Genetics Exam 4 Review

genome:

the set of hereditary information encoded in the DNA of an organism, including both the protein-coding and non-protein coding sequences.

C-value paradox:

is the observation that the amount of DNA in a haploid cell's nucleus does not correlate with an organism's evolutionary or biological complexity

supercoiling:

underwinding/overwinging that occurs when the helix is strained

topoisomerase

prevents supercoiling from happening during DNA replication

LINEs

long interspersed elements

long, repetitive sequences found interspersed in the genomes of higher organisms

SINEs

short interspersed elements

repetitive sequences found in the genomes of higher organisms

nucleotide repeat expansion:

a type of genetic mutation where a short sequence of DNA is repeated too many times in a row

What the composition of the histone?

high in positively charged amino acids (lysine and arginine most common), forms octomers that wraps around chromatin forming a nucleosome. Can have post-translational modifications that modify the tails.

What are the different forms of chromatin?

euchromatin (loosely packed) and heterochromatin (tightly packed)

What is a solenoid structure?

beads on a string- array of nucleosomes coil into compact helical fiber of ~ 30 nm.

What histones are involved in each form of chromatin?

Euchromatin has H2A, H2B, H3, & H4 but does NOT have H1 (linker). Heterochromatin has all 5. Linker histones help pack the DNA in tighter.

What is a D-loop in an eukaryotic chromosome?

a three-stranded (triplex) DNA structure that forms when a single DNA strand invades a double-stranded DNA molecule and base-pairs with one of the strands, displacing the original complementary strand into a loop-like "bubble

Where is the D-loop located in an eukaryotic chromosome?

forms anywhere on gene when double stranded break is present or during homologous recombination

What is the D-loop’s function?

DNA double-strand break repair- invades a strand and makes itself a template, mitochondrial DNA replication, and telomere protection

How is the D-loop formed?

when a single strand of DNA invades a double-stranded DNA duplex and pairs with one of the strands, displacing the original partner strand. DNA strand chewed back on 3’ end. RecA (bacteria) or RAD51 (eukaryotes) coat the single strand to form a filament.

operon:

a genetic unit consisting of one or more structural genes encoding polypeptides, and an adjacent operator gene that regulates the transcriptional activity of the structural gene or genes.

coding strand:

the strand opposite and complementary to the template strand

template strand:

the strand that is transcribed by RNA polymerase during transcription

promoter:

a region of a gene where RNA polymerase binds and initiates transcription, located in the 5’ direction from the coding sequence

-35 box:

a short, conserved sequence of DNA found in bacterial (prokaryotic) promoters; docking site for sigma factor, helps initiate transcription

-10 box:

primarily A-T bonds; bonds to sigma factor, helps initiate transcription

Pribnow box:

6-bp sequence to which the sigma subunit of RNA polymerase binds upstream from the beginning of transcription. (bacterial)

TATA box:

conserved, A-T rich non-coding DNA sequence located in the core promoter region of eukaryotic and archaeal genes that signals where transcription begins

CAAT box:

noncoding sequence; acts as proximal promoter; used as transcription factor binding

polycistronic:

a messenger RNA molecule that encodes the amino acid sequence of two or more polypeptide chains in adjacent structural genes. Characteristic of bacteria.

What is the definition of a gene?

the fundamental physical unit of heredity, whose existence can be confirmed by allelic variants and which occupy a specific chromosomal locus.

What are some similarities and differences between eukaryotic and prokaryotic gene structure?

both use DNA, the ORF (open reading frame) runs 5’-3’ in both, prokaryotes have a singular circular chromosome, prokaryotes have no histones

mRNA:

Carries genetic instructions from DNA in the nucleus to ribosomes in the cytoplasm

What is the primary RNA structure?

linear- amino acids

What is the central dogma?

genetic information flow from DNA —> RNA —> proteins

Who proposed the central dogma?

