Cell/Molecular Biology Notes:

[purple = step 1 drill questions]

Receptors + Hormones:

1. What hormones use cAMP? “G FLAT C2HAMP”

a. Glucagon CRH
Calcitonin
FSH HCG
LH ADH (V2)
ACTH MSH
TSH PTH
2. Hormones that use IP3? “G2OAT”
a. GnRH
b. GHRH
c. Oxytocin
d. ADH (V1)
e. TRH
3. Receptors that use Gq? “HAVe 1 M+M”
a. Histamine1
b. α1
c. V1
d. M1
e. M2
4. Receptors that use Gi? “MAD 2’s”
a. M2, α2, D2
5. Receptors that use Gs?
a. β1, β2, β3, V2, H2, D1
6. What are the steroid hormones? “PET CAT on TV”
a. Progesterone Cortisol
b. Estrogen Aldosterone
c. Testosterone Thyroxine (T3)
d. T4 Vitamin D

DNA + Chromosomes:

1. Structure of DNA + Proteins bound to it?

a. DNA = negatively charged + tightly wound with histones
b. Histones have 8 subunits and a H1 linker
c. Condensed with chromatin in the cells
d. Barr bodies: inactive X chromosomes
2. What is heterochromatin and euchromatin?
a. Heterochromatin – highly condensed and NOT mitotically active
 b. Euchromatin – Less condensed and is transcriptionally active
3. Methylation and acetylation of DNA and histones
a. Template DNA is methylated at cysteine and adenine to allow mismatch repair
enzymes to recognize the old and new DNA
b. DNA methylation at CpG islands ceases DNA replication
c. Methylation of Histones – reversible repression of DNA replication
d. Acetylation of Histones – relaxes DNA coiling making it available for replication
4. Describe the different nucleotides of DNA? Purines, Pyrimidines?
a. Ribose nucleotides are made 1st and then converted to deoxy forms by
ribonucleotide reductase
b. Nucleosides = base + (deoxy)ribose
c. Nucleotides = base + sugar + phosphate
i. Phosphodiester bond 3’  5’
d. Purines:
i. Adenosine, guanine
ii. 2 rings, glycine, aspartate, and glutamine needed for synthesis
e. Pyrimidines:
i. Cytosine, thymine, uracil (RNA)
ii. Require carbonyl phosphate and aspartate
5. Describe the synthesis of pyrimidines:
a. Glutamine + CO2 = Carbamoyl phosphate via carbamoyl phosphate synthetase II
b. Carbamoyl phosphate + aspartate = orotic acid
i. Inhibited by Leflunomide
c. Orotic acid + PRPP = UMP
d. UMP  UDP  CTP
e. UDP  deoxyUDP via ribonucleotide reductase
i. Inhibited by Hydroxyurea
f. deoxyUDP + methylene Tetrahydrofolate (THF)  dTMP + dihydrofolate via
thymidylate synthetase
i. inhibited by 5-fluorouracil (5-FU)
g. THF is made via DHF being reduced by dihydrofolate reductase
i. Inhibited by methotrexate (MTX), trimethoprim (TMP), + pyrimethamine
in humans, bacteria + protozoa)
6. Purine salvage deficiencies:
a. ADA is involved in converting adenosine  inosine
b. ADA def  excess ATP + dATP  inhibition of ribonuclease reductase  this
prevents DNA synthesis and leads to ↓ lymphocyte count
c. This is a major cause of AR SCID
7. Describe Lesch-Nyhan syndrome:
a. Absent hypoxanthine guanine phosphoribosyltransferase (HGPRT)
i. Important in converting hypoxanthine  IMP and guanine  GMP
ii. Leads to ↑↑ uric acid + de novo purine synthesis
b. XR disorder
c. Findings:
 i. Learning disability
ii. Self-harm
iii. Aggressive
iv. Hyperuricemia  gout
v. Dystonia
d. “HGPRT”:
i. Hyperuricemia
ii. Gout
iii. Pissed off (aggressive)
iv. Retardation (mental)
v. dysTonia
e. Treatment?
i. Allopurinol or febuxostat
1. Inhibits xanthine oxidase  prevents hyperuricemia

DNA Replication:

