causing us to commit strange crimes
indeed, made so much worse because they are often secret even to
ourselves. I was, then, prejudiced against the Midwesterner ...
against the Californians too. I felt that the former especially was
curiously hostile to freedom, to the interplay of that rational Western
culture which I had so lovingly embraced in my boyhood and grown
up with, always conscious of my citizenship in the world, of my role
as a humble but appreciative voice in the long conversation. I
resented the automobile manufacturers who thought only of
manufacturing objects, who distrusted ideas, who feared the fine
with the primitive intensity of implacable ignorance. Could this cool
girl be from Detroit? From that same rich suburb which had provided
me with a number of handsome vital classmates at school? Boys
who had combined physical vigor with a resistance to all ideas but
those of their suburb which could only be described as heroic
considering the power of New England schools to crack even the
toughest prejudices, at least on the rational level. That these boys
did not possess a rational level had often occurred to me, though I
did, grudgingly, admire, even in my scorn, their grace and strength
as well as their confidence in that assembly line which had provided
their parents with large suburban homes and themselves with a
classical New England education which, unlike the rest of us, they’d
managed to resist ... the whole main current of Western civilization
eddying helplessly about these youths who stood, pleasantly firm,
like so many rocks in a desperate channel.
Iris Mortimer was one of them. Having learned this there was nothing
to do but find sufficient names between us to establish the
beginnings of the rapport of class which, even in that late year of the
mid-century, still existed: the dowdy aristocracy to which we
belonged by virtue of financial security, at least in childhood, of
education, of self-esteem and of houses where servants had been in
some quantity before the second of the wars; all this we shared and
of course those names in common of schoolmates, some from her
region, others from mine, names which established us as being of an
age. We avoided for some time any comment upon the names,
withholding our true selves during the period of identification. I
discovered too that she, like me, had remained unmarried, an
exceptional state of affairs, for all the names we had mentioned
represented two people now instead of one. Ours had been a
reactionary generation which had attempted to combat the time of
wars and disasters by a scrupulous observance of its grandparents’
customs, a direct reaction to the linking generation whose lives had
been so entertainingly ornamented with self-conscious, untidy
alliances, well-fortified by suspect gin. The result was no doubt
classic but, at the same time; it was a little shocking: their children
were decorous, subdued; they married early, conceived glumly,
surrendered to the will of their own children in the interests of
enlightened psychology; their lives enriched by the best gin in the
better suburbs, safe among their own kind. Yet, miraculously, I had
escaped and so apparently had Iris. Both, simultaneously, were
aware of this: that sort of swift, unstated communication which briefly
makes human relationships seem more potential, more meaningful
than actually they are: it is the promise perhaps of a perfect harmony
never to be achieved in life’s estate.
“You live here alone?” She indicated the wrong direction though
taking in, correctly, the river on whose east bank I did live, a few
miles to the north of Clarissa.
I nodded. “Entirely alone ... in an old house.”
She sighed. “No family?”
“None here. Not much anywhere else. A few in New Orleans, my

family’s original base.” I waited for her to ask if I never got lonely
living in a house on the river, remote from others; but she saw
nothing extraordinary in this.
“It must be fine,” she said slowly. She broke a leaf off a flowering
bush whose branch, heavy with blooming, quivered above our heads
as we sat on the garden bench and watched the dim flash of goldfish
in the muddy waters of the pond.
“I like it,” I said, a little disappointed that there was now no
opportunity for me to construct one of my familiar defenses of a life
alone: I had, in the five years since my days of travel had temporarily
ended, many occasions on which to defend and glorify the solitary
life I had chosen for myself beside this river. I had an ever-changing
repertoire of feints and thrusts: for instance, with the hearty, I
invariably questioned, gently of course, the virtue of a life in the city,
confined to a small apartment with uninhibited babies and breathing
daily large quantities of soot; or then I sometimes enjoyed assuming
the prince of darkness pose, alone with his crimes in an ancient
house, a figure which could, if necessary, be quickly altered to the
more engaging one of remote observer of the ways of men, a stoic
among his books, sustained by the recorded fragments of forgotten
bloody days, evoking solemnly the pure essences of nobler times a
chaste intelligence beyond the combat, a priest celebrating the cool
memory of his race. My theater was extensive and I almost regretted
that with Iris there was no need for even a brief curtain raiser, much
less one of my exuberant galas.
Not accustomed to the neutral response, I stammered something

