Quiz 4 Molecular Genetics

translation

process by which info in mRNA is converted into a protein product

codon

protein coding region of mRNA that are made up of ordered 3 series base units

Aminoacyl-tRNA

tRNA linked to an amino acid

tRNA

75-95 base long adaptor molecule

codon families

4 codons that code for the same amino acid

wobble

some non-regular base pairing tolerated at the 3 position of the codon/anticodon pairing

wobble bases

base that bp irregularly in the tRNA pairing

wobble position

5’ base of the anticodon

inosine

very flexible wobble base that can base pair with C, U, and A

ORF (open reading frame)

long region bound by a start / stop codon that could potentially code for a protein

start codon

first amino acid of the protein and sets the reding frame

Bacterial start codons

AUG, GUG, UUG

eukaryotic start codons

AUG

Stop codons

define the end of the reading frame

what are the stop codons

UAG, UGA, UAA

nonsense mutation

produces a premature stop codon and creates an incomplete protein

Suppressor tRNA

mutations in the tRNA that correct nonsense mutations

frameshift mutations

show that there are no gaps in the code

polysome (polyribosome)

strand of mRNA that has many ribosomes translating it at the same time

ribosome (ribozyme)

catalyze peptide bond formation

tRNA binding sites

in the ribosome, spans both subunits and positions tRNA for peptide bond formation

charging

linking of tRNAs to amino acids, catalyzed by amino acyl tRNA synthase

isoaccepting tRNAs

may recognize and charge more than one tRNA

ribosome binding site

base pair interactions between mRNA and 16srRNA in a small subunit that mediate initiation

SHine-Dalgarno sequence

a ribosome binding site that is 4-9 bp and 8-13 bp upstream of AUG start codon

Start codon

code for methionine

Three tRNA binding sites

A, P, E

The first step of charging

Adenylation, amino acid activated using ATP and forms a peptide bond. Produces an amino-acyl AMP

The second step of charging

Energy used to transfer amino acid to tRNA, either 2’ or 3’ OH of tRNA

Prokaryotic initiation factors

IF1, IF2, IF3

The functions of ribosome binding sites

attract mRNA, position the ribosome, and give a lot of translation

How do eukaryotic ribosomes begin initiation?

they recognize the mRNA cap and then scan for the AUG start codon, the Kozak sequence can help increase efficiency

what is carried on the bacterial initiator tRNA

N-formyl methionine

Elongation factors

3 proteins that help in the process of elongation, two of them use GTP for energy

What are the three elongation factors?

EF-Tu, EF-Ts, EF-G

EF-Tu

binds charged tRNAs 3’ end to mask the amino acid, then when bound to ribosome it hydrolyzes attached GTP after the correct binding is made and releases the tRNA

23SrRNA

on the large subunit of the ribosome, catalyzes peptide bond formation during translation

EF-G

provides energy for translocation of A site tRNA by hydrolyzing attached GTP, occurs after peptidy transferase and the shift uncover the binding site

EF-Ts

works as a GTP/GDP exchanger for EF-Tu

What allows elongation to begin?

Ribosome assembled, charged tRNA at the P site, and A site is empty

Translation error rate

10^-3 to 10^-4

termination in translation

starts when one of the stop codons is at the A site of the ribosome

Class I release factors

recognize stop codons and trigger hydrolysis of the peptide chain from tRNA at the P site

RF1

prokaryotic release factor, recognizes UAG and UAA

RF2

prokaryotic release factor, recognizes UGA and UAA

Class II release factors

stimulate disassociation of class I factors from the ribosome after the release of the polypeptide chain

RRF (ribosome recycling factor)

removes ribosomes from the mRNA

EF-G

releases the uncharged tRNA from the P and E sites

Truncated mRNA

mRNA that has been shortened/cut off early and does not have a stop codon

tmRNA

a tRNA charged with alanine and an mRNA molecule that recognizes a ribosome stuck on the end of truncated mRNA, it allows the ribosome to be released and signals the protein to be destroyed

Non-stop decay

eukaryotic way of releasing a ribosome from an mRNA with no stop codon

Ski7

recognizes the lysine tail on the protein, released the ribosome, and degrades both mRNA and protein

Nonsense mediated mRNA decay

exon junction complexes are not displaced after the first round of translation and signals that the protein and mRNA need to be degraded

regulation of transcription

most common, involves how RNA polymerase interacts/recognizes promoters

constitutive genes

not regulated, constant expression in the cell and controlled only by promoter strength

Housekeeping genes

code for the products the cell needs at all times

Regulated gene expression

amount of the gene product rises and falls with the cells needs

Regulatory proteins

control the expression of other genes

Activators

help recruit the RNA polymerase to the promoter

Repressor

inhibit transcription

positive regulation

binding of an activator protein enhances gene expression

Negative regulation

binding of repressor protein inhibits gene expression

Distant regulatory sites (enhancers)

can result in activator or repression

Co activator

helps activators and RNA polymerase interact but does not bind DNA

Co repressors

bind activator proteins and prevents them from working on RNA polymerase

Insulators

prevent activators from interacting with the wrong promoter

Signal integration

many genes regulated by more than one regulatory protein

effectors

molecular signal that regulates activator/repressor function

Operons

bacteria, related functions clustered together so they can be coordinately controlled, produce polycistronic messages

Polycistronic messages

one promoter controls transcription of several genes, one mRNA has multiple reading frames

Regulon

group of operons that are controlled together

Combinatorial control

a specific combination of regulators unlock each particular gene

LacZ gene

codes for beta galactosidase

LacY gene

codes for a permease protein that brings lactose into the cell

Constitutive mutants

produced all three gene products all the time in the Jacob and Monod experiment

Merodiploid analysis

makes bacteria a little bit diploid to reveal types of mutants and if they are recessive/dominant

Complementation

normal gene can mask the presence of a defective one

Lac I- mutations

can be masked by a merodiploid, aka recessive and can be complemented in trans

complimented in trans

functional copy of the gene from a separate source can restore the wild-type phenotype

Trans acting factors

anything that is diffusible and can perform its function at many places in the cell

Lac I gene

codes for a protein that regulates the rest of the genes in the lactose operon, the product repressed expression of structural genes in the absence of lactose

Lac O mutations

cannot be rescued/complimented in merodiploid, a mutation in the DNA sequence where the lac repressor protein binds to regulate gene expression

Lac repressor

binds to the operator site in the absence of lactose and blocks transcription

Allolactose

produced in a small amount when lactose is present and acts as an effector molecule, inducer, that binds the repressor and release it from the DNA so the operon can become active

Catabolite repression

limits expression of genes for alternative carbon sources if glucose is present

CRP

positive regulator with little effect with lactose repressor is bound

What are the prokaryotic class I release factors

RF1 & RF2

What are the three stop codons

UAG, UGA, UAA

What is the eukaryotic class I release factor?

eRF1

What are the prokaryotic and eukaryotic class II release factors?

RF3 and eRF3

Another name for activators and repressors

specific transcription factors

Who did the experiment that discovered the Lac operon

Jacob and Monod

What controls the lac operon

a protein repressor and a DNA sequence (lac I and operator site)

What two molecules have an inverse relationship?

Glucose and cAMP