1. Semi-conservative
a. Keeps a parent strand in each new double strand of DNA
2. Both continuous and discontinuous using okazaki fragments (short newly synthesized
DNA strands)
3. Origin of replication:
a. Where DNA replication begins
4. Replication fork:
a. Y-shaped region where DNA separates into leading and lagging strands that can
be synthesized
5. Helicase:
a. Unwinds DNA template at replication fork
6. Single stranded proteins:
a. Bind to DNA preventing it from reannealing
7. DNA topoisomerases. ID drug that inhibits prokaryote enzymes:
a. Add/remove supercoils
b. Fluoroquinolones (i.e. Ciprofloxacin) bind to II/IV topoisomerases inhibiting
prokaryote DNA replication
8. DNA primase:
a. Makes RNA primer for DNA polymerase to initiate replication
9. DNA polymerase III:
a. Prokaryote only!
b. Elongates DNA strand by adding deoxy nucleotides to 3’ end (5’  3’)
c. Elongates until it reaches the lagging strand of the primer preceding it
d. Proof reads in 3’  5’ direction
10. DNA polymerase I:
a. Degrades RNA primer and replaces it with DNA
b. 5’  3’ synthesis with excision of RNA primer
 11. DNA ligase:
a. Catalyzes formation of phosphodiester bond within a dsDNA
b. Joins up okazaki fragments
12. Telomerase:
a. RNA depended DNA polymerase
b. Adds DNA to 3’ ends of chromosomes to avoid loss of genetic material at end of
replication

Mutations in DNA and Repair:

[[put in examples here‼]]

1. Silent mutation:
a. Nucleotide substitution but codes for the same amino acid
b. Often a base change in 3rd position of codon (tRNA wobble)
2. Missense mutation:
a. Substitution leading to change in amino acid
i. Conservative if amino acid is similar in structure
b. Ex. sickle cell anemia: glutamic acid  valine
3. Nonsense mutation:
a. Substitution leads to early stop codon leading to shortened reading frame
4. Frameshift mutation:
a. Deletion of insertion of nucleotide leading to alteration of reading frame
b. Causes misreading of all nucleotides DOWNstream of mutation and causes a
truncated or non-functional protein
5. Transition:
a. A  G or C  T
6. Transversion:
a. A/G  C/T
7. DNA repair: ssDNA needs to be repaired sometimes by what methods?
a. Nucleotide excision repair – endonucleases cut out mutations, polymerase and
ligase fill and reseal the gap
i. This repairs large helix distorting lesion + occurs in G1 cell cycle
ii. This mech is defective in Xeroderma Pigmentosa (XP) – pyrimidine dimers
not repaired after UV exposure
8. Base excision repair: [[put examples here‼]]
a. Base specific glycosylase removes altered base and creates empty site
b. Nucleotides are removed by AP-endonucleases which cleaves 5’ end
c. Lyase cleaves 3’ end and DNA polymerase β fills the gap and DNA ligase seals it
9. Mismatch repair: [[put examples here‼]]
a. Newly synthesized strand is recognized, mismatched nucleotides removed, and
gap is filled and resealed
b. Occurs in G2 phase
c. Defective in HNPCC
10. Double stranded repair: non homologous end joining:
 a. 2 ends of DNA together to repair double stranded breaks
b. defective in ataxia telangiectasia + fanconi anemia
11. DNA/RNA/protein synthesis direction?
a. DNA and RNA both synthesized in 5’  3’
i. 5’ has triphosphate energy source, 3’ hydroxyl attack)
ii. Drugs that block DNA replication often have modified 3’-OH in order to
block this (chain termination)
b. mRNA read 5’  3’
c. Protein synthesis occurs N-terminus  C-terminus
12. Stop and start codons are:
a. mRNA – AUG (methionine sometimes removed before translation is completed)
b. in prokaryotes – fMet – this stimulates neutrophil chemotaxis
c. Stop codons – UGA, UAA, UAG – “U Go Away! U Are Away! U Are Gone!”

Lac Operon: [[NOT High Yield – waste of time!]]

1. Lac operon is an example of genetic response to environmental change. What happens

when glucose is absent and lactose available?
a. Lac operon activated to switch to lactose metabolism
b. Low GLU  ↑ adenylyl cyclase activity  cAMP generated  activation of
catabolite activator protein (CAP)
c. CAP binds to lac operon  +transcription
d. When lactose available, allolactose binds to repressor protein allowing RNA
polymerase to bind and LAc genes are strongly expressed
e. If lactose is NOT available, repressor binds to Operator region  inhibiting
transcription
2. Organization of eukaryote gene: promoter region
a. Where RNA polymerase II and other transcription factors bind to DNA UPstream
from the gene
b. AT-rich area – TATA or CAAT boxes
c. If mutated?  ↓ gene expression
3. Enhancer/Silencer region:
a. Lies UPstream to gene and alters gene expression through binding of
transcription factors

RNA production and processing:

1. Eukaryotes: RNA polymerase I

a. Makes rRNA (ribosomal RNA that’s needed for protein synthesis)
b. 2 subunits involved in forming peptide bonds between amino acids
2. RNA polymerase II:
a. Makes mRNA (messenger RNA), which is a transcription of DNA
b. Pre-mRNA made, then spliced together to make mature mRNA, which is moved
to the ribosomes for translation
 c. Inhibited by Death cap (amanita phalloides) mushroom
3. RNA polymerase IIIL:
a. Makes tRNA (transfer RNA), for protein synthesis for individual codons
b. Brings individual amino acids to ribosome for protein synthesis
4. In prokaryotes?
a. One 1 multiunit RNA polymerase used to create all 3 types of RNA
b. Rifampicin disrupts prokaryotic RNA
c. Actinomycin D inhibits RNA polymerase in both prokaryotes and eukaryotes
5. Initial transcription product of DNA is called?
a. Heterogeneous nuclear RNA (hnRNA)
b. This is modified to mRNA
6. RNA processing:
a. hnRNA is capped at 5’ end with Gppp (7-methylguanosine cap)
i. Then, polyadenylation of 3’ (200-A’s) spliced out of introns
b. hnRNA  capped, tailed, and then spliced = mRNA
7. Splicing is a process whereby pre-mRNA is…
a. Combined with small nuclear RiboNuclearProteins (RNP) form a spliceosome
b. Formed into a lariat knot, then lariat released thereby removing the intron
8. Problems in splicing:
a. Antibodies to snRNPs (anti-Smith antibodies) = specific for SLE
b. Antibodies to U1 RNP = Mixed connective tissue disease
c. Abnormal splicing = β-thalassemia
9. Introns are:
a. Non-coding segments of DNA (not expressed; in between)
10. Exons are:
a. Coding segments of DNA (expressed as proteins)
b. Different exons can be combined in alternative patterns to form huge number of
different proteins
11. What is tRNA and its structure?
a. RNA responsible for transporting individual amino acids into ribosomes for
protein synthesis
b. Clover leaf structure
c. Contains anti-codon (of mRNA codon specific for amino acid)
d. T-arm is necessary for tRNA-ribosome binding
e. D-arm with dyhydrouracil residues for aminoacyl-tRNA synthetase recognition
f. 5’-CCA-3’ acceptor stem where amino acid binds
12. What enzyme binds the amino acids to tRNA acceptor arm?
a. Aminoacyl-tRNA synthetase binds amino acid to the cca-3’ acceptor site
13. What is a wobble?
a. Accurate amino acid pairing requires the first 2 nucleotide position
b. 3rd position = wobble position, where a different amino acid may code for same
amino acid

Protein synthesis:
[[give examples of drugs‼]]
1. Ribosomes involved in eukaryotic protein synthesis:
a. 40S + 60S subunits  80S ribosome
2. Ribosomes involved in prokaryotic protein synthesis:
a. 30S + 50S  70S ribosome
3. describe initiation of protein synthesis:
a. GTP hydrolysis and initial factors assemble 40S ribosome subunits and the 60S
subunit with mRNA
4. Describe elongation of protein:
a. Aminoacyl-tRNA binds to A site in ribosome complex
b. rRNA catalyzes peptide bond formation binding polypeptide to new amino acid
in A site
c. Ribosome advances 3 nucleotides along the mRNA (5’  3’) with the peptidyl
tRNA moving into P site
5. Describe termination of protein synthesis:
a. Stop codon (UAA/UGA/UAG) recognized and polypeptide released
6. Describe A, P, and E sites of the ribosome:
a. A = Accommodates incoming Aminoacyl-tRNA
i. tRNA + amino acid
b. P = Peptide bond
c. E = Exit of used tRNA
7. Describe post-translational modifications of proteins:
a. Occur within Golgi apparatus
b. Trimming = removal of N-/C-terminus
c. Covalent alterations = phosphorylation, glycosylation, hydroxylation,
methylation, acetylation, and ubiquitination
8. What does the rough endoplasmic reticulum (RER) do?
a. Has many ribosomes present
b. Site of synthesis of secretory proteins + adds N-linked oligosaccharides to
proteins
c. Mucous secreting cells + plasma cells are rich in RER
9. What is a Nissl body?
a. RER in neurons that synthesize neurotransmitters
10. Describe Smooth endoplasmic reticulum (SER):
a. No ribosomes!
b. Site of steroid synthesis in adrenal cortex and gonads
c. Detoxification of drugs/poisons in hepatocytes
11. What is the function of the Golgi apparatus?
a. Involved in cell trafficking and distribution of proteins and lipids from ER to
vesicles and the plasma membrane
b. Modifies proteins for packaging
c. Endosomes sort incoming material and can send it to lysosomes for destruction
or to Golgi for use
 12. What is I-cell disease?
a. Inclusion cell disease – inherited lysosomal storage disorder
b. Defect in N-acetylglucosamine-1-phosphotransferase (GNPTA)  Golgi unable
to phosphorylate mannose residues (↓ mannose-6-phosphate) on glycoproteins
 excretion (instead of lysosome packaging)
13. What are the characteristics of I-cell disease?
a. Coarse facial features
b. Clouded corneas
c. Restricted joint movement
d. High plasma levels of lysosomal enzymes
e. Often fatal in childhood
14. What are peroxisomes and proteasomes? [[DZ???]]
a. Peroxisome = membrane enclosed organelle involved in catabolism of VLCFAs,
amino acids, and other branched fatty acids
b. Proteasome = protein complex that degrades damaged or ubiquitin-tagged
proteins
c. Problems in this system indicated in Parkinson’s disease

