Biochem Exam 3: Transcription And Translation

Front 1

RNA polymerases (do/do not) require a primer.

Back 1

do not

*must recognize a start point for transcription and a DNA strand to use as a template

Front 2

RNA polymerases synthesize mRNA from DNA in the _________ direction.

What building blocks does this require (4)?

Back 2

5' to 3'


ATP, GTP, CTP, & UTP

Front 3

RNA polymerases lack a ____________________ activity.

Back 3

3' to 5' exonuclease activity

Front 4

Bacterial cells have (a single/multiple) RNA polymerase(s).

Back 4

a single

Front 5

What are the 4 subunits of the E.coli core RNA polymerase enzyme? What binds to this core enzyme and directs the enzyme to bind at a promoter?

Back 5

alpha2-beta-beta prime

sigma

Front 6

Describe the three eukaryotic RNA polymerases.

Back 6

1. Polymerase I produces rRNA
2. Polymerase II produces mRNA
3. Polymerase III produces tRNA and 5s rRNA

They all have the same mechanism of action but recognize different promoters

Front 7

RNA polymerase binds to the _________ on DNA.

Back 7

promoter

*promoter, promoter-proximal elements, & enhancers are all regulatory sequences on genes

Front 8

The start point and termination signal on DNA are contained in the...

Back 8

coding region, located after the promoter

Front 9

What DNA strand, coding or template, is used by RNA polymerase to make mRNA?

Back 9

template strand

Front 10

The _________ strand of DNA is the same sequence as the mRNA strand except T's are replaced with U's (there are no T's in RNA).

Back 10

coding

Front 11

During translation, where can you find the codons?

Back 11

they are the sequence of 3 nucleotides found on the mRNA, read from 5' to 3'

Front 12

The AT rich consensus sequence in E. coli that determines the start of transcription is called the...

Back 12

Pribnow box

Front 13

The AT rich consensus sequence in eukaryotes that determines the start of transcription is called the...

Back 13

TATA box

Front 14

In addition to the TATA box, you can find consensus sequences such as the _______, ________, and _________ in eukaryotes.

Back 14

CAAT box, GC-rich sequences, enhancers

Front 15

When DNA is unwound by the RNA polymerase holoenzyme, what enzyme is used to remove supercoils?

Back 15

DNA topoisomerase

Front 16

Termination of transcription at the termination signal through the formation of a hairpin loop in DNA is called...

Back 16

Rho-independent transcription termination

Front 17

Termination of transcription through the binding of rho factor is called...

Back 17

Rho dependent transcription termination

Front 18

The unit of a promoter and all the genes it controls is called an

Back 18

operon

Front 19

mRNA generated from an operon containing many genes produces a _____________ transcript.

Back 19

polycistronic

*cistron is a region of DNA that encodes a single polypeptide chain

Front 20

In bacteria, ___________ allows the coupling of transcription and translation.

Back 20

the absence of a nucleus

Front 21

Many transcription factors, nucleosome-modifying complexes, chromatin remodeling complexes, elaborate transcript modification through splicing are all processes found in...

Back 21

eukaryotic cells (more elaborate than bacterial cells)

Front 22

Eukaryotic mRNA usually contains information for (one/many) polypeptides.

Back 22

one

Front 23

____________ interact w/ each other and RNA pol II to initiate transcription.

Back 23

General transcription factors (GTFs)

*promoters contain GTF binding sites

Front 24

____________ bind elements to help stimulate transcription initiation.

Back 24

Enhancers

*can be far from promoter

Front 25

Pol II synthesizes a primary transcript of mRNA. The initial mRNA transcript is capped at the _____ end.

Back 25

5'

Front 26

The 5' end cap of mRNA serves as a...

Back 26

recognition site for binding to ribosome and decreases degradation

Front 27

The initial mRNA transcript is processed to have a poly A tail at the _____ end (for stability). The poly A tail is added by the ____________ enzyme.

