Ch.

16 Molecular Basis of Inheritance

 Important people
o Fred. Griffith - transformation
o Alfred Hershey, Marta Chase - only phage DNA entered host
o Rosalind Franklin - DNA images through X-ray crystallography
 Enzymes in Replication
o Helicase
o Single stranded binding proteins - prevent re-pairing
o Topoisomerase
o RNA primer
 RNA primase - molecular brake
o DNA polymerase
 only adds to 3' end (5 - 3 manner)
 replaces RNA w/ DNA
 proofreads
o DNA ligase

Definitions:

o Semiconservative model: two parent strands separate and each is a template for a new
complementary strand
o Leading: towards fork
o Lagging: away from fork
o Mismatch repair: other enzymes repair nucleotide errors evaded by DNA polymerase; if
replicated, it's a mutation
 Nucleotide excision repair: nuclease cuts out faulty DNA; DNA polymerase and ligase
replaces the nucleotides
o Telomeres: repetitive DNA at end of eukaryote chromosome; provide protection against
genes shortening after successful replication and from fusion of chromosomes
o Telomerase: lengthens telomeres in germ cells using RNA to extend leading strand
o Nucleosome: protein core with 8 histones; joined by linker DNA
o Heterochromatin: compact during interphase; not transcribed; methylated
 Opposite of euchromatin

CH. 17 Gene Expression

 Gene - transcription - mRNA - translation - protein - metabolic pathway - phenotype

 Important people
o Beatle and Tatum - mutant Neurospora needed complete medium to grow
 Not all proteins are enzymes
 Many proteins made from many genes
 1 gene can code for closely related polypeptide
 Some genes code for RNA
 Transcription stages - general to bacteria and eukaryotes
o Initiation
  Involves: promoter, start point, transcription initiation complex (transcription factors
+ RNA polymerase)
o Elongation
 RNA polymerase unwinds DNA and pairs it with RNA bases
o Termination
 Bacteria - transcribed terminator sequence acts as a signal for RNA polymerase to
detach
 Eukaryotes - polyadenylation sequence acts as a signal to cut mRNA from RNA pol.
RNA pol continues until enzymes degrade it
 5' cap - 5' UTR - start codon - intron/exon - stop codon - 3' UTR - poly-A tail
 5' cap and poly-A tail
o Speed export
o Protect from hydrolytic enzymes
 Untranslated regions (UTRs) bind to ribosome
 RNA functions as enzyme because
o Can base pair with itself
o Functional groups act like catalysts
o Can pair with other nucleic acids
 Translation stages - general to bacteria and eukaryotes; energy from GTP hydrolysis
o Initiation - requires initiation factors
 Small subunit and initiator tRNA bind to start codon
 Large subunit attaches
 Completes Translation Initiation Complex
o Elongation - requires elongation factors
 Anticodon recognizes codon; aminoacyl tRNA enters A site
 Polypeptide moved to attach to amino in A site
 Translocation from A to P site and P to E site; mRNA moves with bound tRNA
o Termination
 Release factor binds to stop codon and cleaves off polypeptide from P site
 Post translational modifications
o Attachment of molecules
o Removal of amino acids
o Polypeptide chain cleaved
o Accumulation of polypeptides
 Translation always begins in cytosol
 Making multiple polypeptides
o Polysomes
o Alternate RNA splicing
 Mutations
o Chromosomal rearrangements
o Substitutions - silent, missense, nonsense
o Insertions or deletions - frameshift
 Cause excessive missense/nonsense
o Spontaneous - errors in DNA replication and recombination
 Caused by mutagens (X-Ray, UV, carcinogens, nucleotide analogs)

Definitions:
  Gene expression: process by which DNA directs synthesis of proteins or RNA
o Central dogma: DNA - mRNA - Protein
 Codons: written in 5-3
 Coding strand: non-template DNA
o Genes sequence reported as non-coding strand
 RNA polymerase: unwinds DNA and adds RNA bases
 Promoter: DNA sequence where transcription begins; RNA pol binds here
o Start point: nucleotide downstream of promoter
 Terminator: DNA sequence where transcription ends; BACTERIA only
 TATA box: promoter in EUKARYOTES only
 Ribozyme: RNA as enzyme
o Ex. Spliceosome, intron
o Spliceosome: cut out introns, join together exons
 Alternate RNA splicing: final transcript differs based on which portions of pre-mRNA treated as
exons and introns
 Exon-shuffling: mix and match of different exons within a gene or two different genes during
meiosis
 tRNA: reads a mRNA codon and interpret it as an amino acid
 Wobble: flexibility in base pair rules, 3rd base in codon can pair with more than one base in
anticodon
 Aminoacyl-tRNA synthetase: enzyme family of 20 enzymes that match tRNA with amino, forming
aminoacyl-tRNA/charged tRNA
 A-Site: holds aminoacyl tRNA
 P-Site: holds peptidyl tRNA
 E-Site: exit site for tRNA
 Initiation factors: required to bring all components of translation initiation together
 Elongation factors: add amino acids from N-C terminus
 Signal recognition particles (SRPs): recognize signal peptides on free ribosomes and bring
ribosome to receptor in ER membrane
 Polysomes: ribosome chain that enable cell to make many polypeptides from 1 mRNA

