biol 3250 - chapter 13 and 14

the genetic information is coded within mRNA in groups of three nucleotides known as…

codons

DNA start codon

ATG

DNA stop or nonsense codon

TAA

TAG

TGA

RNA start codon

AUG

RNA stop or nonsense codon

UAA

UAG

UGA

AUG, specifies what?

methionine

start codon

UAA, UAG, UGA signify what?

termination

stop codons

with respect to a growing polypeptide chain, the linkage between the amino group of the incoming amino acid and the carboxyl group of the existing polypeptide bond is known as ?

peptide bond

polar

hydrophilic

water loving

non-polar and aromatic

hydrophobic or water hating

what are the four levels of structure in proteins ?

primary

secondary

tertiary

quaternary

• not all proteins have a quaternary structure

primary

protein structure

amino acid sequence

secondary

protein structure

formation of alpha helices and beta sheets

tertiary

protein structure

final three-dimensional structure

quaternary

protein structure

proteins made up of two or more polypeptides

proteins that do not form quaternary structures are called ?

monomeric proteins

tRNAs incorporate the incoming amino acids during ?

translation of mRNA into proteins by the ribosome

the 3’ ACC acceptor stem where the amino acid is added is found in all ?

tRNAs

the actual tRNA is a ribbon shape twisted molecule in which the 5’ to 3’ orientation of the anticodon is ? to the 5’ to 3’ orientation of the codons in the mRNA

antiparallel

the enzymes that attach amino acids to tRNAs are known as ?

aminoacyl-tRNA synthetases

how many aminoacyl-tRNA synthetases are there ?

20 ; one for each amino acid

the genetic code is degenerate at ? of codons for most amino acids

the third position

the wobble position is the ? of the codon and the ? of the anticodon

third base

first base

third base of mRNA codon

A

base in anticodon

• I

• U

• xm⁵s²U

• xm⁵ Um

• Um

• xm⁵U

• xo⁵U

• k²C

third base of mRNA codon

U

base in anticodon

• A

• G

• U

• I

• xo⁵U

third base of mRNA codon

G

base in anticodon

• C

• A

• U

• xo⁵U

third base of mRNA codon

C

base in anticodon

• G

• A

• I

a ribosome is composed of two subunits…

large and small subunits

each submit is formed by ?

the assembly of multiple proteins and rRNA

the A site is where ?

the next aminoacyl tRNA with an incoming amino acids loads into the ribosome

the P site is where ?

the peptidyl transfer takes place and the peptide bond is formed

the E site is where ?

the empty tRNA exits the ribosome after the peptide bond has been formed

where does peptide bond initiate ?

where is the tRNAMet loaded?

occurs at the P site

there are a number of helper proteins involved in ?

each stage of translation

the start codon for eukaryotic translation is usually first AUG after the ?

5’ cap of the mRNA

as soon an mRNA strand is long enough, a ribosome will attach to its ? so translation begins before transcription ends

this is known as ?

5’ end

transcriptional/translational coupling

the initiation, elongation and termination stages of translation in both bacteria and eukaryotes require ?

auxiliary proteins in addition to the ribosome

the antibiotics chloramphenicol, erythromycin, puromycin, tetracycline and streptomycin act by ?

inhibiting the process of translation in bacteria

constitutive

genes that are unregulated and always on

gene regulation can occur at the level of ?

transcription, translation, posttranslationally or after translation

transcription

genetic regulatory proteins such as activators or repressors

• attenuation

translation

translational repressor proteins

riboswitches

antisense RNA

posttranslational

feedback inhibition by the first product of a pathway

covalent protein modifications

regulation can occur as the gene is copied into mRNA by RNA polymerase during ?

transcription

• genetic regulatory proteins bind to the DNA and control the rate of transcription

• in attenuation, transcription terminates soon after it has begun due to formation of a transcriptional terminator

regulation can occur as the mRNA is ?

translated into protein by the ribosome during translation

• translational repressor proteins can bind to the mRNA and prevent translation from starting

• riboswitches can produce an mRNA confirmation that prevents translation from starting

• antisense RNA can bind to the mRNA and prevent translation from starting

regulation can occur as the protein undergoes ?

posttranslational changes to make it a functional protein

• in feedback inhibition, the product of a metabolic pathway inhibits the expression of the first enzyme in the pathway