about the pleasures of gardens; Iris’s calm indifference saved me
from what might have been a truly mawkish outburst calculated to
interest her at any cost (mawkish because, I am confident, that none
of our deepest wishes or deeds is, finally, when honestly declared,
very wonderful or mysterious: simplicity not complexity is at the
center of our being; fortunately the trembling “I” is seldom revealed,
even to paid listeners, for, conscious of the appalling directness of
our needs, we wisely disguise their nature with a legerdemain of
peculiar cunning). Much of Iris’s attraction for me ... and at the
beginning that attraction did exist ... was that one did not need to
discuss so many things: of course the better charades were not
called into being which, creatively speaking, was a pity; but then it
was a relief not to pretend and, better still, a relief not to begin the
business of plumbing shallows under the illusion that a treasure
chest of truth might be found on the mind’s sea floor ... a grim ritual
which was popular in those years, especially in the suburbs and
housing projects where the mental therapists were ubiquitous and
busy.
With Iris, one did not suspend, even at a cocktail party, the usual
artifices of society. All was understood, or seemed to be, which is
exactly the same thing. We talked about ourselves as though of
absent strangers. Then: “Have you known Clarissa long?” I asked.
She shook her head. “I met her only last winter.”
“Then this is your first visit here? to the valley?”
“The first,” she smiled, “but it’s a little like home, you know. I don’t
mean Detroit, but a memory of home, got from books.”
I thought so too. Then she added that she did not read any longer
and I was a little relieved; somehow with Iris one wanted not to talk
about books or the past. So much of her charm was that she was
entirely in the present. It was her gift, perhaps her finest quality, to
invest the moment with a significance which in recollection did not
exist except as a blurred impression of excitement. She created this
merely by existing. I was never to learn the trick, for her conversation
was not, in itself, interesting and her actions were usually calculable
in advance, making all the more unusual her peculiar effect. She
asked me politely about my work, giving me then the useful
knowledge that, though she was interested in what I was doing, she
was not much interested in the life of the Emperor Julian.
I made it short. “I want to do a biography of him. I’ve always liked

history and so, when I settled down in the house, I chose Julian as
my work.”
“A life’s work?”
“Hardly. But another few years. It’s the reading which I most enjoy,
and that’s treacherous. There is so much of interest to read that it
seems a waste of time and energy to write anything ... especially if
it’s to be only a reflection of reflections.”
“Then why do it?”
“Something to say, I suppose; or at least the desire to define and

illuminate ... from one’s own point of view, of course.”
“Then why ... Julian?”
Something in the way she said the name convinced me she had
forgotten who he was if she had ever known.
“The apostasy; the last stand of paganism against Christianity.”
She looked truly interested, for the first time. “They killed him, didn’t
they?”
“No, he died in battle. Had he lived longer he might at least have

kept the Empire divided between the old gods and the new messiah.
Unfortunately his early death was their death, the end of the gods.”
“Except they returned as saints.”
“Yes, a few found a place in Christianity, assuming new names.”
“Mother of God,” she murmured thoughtfully.
“An unchristian concept, one would have thought,” I added, though

the beautiful illogic had been explained to me again and again by
Catholics: how God could and could not at the same time possess a
mother, that gleaming queen of heaven, entirely regnant in those
days.
“I have often thought about these things,” she said, diffidently. “I’m
afraid I’m not much of a student but it fascinates me. I’ve been out in
California for the past few years, working. I was on a fashion
magazine.” The note was exactly right: she knew precisely what that
world meant and she was neither apologetic nor pleased. We both
resisted the impulse to begin the names again, threading our way
through the maze of fashion, through that frantic world of the
peripheral arts.
“You kept away from Vedanta?” A group of transplanted English
writers at this time had taken to oriental mysticism with great
eagerness, an atonement no doubt for their careers as movie
writers. Swamis and temples abounded among the billboards and
orange trees; but since it was the way for some it was, for those few
at least, honorable.
“I came close.” She laughed. “But there was too much to read and
even then I always felt that it didn’t work for us, for Americans, I
mean. It’s probably quite logical and familiar to Asiatics, but we come
from a different line, with a different history; their responses aren’t
ours. But I did feel it was possible for others, which is a great deal.”
“Because so much is really not possible?”
“Exactly. But then I know very little about these things.” She was
direct: no implication that what she did not know either did not exist
or was not worth the knowing, the traditional response in the
fashionable world.
“Are you working now?”
She shook her head. “No, I gave it up. The magazine sent somebody
to take my place out there (I didn’t have the 'personality’ they
wanted) and so I came on to New York where I’ve never really been,
except for week ends from school. The magazine had some idea
that I might work into the New York office, but I was through. I have
worked.”
“And had enough?”
“For that sort of thing, yes. So I’ve gone out a lot in New York, met
many people; thought a little....” She twisted the leaf that she still
held in her fingers, her eyes vague as though focused on the leaf’s
faint shadow which fell in depth upon her dress, part upon her dress
and more on a tree’s branch ending finally in a tiny fragment of
shadow on the ground, like the bottom step of a frail staircase of air.
“And here you are, at Clarissa’s.”
“What an extraordinary woman she is!” The eyes were turned upon
me, hazel eyes, very clear, the whites luminous with youth.
“She collects people, but not according to any of the usual criteria.
She makes them all fit, somehow, but what it is they fit, what design,
no one knows. I don’t know, that is.”
“I suppose I was collected. Though it might have been the other way
around, since I am sure she interests me more than I do her.”
“There is no way of telling.”
“Anyway, I’m pleased she asked me here.”
We talked of Clarissa with some interest, getting nowhere. Clarissa