Back 27

3' end

poly(A) polymerase

Front 28

Toxin alpha-amanitin blocks _________ and is fatal at low doses.

Back 28

RNA polymerase II

Front 29

Introns are removed from premature mRNA by...

Back 29

splicing

Front 30

Describe the progression of rRNA transcripts to their final cleaved forms.

Back 30

First you make a 45S precursor rRNA strand from a set of tandemly repeated genes on DNA. This large transcript gets cleaved into 18S, 28S and 5.8S rRNAS.

Front 31

What 4 things must be done to immature tRNAs before they can leave the nucleus?

Back 31

1. cleavage of 5' and 3' ends
2. splicing of intron
3. replacement of 3' UU with CCA
4. Modification of bases

Front 32

Thalassemias are caused by mutations that affect the synthesis of __________.

Back 32

alpha or beta chains of hemoglobin

Front 33

Mutations that cause beta thalassemias are found in the...

Back 33

TATA box (w/i promoter), reducing the accuracy of the transcription starting point

Front 34

There is only one codon combination for ___________ and ___________.

Back 34

-Trp
-Met (start codon)

Front 35

tRNA's bind amino acids at their ______ end and transport them to the ribosome.

Back 35

3'

tRNA is a link btwn mRNA codon and specific AA

Front 36

The ________ of the tRNA interacts with the codon of mRNA.

Back 36

anticodon

Front 37

tRNAs recognize (one/more than one) codon per amino acid. This property is called the ____________

Back 37

more than one

wobble hypothesis
*reason fewer than 61 tRNAs required

Front 38

In a silent mutation, a changed codon may code for

(point mutation, one base altered)

Back 38

the same amino acid

Front 39

In a missense mutation, a changed codon may code for

(point mutation, one base altered)

Back 39

a different amino acid

Front 40

In a nonsense mutation, the changed amino acid may code for

(point mutation, one base altered)

Back 40

termination (stop codon)

Front 41

Sickle-cell anemia is caused by a (missense/nonsense/silent) mutation.

Back 41

missense

Front 42

In sickle-cell anemia, the amino acid _____ replaces the normal amino acid ______.

Back 42

Val replaces Glu
(GAG) (GTG)

Front 43

In translation, ATP is used to...

Back 43

attach AA onto the tRNA

Front 44

In translation, GTP is used to...

Back 44

bind the aminoacyl-tRNA to the A site and for subsequent translocation

Front 45

mRNA is translated from its 5' end, producing a polypeptide synthesized from its _______ terminal.

Back 45

amino

Front 46

Prokaryotic mRNA is polycistronic while eukaryotic mRNA is __________.

Back 46

monocistronic
(mRNA codes for only one polypeptide chain)

Front 47

The attachment of amino acids to tRNA is catalyzed by specific ______________ and requires _______.

Back 47

aminoacyl-tRNA synthetases, requires ATP

Front 48

Aminoacyl-tRNA synthetases have a high fidelity of translation due to their ________ and ______ activities.

Back 48

specificity

proofreading
(only enzyme that proofreads)

Front 49

In order, the 3 sites where tRNA binds on the ribosome are the..

Back 49

1. A site (initial binding)
2. P site
3. E site (exit)

Front 50

In prokaryotes, the 16S rRNA contains a sequence that is complementary to the ___________ sequence of mRNA. The binding of these 2 sequences positions mRNA on the _________.

Back 50

-Shine-Delgarno

-30S subunit

Front 51

In eukaryotes, what subunit binds to the cap structure of mRNA?

Back 51

40S

Front 52

In prokaryotes, the initiator tRNA carries a ________________.

Back 52

N-formylated methionine

Front 53

In eukaryotes, the initiator tRNA carries a ______________.

Back 53

regular methionine (not formylated)

Front 54

During elongation, amino acids are added to the __________ terminus of the growing chain. This addition is catalyzed by the enzyme _________.