• covalent modifications to the structure of a protein can alter its function

transcriptional regulation involves the actions of two main types of regulatory proteins…

repressors and activators

repressors

bind to DNA and inhibit transcription, usually bind downstream of the promoter

activator

bind to DNA and increase transcription, usually bind upstream of the promoter

negative control

refers to transcriptional regulation by repressor proteins

positive control

refers to regulation by activator proteins

small effector molecules that increase transcription are called ?

inducers

genes that are regulated by inducers are called ?

inducible

small effector molecule may ? transcription

inhibit

corepressors

bind to repressors and cause them to bind to DNA

inhibitors

bind to activators and prevent them from binding to DNA

genes that are regulated by small effector molecules that inhibit transcription are called ?

repressible

when the cell has other sugars available as carbon sources, such as glucose or glycerol , the lac operon is ?

off

when the cell only has lactose available as a carbon sources, the lac operon is ?

on

there are three DNA binding sites in the lac operon

1. CAP binding site

2. lac promoter

3. lac (o1) operator

three proteins are involved in the regulation of the transcription of the lac operon and they bind to different sites on the DNA

1. RNA polymerase

2. CAP*

3. lac repressor (lacl)

RNA polymerase binds to the ?

promoter

CAP* but not CAP protein binds to ?

the CAP binding site

lac repressor (lacl) binds to ?

the main lac operator (o1) and either auxiliary lac operators (o2 or o3)

control via sugar metabolism

if there is a preferred sugar (glucose), they do not want lac genes off

if cells are grown in glucose, there are low levels of cAMP

if the cells are grown in a poor carbon source there are high levels of cAMP

• CAP -cAMP will not bind to CAP site so RNA polymerase cannot bind to the weak lac promoter

  • CAP +cAMP binds to the CAP site and helps RNA polymerase bind to the weak lac promoter

control via Lacl, the lac repressor

does not want to make genes catabolize lac unless needed to

lac repressor binds to operator which prevents movement of RNA polymerase

allolactose

• made when the lacZ gene product acts on lactose, binds to lac repressor and prevents it from binding to the operator do RNA polymerase is free to move

control via the stem loop structure of the operator

the operator (o1) forms a stem loop structure that helps recruit lac repressor, which is further aided by two additional operators (o2) in the lacZ gene and (o3) in the Lacl gene that also interacts with the lac repressor

trans-effect or trans-acting factor

genetic regulation that can occur even though DNA segments are not physically adjacent

mediated by genes that encode regulatory proteins

ex. the action of the lac repressor on the lac operon

cis-effect or cis-acting element

a DNA sequence that must be adjacent to the genes it regulates

mediated by sequences that bind regulatory proteins

ex. the lac operator binding site

the lac operon uses two regulatory proteins

lacl repressor

inducing CAP* general transcription factor

• impacted by two effector molecules

  • allolactose and cAMP

lacl repressor binds to the lac operator (lacO) and prevents transcription of the lac promoter (lacP) by RNA polymerase but the ?

effector molecule - allolactose inactivates the lacl repressor and prevents binding to lacO

CAP* protein (CAP protein bound by the effector molecule cAMP) binds to the CAP binding site but ?

CAP proteins without cAMP cannot bind to the CAP binding site

RNA polymerase cannot bind to the weak lac promoter (lacP) but ?

RNA polymerase can bind to the CAP* protein, this helps the RNA polymerase bind to the weak lac promoter (lacP)

when tryptophan levels are low in the cell ?

the trp operon is on so more tryptophan can be made

when tryptophan levels are high in the cell ?

the trp operon is off so no more tryptophan can be made

when tryptophan levels are low, tryptophan does not ?

bind to the trp repressor protein

• prevents the repressor protein from binding to the operator site

when tryptophan levels are high, tryptophan acts as ?

a corepressor that binds to the trp repressor protein

the tryptophan-trp repressor complex binds to ?

the operator site to inhibit transcription

when attenuation occurs…

the RNA is transcribed only to the attenuator sequence and transcription is then terminated

attenuation is a second method that can turn what operon off ?

trp operon

just as in regulation by the trp repressor

low levels of tryptophan ?

high levels of tryptophan ?

low levels - prevents attenuation and starts transcription

high levels - causes attenuation and stops transcription

operons involved in catabolism (breakdown) are usually off and typically inducible and the substance to be broken down as as ?

the inducer

operons involved in anabolism (synthesis) are usually on and typically repressible and the inhibitor or corepressor is the small molecule that is ?

the product of the operon

antisense RNA acts to control ?

gene expression at the transcription level