was truly enigmatic. She had lived for twenty years on the Hudson.
She was not married but it was thought she had been. She
entertained with great skill. She was in demand in New York and also
in Europe where she often traveled. But no one knew anything of her
origin or of the source of her wealth and, oddly enough, although
everyone observed her remarkable idée fixe, no one ever discussed
it, as though in tactful obedience to some obscure sense of form. In
the half-dozen years that I had known her not once had I discussed
with anyone her eccentricity. We accepted in her presence the reality
of her mania, and there it ended. Some were more interested by it
than others. I was fascinated, and having suspended both belief and
doubt found her richly knowing in matters which interested me. Her
accounts of various meetings with Labianus in Antioch were quite
brilliant, all told most literally, as though she had no faculty for
invention which perhaps, terrifying thought, she truly lacked, in which
case ... but we chose not to speculate. Iris spoke of plans.
“I’m going back to California.”
“Tired of New York?”

“No, hardly. But I met someone quite extraordinary out there,
someone I think I should like to see again.” Her candor made it
perfectly clear that her interest was not romantic. “It’s rather in line
too with what we were talking about. I mean your Julian and all that.
He’s a kind of preacher.”
“That doesn’t sound promising.” A goldfish made a popping sound as

it captured a dragonfly on the pond’s surface.
“But he isn’t the usual sort of thing at all. He’s completely different
but I’m not sure just how.”
“An evangelist?” In those days loud men and women were still able
to collect enormous crowds by ranging up and down the country
roaring about that salvation which might be found in the bosom of
the Lamb.
“No, his own sort of thing entirely. A little like the Vedanta teachers,
only he’s American, and young.”
“What does he teach?”
“I ... I’m not sure. No, don’t laugh. I only met him once. At a friend’s
house in Santa Monica. He talked very little but one had the feeling
that, well, that it was something unusual.”
“It must have been if you can’t recall what he said.” I revised my first
estimate: it was romantic after all; a man who was young, fascinating
... I was almost jealous as a matter of principle.
“I’m afraid I don’t make much sense.” She gestured and the leaf fell
into its own shadow on the grass. “Perhaps it was the effect he had
on the others that impressed me. They were clever people, worldly
people yet they listened to him like children.”
“What does he do? does he preach? work?”

“I don’t know that either. I met him the night before I left California
and I haven’t seen anyone who was there that evening since.”
“But now you think you want to go back to find out?”
“Yes. I’ve thought about him a great deal these last few weeks. You’d
think one would forget such a thing, but I haven’t.”
“What was his name?”
“Cave, I think. John Cave.”
“A pair of initials calculated to amaze the innocent.” Yet even while I

invoked irony, I felt with a certain chill in the heat that this was to be
Clarissa’s plot, and for many days afterwards that name echoed in
my memory, long after I had temporarily forgotten Iris’s own name,
had forgotten, as one does, the whole day, the peony in the
boxwood, the leaf’s fall and the catch of the goldfish; instants which
now live again in the act of recreation, details which were to fade into
a yellow-green blur of June and of the girl beside me in a garden and
of that name spoken in my hearing for the first time, becoming in my
imagination like some bare monolith awaiting the sculptor’s chisel.
Two
1
I did not see Iris again for some months. Nor, for that matter, did I
see Clarissa who, the day after our lunch, disappeared on one of her
mysterious trips ... this time to London, I think, since she usually got
there for the season. Clarissa’s comings and goings doubtless
followed some pattern though I could never make much sense of
them. I was very disappointed not to see her before she left because
I had wanted to ask her about Iris and also ...
It has been a difficult day. Shortly after I wrote the lines above, this
morning, I heard the sound of an American voice on the street-side
of the hotel; the first American voice I’ve heard in some years for,
excepting me, none has been allowed in Upper Egypt for twenty
years. The division of the world has been quite thorough, religiously
and politically, and had not some official long ago guessed my
identity it is doubtful that I should have been granted asylum even in
this remote region.
I tried to continue with my writing but it was impossible: I could recall

nothing. My attention would not focus on the past, on those wraiths
which have lately begun to assume again such startling reality as I