Francis Crick

What are the general properties of RNA polymerase in prokaryotes?

synthesizes all classes of RNA (mRNA, rRNA, and tRNA) in bacteria; no primer required, lack of proofreading, used commonly in antibiotics

What are the general properties of RNA polymerase in eukaryotes?

(Pol I, Pol II, and Pol III) that synthesize different classes of RNA without requiring a primer, reading DNA templates from 3′ to 5′ while building chains from 5′ to 3′, require general transcription factors (GTE)

What is the role of the sigma factor?

enable bacteria to initiate transcription by directing RNA polymerase to specific promoter sequences on DNA, helps single strand of DNA to “melt” (unwind)

What DNA sequences does the sigma factor bind to?

-35 & -10 typically

What is Rho dependent termination in prokaryotes?

The Rho factor binds to a Rho utilization (rut) site, unwinds the DNA-RNA hybrid, pulling the RNA away and releasing the RNA polymerase via ATP hydrolysis

What is TBP?

encodes the TATA-box binding protein

Which RNA transcribes tRNA?

RNA Pol III

Which RNA transcribes mRNA?

RNA Pol II

What are the major general transcription factor components of the PIC?

TFIID, TFIIA, TFIIB, TFIIF, TFIIE, TFIIH, RNA Pol II

What is the function of the 5’-methyl-guanosine cap?

Protection from Degradation, Translation Initiation, & Nuclear Export & Processing

What is the 5’-methyl-guanosine cap?

a modified nucleotide added to the 5′ end of eukaryotic primary messenger RNA (pre-mRNA) transcripts

What is the function of the Poly-A tail?

mRNA stability, nuclear export, lifespan regulation, & translation efficiency

What is the Poly-A tail?

a long chain of adenine nucleotides (typically 100 to 250 bases) added to the 3' (three-prime) end of a eukaryotic messenger RNA (mRNA) molecule; added during polyadenylation (PTM)

How is the Poly-A tail added to the transcript and to which end?

3’ end; poly-A-polymerase adds a “tail” of 100-250 adenine nucleotides

Which Kornberg worked on RNA PolII?

Roger D. Kornberg

What is intron splicing?

What factors perform intron splicing?

What do we know about how splice sites are chosen?

What is alternative splicing?

How does alternative splicing increase the number of proteins a genome can produce?

Can altered mRNA splicing cause aberrant phenotypes?

What is RNA editing?

What is the Ames test for?

How many nm is naked DNA?

2 nm

How many nm is a nucleosome?

11 nm

How many nm is a chromatin D-loop?

300 nm

How many nm is a metaphase chromosome?

1,400 nm

tRNA:

Acts as an adaptor molecule that brings specific amino acids to the ribosome (has an anticodon).

rRNA:

Forms the structural and catalytic core of ribosomes and catalyzes peptide bonds

regulatory RNAs

(siRNA, miRNAs)

Controls gene expression at transcriptional and post-transcriptional levels (e.g., gene silencing, mRNA degradation)

What is RNA secondary structure?

stems (helices) and loops

What is RNA tertiary structure?

3D folded structure

What is Rho independent termination?

RNA transcript folds back on itself to form hairpin (stem) loop, followed by Uracil nucleotides. The loop stops RNA Pol, transcript falls off, RNA is free.

What is TFIID?

a multi-subunit general transcription factor essential for initiating gene transcription by RNA polymerase II in eukaryotes

What is TFIIH?

(Transcription Factor II H) is a large, multi-protein complex in eukaryotic cells that plays an essential role in two fundamental cellular processes: gene transcription (reading DNA to make RNA) and DNA repair

What is TFIIE?

general transcription factor that plays a critical role in the initiation of mRNA synthesis by RNA polymerase II

What is RNA Pol III?

a multi-subunit protein enzyme in eukaryotic cells that transcribes DNA into small, functional non-coding RNAs essential for cell growth, protein synthesis, and regulation