Genetics Exam #1 Review

Structure of a nucleotide

1.)Phosphate

2.)Sugar

3.)Nitrogenous Base

Phosphate and sugar make up the backbone

How many hydrogen bonds is in a C-G pair?

3

How many hydrogen bonds are in a A-T pair?

2

What is the most common DNA structure

B-DNA

Right handed helix (clockwise)

Where does Transcription start in a gene?

+1

After initiation site:

Downstream (+)

Before initiation site:

Upstream (-)

Eukaryote or Prokaryote?: Each gene is controlled by its own promoter and the resulting mRNA is translated into one protein in most cases

Eukaryote

Eukaryote or Prokaryote?: Some sets of genes are controlled by the same promoter and transcribed together, then translated separately

Prokaryote

Eukaryote or Prokaryote?: Polycistronic mRNAs

Prokaryote

Eukaryote or Prokaryote? Initiation of transcription:

One type of RNA polymerase that transcribes all the genes

Sigma enzyme controls the specificity of where it would synthesize

Promoter consensus sequences bound by sigma (-10 facilitates unwinding of the DNA strand, -35 region)

Prokaryote

Eukaryote or Prokaryote? Elongation:

Sigma factor is released

Abortive initiation

RNA polymerase repeatedly starts and releases short transcripts

After a few attempts, a longer transcript is achieved that allows for proper elongation

Prokaryote

Eukaryote or Prokaryote?: Termination

Rho-Dependent: Controlled by Rho protein. Ribosomes translate as the Rho tracks along the RNA behind the RNA polymerase. RNA polymerase runs into string of Gs (terminator site) and stalls. Rho catches up and collides with the polymerase, unwinding the RNA from the template, causing it to dissociate

Rho-Independent: Controlled by specific sequences in the DNA template strand/RNA(G-C rich inverted repeats followed by a string of adenines). Inverted repeats in the RNA form a stable hairpin, causing polymerase to pause as its transcribing the adenines to uracils. String of U-A pairs are weak, that long with hairpin destabilize RNA polymerase and cause core enzyme to dissociate from template strand

Prokaryote

Eukaryotic promoters - RNA pol 1, 2, or 3

Location: Nucleus

RNA products: Large rRNAs

Notes: Nucleolus is where rRNA processing and assembly occur; a-amanitin insensitive

RNA polymerase 1

Eukaryotic promoters - RNA pol 1, 2, or 3

Location: Nucleus

RNA products: pre-mRNAs, some snRNAs, snoRNAs, some miRNAs

Notes: Transcribes the majority of genes; extremely a-amanitin sensitive

RNA polymerase 2

Eukaryotic promoters - RNA pol 1, 2, or 3

Location: Nucleus

RNA products: 5S rRNA, tRNAs, some snRNAs, some miRNAs

Notes: Moderately a-amanitin sensitive

RNA polymerase 3

Eukaryotic promoters - RNA polymerase 1, 2, or 3

Core vs regulatory promoter

TATA box located at -25 to -35, helps with unwinding

Some have CAAT box around -80

Some have GC rich boxes and octamer boxes: increases initiation efficiency

Basal/general transcription factors bind to the promoter

RNA polymerase 2

Eukaryotic promoters - RNA polymerase 1, 2, or 3

In general, require less transcription factors than RNAP II initiation transcription

Require transcription factors to bind conserved sequences, but those sequences differ based on polymerase

RNA polymerase 1 and 3

Eukaryote or Prokaryote?: Elongation

RNA polymerase is released from the rest of the pre-initiation complex and proceeds to generate the RNA

DNA template is more complex because of chromatin

Eukaryote

Eukaryote or Prokaryote?: Termination

Termination is different depending on the RNA polymerase

RNAP 1: 18nt template sequence that is recognized by a termination protein

RNAP 2: Elongation goes 1000-2000nt past the gene, ore-mRNA tail is processed and removed, exact mechanisms vary by gene

RNAP 3: RNA hairpin structure forms followed by a string of uracils (similar to rho-independednt terimnation)

Eukaryote

What is: A modified guanine nucleotide called 7-methylguanosine added to the 5’ end of mRNA

5’ cap

When does 5’ capping occur?

Shortly after transcription begins (co-transcriptionally)

Which RNA polymerase produces capped mRNA?

RNA polymerase 2

What are the two main functions of the 5’ cap?