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First Aid 2022 32nd Edition Edition Tao

First Aid for the USMLE Step 1 2022, 32e Tao Le

First Aid for the USMLE Step 1 2022 - A Student-to-

First Aid For The USMLE Step 1 2018 Tao Le

First Aid for the Basic Sciences. General Principles

First Aid Cases For The USMLE Step 1 4th Edition

First Aid for the USMLE Step 1 2019, Twenty-Ninth

First Aid for the USMLE Step 1 2020, 30th Anniversary

First Aid for the USMLE Step 1 2019, Twenty-Ninth

Contributing Authors vii General Acknowledgments xiii

Introduction 2 Test-Taking Strategies 19

` SECTION I SUPPLEMENT S P E C I A L S I T UAT I O N S 25

` SECTION II HIGH-YIELD GENERAL PRINCIPLES 27

How to Use the Database 28 Pathology 203

FAS1_2022_00_Frontmatter.indd 5 11/10/21 10:50 AM

How to Use the Database 738 Biochemistry 742

FAS1_2022_00_Frontmatter.indd 6 11/10/21 10:50 AM

DNA was the first three-dimensional Xerox machine.

This high-yield material includes molecular biology, genetics, cell

Do not spend time learning details of organic chemistry, mechanisms, or

FAS1_2022_01-Biochem.indd 31 11/4/21 11:59 AM

Chromatin structure DNA exists in the condensed, chromatin form to

Heterochromatin Condensed, appears darker on EM (labeled H Heterochromatin = highly condensed.

Euchromatin Less condensed, appears lighter on EM (labeled Eu = true, “truly transcribed.”

FAS1_2022_01-Biochem.indd 32 11/4/21 11:59 AM

Nucleotides Nucleoside = base + (deoxy)ribose (sugar).

Purines (A,G)—2 rings. Pure As Gold.

N10–Formyl- Nitrogenous base CH₂

FAS1_2022_01-Biochem.indd 33 11/4/21 11:59 AM

Hydroxyurea AMP GMP monophosphate dehydrogenase

Purine and pyrimidine synthesis:

5-FU, and pyrimethamine: inhibit dihydrofolate

CPS1 = m1tochondria, urea cycle, found in liver

FAS1_2022_01-Biochem.indd 34 11/4/21 11:59 AM

Purine salvage deficiencies

Nucleic acids Ribose 5-phosphate Nucleic acids

Genetic code features

FAS1_2022_01-Biochem.indd 35 11/4/21 11:59 AM

FAS1_2022_01-Biochem.indd 36 11/4/21 11:59 AM

joining repair double-stranded breaks. 3´ 5´ 3´

homologous dsDNA as a template. Homologous recombination

UV exposure Pyrimidine dimer Deaminated C

Newly replaced segment

Nucleotide excision repair Base excision repair Mismatch repair

FAS1_2022_01-Biochem.indd 37 11/4/21 11:59 AM

Altered amino acids

AUG AUG AUG

FAS1_2022_01-Biochem.indd 38 11/4/21 11:59 AM

DNA 5´ CAAT TATAAA GT AG GT AG AATAAA 3´

Regulation of gene expression

FAS1_2022_01-Biochem.indd 39 11/4/21 11:59 AM

Cleavage at 5′ splice site; lariat-

FAS1_2022_01-Biochem.indd 40 11/4/21 11:59 AM

Exon 1 Exon 2 Exon 3 Exon 4 Exon 5 Exon 6

FAS1_2022_01-Biochem.indd 41 11/4/21 11:59 AM

Start and stop codons

FAS1_2022_01-Biochem.indd 42 11/4/21 11:59 AM

FAS1_2022_01-Biochem.indd 43 11/4/21 11:59 AM

Cell cycle arrest

Caspase activation E2F G2

FAS1_2022_01-Biochem.indd 44 11/4/21 11:59 AM

COPII Vesicular trafficking proteins

FAS1_2022_01-Biochem.indd 45 11/4/21 11:59 AM

Peroxisome Membrane-enclosed organelle involved in:

Fibroblast Preprocollagen S ynthesis—translation of collagen α

enaturation—DNA template, DNA primers, a heat-stable DNA polymerase, and