CH. 18 Regulation of Gene Expression

 Feedback inhibition faster than negative/positive control

 Bacteria - operon model
o Operator: DNA segment that regulates enzyme production; controls binding of RNA
polymerase to promoter
o Operon: includes operator, promotor, and all genes they control
o Repressor: binds to operator to prevent transcription; allosteric enzyme
o Coded by regulatory gene: codes from proteins that control transcription
o Corepressor: activates repressor
o Inducer: inactivates repressor
o Negative gene control: operons switched on/off by repressor
o Repressible operon: transcription already on
 Repressible enzyme: produced continuously until stopped by corepressor
o Inducible operon: transcription already off by repressor
 Inducible enzyme: synthesis induced by inducer
 o Positive Gene control: activator directly binds to DNA to control rate of transcription
(volume control)
 Eukaryotes - more control over gene expression
o Chromatin modification
o Histone acetylation/methylation
o DNA methylation
o Epigenetic inheritance - chromatin modifications reversible, DNA modifications
permanent
o Transcription - DNA-binding proteins either promote/inhibit
o Control elements: noncoding DNA that serves as binding site for transcription factors
o General transcription factor: essential for transcription for all protein-coding genes;
low rate of transcription
o Specific transcription factor: bind to enhancer; high rate of transcription
 Activators and repressors
o Proximal control elements: near promoter
o Distal control elements/enhancer: bind to specific transcription factors
o Activators: promote simultaneous transcription of genes w/ same combo of control
elements
 DNA binding domain, activation domain
 Acetylate histones
o Repressor
 Bind directly to control element or block activators
 Un-acetylate histones
o Mediator proteins: connect specific to general transcription factors through DNA
bending protein
o RNA processing - adds complexity to form
o mRNA degradation/translation
o Regulatory proteins bind to UTR, preventing ribosomal attachment
o Bacteria mRNA degraded quickly, Eukaryotic mRNA lasts longer
o Protein degradation/secretion
o Proteasomes recognize proteins tagged with ubiquitin
o Phosphorylation activates proteins
o Post translational modifications
 Protein-coding DNA - 1.5%
 Non-Protein-coding DNA - forms ncRNAs
o rRNA, tRNA
o Small RNAs
o microRNAs: degrades mRNA
o siRNAs - lead to RNAi: silencing of gene expression
o Piwi-interacting RNAs: heterochromatin; gamete formation
o Long noncoding RNAs: X-inactivation
 Post-fertilization
o Cell division
o Differentiation
o Morphogenesis
 Which genes to express? Positional information provided by..
o Cytoplasmic determinants: maternal substances in egg
o Induction: cells influence differentiation of each other through close range interactions
  What causes proto-oncogenes to turn into oncogenes
o DNA movement
o Amplification of proto-oncogene
o Mutation
o All result in excess/hyperactive protein
 Tumor suppressor gene
o Repair DNA
o Control cell-cell adhesion
o Stop cell cycle

Definitions:

 Differential gene expression: expression of different genes by cells with same genome; in
eukaryotes, depends the combination of control elements and activators
 Histone acetylation: promotes transcription
 Histone methylation: condenses chromatin; slows transcription
 DNA methylation: inactive Barr body, passed on to daughter cells; embryonic development;
genomic imprinting
 Epigenetic inheritance: inheritance of traits transmitted through mechanisms not involving DNA
sequence
 Transcription factories: formed by loops of chromatin; rich in RNA pol and transcription factors
 Determination: embryonic cell irreversibly committed to becoming cell type; tissue specific
proteins, observably different
o Master-regulatory genes: make tissue specific proteins (primary transcription factors)
 Pattern formation: development of spatial structure in a 3D form
o Positional info: cues that control pattern formation by indicating cell location relative to
axes
o Homeotic genes: control pattern formation
 Maternal effect/egg polarity genes: gene, when mutant in mother, results in mutant phenotype
in offspring no matter what; embryonic lethal
 Morphogen: substance that establishes embryo's form in gradients (Bicoid)
 Oncogenes: cancer-causing
 Proto-oncogenes: normal cell growth
 Ras gene (proto-oncogene): Ras protein relays info from growth factor kinases, causing mitosis
 P53 gene (tumor-suppressor): codes for specific transcription factor that promotes synthesis of
proteins that inhibit cell cycle