Protect mRNA from degradation and helps initiate translation

What is polyadenylation?

Addition of a poly (A) tail to the 3’ end of mRNA

How long is a newly added eukaryotic poly A tail?

200 to 250 adednine nucleotides

What sequences signal polyadenylation?

An upstream poly A signal and a downstream U/GU rich sequence

What are the three main functions of the poly A tail?

1.) Increase mRNA stability

2.) Promotes nuclear export

3.) Helps initiate translation

How does polyadenylation differ in prokaryotes

It is less common, generally uses shorter tails, and often promotes RNA defradation

What happens during RNA splicing

Introns are removed and Exons are joined together

What is the 5’ splice site?

the begining of an intron, typically containing GU

What is the 3’ splice site?

The end of an intron, typically containing AG

What is the branch point?

An adenine usually located about 18-40 nucleotides upstream of the 3’ splice site

What is the splicesome?

A complex of RNA and proteins that removes introns and joins exons

What do snRNAs do during splicing?

Recognise splice sites and help position and stabilize the spliceosome

What is alternative splicing

Processing one pre-mRNA into different mature mRNAs by including or excluding certain exons

What percentage of human multi-exon genes undergo alternative splicing

95%

Where are splicing enhancers and silencers located?

In either exons or introns

What can alternative 3’ cleavage sites produce?

mRNAs with different 3’ ends, changing stability or translation

What produces multiple gene varients, including tissue specific proteins?

Alternative splicing

What is the function of tRNA

Recognizes mRNA codons and delivers the corresponding amino acids during translation

What is the function of rRNA

Provides structural and catalytic functions within ribosomes

Where are eukaryotic tRNAs transcribed and processed?

In the nucleus before being exported into the cytoplasm

Why i conserved shape of tRNA important?

It allows proper recognition and function during translation

Where are most eukaryotic rRNAs processed and assembled into ribosomal subunits?

The nucleolus

How is rRNA processed?

It undergoes chemical modifications, cleavage, and trimming with help from snoRNAs and snoRNPs

What are the three stages of translation?

Initiation, elongation, termination

What happens during translation initiation (post transcriptional)?

The initiator tRNA recognizes the start codon, and the ribosome assembles

Why is identifying the correct start codon important?

Starting at the wrong position can change the reading frame and protein sequence

What is the shine-Delgarno sequence?

A prokaryotic mRNA sequence that helps position the small ribosomal subunit

How does eukaryotic translation initiation work?

The initiation complex binds neat the 5’ cap and scans for AUG

What is the Kozak sequence

A eukaryotic sequence surrounding AUG that helps the ribosome identify the start codon

How does the poly A tail help with translation initiation?

It interacts with cap-associated proteins, promoting efficient initiation

What happens during translation elngation?

The ribosome moves along mRNA, adding amino acids to the growing polypeptide

What will be on the outside and what will be on the inside when a polypeptide chain enters the cytosol?

Outside - Hydrophilic molecules (Polar or charged)

Inside - Hydrophobic molecules (nonpolar)

Where does incoming tRNA carring enter the ribosome?

The A site

Which site holds the tRNA carring the growing polypeptide chain?

The P site

Which site allows empty tRNA to exit the ribosome?

The E site

Do stop codons code for amino acids?

No

True or false: Multiple codons can code for the same amino acid

True (degeneracy of the genetic code)

True or fasle: Different tRNAs can carry the same amino acid but have different codons

True (isoaccepting tRNAs)

What is wobble base pairing?

Flexible pairing between the third codon position and the first anticodon position

Why can cells function with only 30-50 tRNA types?

Wobble pairing allows some tRNAs to recognize multiple codons

Why is protein structure important?

A proteins shape determines its function

What are the four main components of an amino acid

Central carbon, amino group, carboxyl group, R group

What is primary structure/

The linear sequence of amino acids in a polypeptideWha

Where are peptide bonds between amino acids?

Between the carboxyl groups

How do R groups influence proteins

Affect how a protein folds and functions

What are the two main types of secondary structure?

Alpha helices and beta sheets

What is the tertiary protein structure?

The overall 3D shape of a single polypeptide

What interactions stabilize the tertiary structure?

Hydrogen bonds, ionic interactions, hydrophobic interactions, and disulfide bridges

What is quaternary protein structure?

The arrangement of multiple polypeptide subunits into a functional protein