Cell cycle:

1. Name the 5 phases of the cell cycle:

a. M phase = mitosis (prophase, prometaphase, metaphase, anaphase, telophase)
and cytokinesis (cell division)
b. G0 phase = cells inactive and repair occurs here
c. G1 phase = growth phase, where cell primes itself for DNA synthesis
d. S phase = DNA synthesis
e. G2 phase = growth phase prior to mitosis
2. How is the cell cycle regulated?
a. Cyclins and cyclin dependent kinases (CDKs) bind together to form complexes
that phosphorylate different proteins in order to progress through cycle
b. Tumor suppressor genes (like p53 or Rb) involved in restricting cell progression
from G1  S if DNA damage is present
i. Damaged in Li Fraumeni syndrome
3. Cell types: Permanent
a. Generated from stem cells and remain in G0, do not undergo division after
production after production
b. Neurons, cardiac and skeletal muscle, RBCs
4. Cell types: Stable (Quiescent)
a. Cells that enter G1 if stimulated by damage or environmental factors
b. Ex: hepatocytes and lymphocytes
5. Cell types: Labile
a. NEVER enter G0
b. Constantly renewing and reproducing
c. Affected by chemotherapy
 d. Ex: bone marrow, gut epithelium, skin, hair follicles, germ cells

Cell structures:

1. What is the function and an example of a microfilament?

a. Function = muscle contraction – actin
b. Ex: cytokinesis
2. …Intermediate filaments?
a. Function = maintain cell structure
b. Ex: vimentin, desmin, neurofilaments, cytokeratin
3. …microtubules?
a. Function = movement and cell division
b. Ex: cilia, flagella, mitotic spindles, centrioles
4. Name some immunohistochemical stains for intermediate filaments.
a. Vimentin = connective tissue stain = Raynaud, SLE, Mixed Connective Tissue Dz
(anti-U1 RNP antibody)
b. Desmin = muscle stain = Duchenne, Becker
c. GFAP = neuroglial stain
5. Describe the microtubule structure.
a. Made up of heterodimers of α and β tubulin – each dimer has 2 GTP
b. Involved in axoplasmic transport in neurons
c. Dynein moves cargo from pos  neg (Retrograde)
d. Kinesin moves cargo from neg  pos (Anterograde)
6. Name 5 drugs that act on microtubules.
a. Mebendazole = antihelminthic
b. Griseofulvin = antifungal
c. Colchicine = antigout
d. Vincristine/vinblastine = anticancer
e. Paclitaxel = anticancer
7. Describe the structure of cilia.
a. 9 microtubule doublets in periphery + 2 centrally
b. Axonemal dynein =ATPase that links peripheral doublets causing bending of
cilium
8. What is Kartegener syndrome?
a. Aka Primary ciliary dyskinesia
b. Immotile cilia d/t defect in dynein arm
c. Leads to male and female infertility d/t immotile sperm and dysfunctional
fallopian tubes
d. ↑ risk of ectopic preg, bronchiectasis, recurrent sinusitis, situs inversus
(dextrocardia)
e. “radial spoke problem”  descriptor for Kartagener on Step 1 exam ‼
9. Plasma membrane composition:
a. Asymmetrical phospholipid bilayer
b. Contains cholesterol, phospholipids, sphingolipids, glycolipids, and proteins
 c. Fungal cell walls contain ergosterol (disrupted by amphoB, itraconazole, and
miconazole)
10. Describe the Na+/K+ ATPase pump.
a. Transmembrane transporter
b. 3 Na+ out of the cell and 2 K+ into the cell
c. 3 Na+ enter  ATP binds  Na+ exit cell  2 K+ bind  dephosphorylation of
pump  2 K+ released inside cell
d. Inhibitor: Digoxin/digitalis
i. Binds to pump  ↑ intracellular Ca2+ (prevents Ca2+ from leaving cell) 
prolonged cardiac cycle and ↑ cardiac contractility