CH. 19 Viruses

 Viral replication in animal cells

o Attachment and entry
o Genome replication
o Gene expression - viral proteins
o Virus assembly
o Exits (doesn’t kill cell due to envelope)
 CRISPR-CAS and restriction enzymes cut up viral DNA - prokaryotes
 Emergence of viral diseases
o Frequent mutations
 o Small population - large population
o Animal - humans
 Plant viruses - RNA genome; same structure and cycle as animal virus; enlarge plasmodesmata

Definitions:

 Capsid: protein shell enclosing virus, made from capsomeres

 Viral envelopes: made from host cell; animal cells; doesn’t kill
 Lytic cycle: bacterium breaks open and releases phages
o Virulent phage: only replicates by lytic cycle
 Lysogenic cycle: coexists with cell
o Temperate phage: uses both cycles
 Prophage: inserted into bacterial chromosome; can turn lytic; passed on
 Reverse transcriptase: RNA to DNA; used by retrovirus (ex. HIV)
o Retrovirus is provirus: never leaves cell
 Vaccine: harmless derivative of pathogen
 Antiviral drugs: resemble nucleosides (no P) and interfere with viral genome synthesis
 Horizontal transmission: plant infected by external source
 Vertical transmission: plant inherits virus
 Prions: misfolded proteins that build up into a complex by converting other proteins into prions

CH. 20 Biotechnology

 Amplifying DNA
o Plasmids as cloning vectors - DNA from a source combined with plasmid and then allowing
recombinant plasmid to replicate in host cell
o PCR - provides specific DNA fragment for cloning
o Denaturation - DNA heated to separate strands
o Annealing - strands cooled; primers added
o DNA polymerase adds nucleotides
o Cycles over and over (2n)
 Analyzing gene expression - analyze the mRNA
o In situ hybridization
o Reverse transcriptase PCR
o cDNA synthesis - uses mRNA
o PCR of cDNA
o Gel electrophoresis of amplified DNA
 Embryonic stem (ES) cells - reproduce indefinite, wide variety of cell types
 Adult stem cells - only some cell types
 Transgenic animals - pharmaceutical factories

Definitions:

 Nucleic acid hybridization: pairing two complementary, different nucleic acids (ex. DNA with
RNA); basis of DNA tech.
 DNA sequencing: using complementary bases to find entire sequence
 Plasmids: in bacteria; replicated separate; can act as cloning vectors
 Restriction enzyme: cuts DNA at restriction sites to yield restriction fragments with sticky ends
 o Fragments bind to any other DNA cut with same enzyme
 Expression vector: contain regulatory sequences (ex. Promoter) to aid direct expression of the
inserted DNA
 Complementary DNA (cDNA): only has exons; used in cloning vectors
 Electroporation: pulse added to solution of cells that creates holes in which DNA can enter
 Nucleic acid probe: single stranded nucleic acid used to locate complementary sequences
o In situ hybridization: used to locate specific mRNA to track gene expression using probes
 Reverse-transcriptase PCR: used to compare the amount of specific mRNA in several samples at a
time
 DNA microarray assays: used to determine whether DNA contains mutation
 RNA sequencing: involves making cDNA and sequencing them; can show levels of RNA processing
 In vitro mutagenesis: editing cloned gene and inserting it into cell and studying mutant
 CRISPR-Cas 9 System: technique of editing gene involving Cas 9 protein and guide RNA
o Cas 9 cuts DNA at target location
o Mutant forms of DNA can be repaired
 Genome-wide association study: researchers look for DNA sequences that vary in population
o Single Nucleotide Polymorphism (SNP): single base pair where variation found; next to
disease associated allele
 Stem cell: undifferentiated; basis of cloning; repair damaged tissue
 Totipotent cell: can grow into all parts of embryo and adult
 Nuclear transplant/somatic cell nuclear transfer: nucleus of donor cell placed in target cell (egg)
with nucleus removed; basis for animal cloning; depends on chromatin modification of donor
nucleus
 Pluripotent: embryonic stem cells; many but not all parts of organism
 Therapeutic cloning: cloning used to produce ES cells to treat diseases
 Induced pluripotent stem (iPS) cells: uses retrovirus ; can be used as model cells for studying
diseases or replace nonfunctional cells
 Gene therapy: replacing genes; uses a viral vector
 Short tandem repeats: variation in genetic markers; repeats of nucleotides; varies among
population
 GMO: transgenic crops; might cause allergies