Back 54

carboxyl

peptidyltransferase

Front 55

During translation, the first tRNA (initiator tRNA of the AUG start codon) enters the ___ site.

Back 55

P site (NOT A!)

Front 56

Elongation of the amino acid chain continues until a _________ is read at the A site, causing _________ to hydrolyze the bond between the peptide and tRNA as well as the binding of _________.

Back 56

stop codon

peptidyltransferase

release factors

Front 57

Gene transcription is mostly regulated on the level of __________.

Back 57

transcription

Front 58

_____________ can target mRNA for degradation.

Back 58

small interfering RNA

Front 59

In prokaryotes, the chaperones that are members of the heat-shock protein family that help the growing protein to fold are __________ and _________.

Back 59

DnaJ and DnaK

Front 60

In eukaryotes, the chaperones that are members of the heat-shock protein family that help the growing protein to fold are __________ and _________.

Back 60

Hsp40 and Hsp70

Front 61

When a new protein is folding, disulfide bonds are formed between ______ residues by the __________ enzyme.

Back 61

Cys

disulfide isomerase

Front 62

Posttranslational modifications: Ser, Thr, and Tyr can be

Back 62

phosphorylated or dephosphorylated

(phosphorylation most common modification)

Front 63

Posttranslational modifications: Lys and Arg can be

Back 63

methylated (methylation of histone is involved in regulation of transcription)

Front 64

Posttranslational modifications: Pro and Lys can be

Back 64

hydroxylated (Stabilization of collagen)

Front 65

Posttranslational modifications: how is blood coagulated (clot formation)?

Back 65

carboxylation

Front 66

Posttranslational modifications: the attachment of fatty acids does what?

Back 66

anchors proteins in membrane

Front 67

Posttranslational modifications: Ser, Thr, or Asn residues of membrane or secreted proteins can be...

Back 67

glycosylated

Front 68

Posttranslational modifications: Lys in carboxylases can be

Back 68

biotinylated

Front 69

What is needed for the translation of proteins on the ER surface for insertion into the ER?

Back 69

A signal peptide is translated--this attracts a SRP (signal recognition particle) that stops translation, binds the ribosome to the SRP receptor on the ER, and translation then resumes

Front 70

Amino acids synthesized in the cytosol that are destined for the nucleus contain a...

Back 70

nuclear localization signal

Front 71

Amino acids synthesized in the cytosol that are destined for the mitochondria contain a...

Back 71

mitochondria entry signal

Front 72

Proteins destined for secretion outside the eukaryotic cell are synthesized on the...

Back 72

ER surface and then released inside the ER

Front 73

Why do we need transcription?

Back 73

to protect DNA from cytoplasmic environment (eukaryotes)

cell does not have enough copies of genome to serve cell's metabolic needs

to regulate the rate of protein synthesis (control mRNA #, life-time, and RNA binding factors)

Front 74

Describe the structural elements of the gene and their function in transcription

Back 74

Promoter sequence of DNA binds RNA polymerase and proceeds coding region. Coding region contains start point and termination signal for transcription

Front 75

Difference between template and coding strand

Back 75

coding strand is used to determine AA sequence
template strand is used to produce mRNA
-they are complementary and antiparallel to one another

Front 76

Describe the role of transcription factors in initiation of transcription

Back 76

Transcription factors bind to promoters and interact with each other and RNA pol II to initiate transcription. Enhancers bind to transcription factors to make transcription MUCH more efficient.

Front 77

Differences between eukaryotic and prokaryotic primary transcripts

Back 77

In prokaryotes transcription & translation are coupled, no nucleus

In eukaryotes, more transcription factors, 3 RNA polymerases, modification of transcript, uncoupled, occurs in chromatin w/i nucleus
Eukaryotic Transcription:
1. initiation
2. elongation
3. termination
4. posttranslational modification

Front 78

Explain the function of Cap structure and poly-A tail in eukaryotic mRNA

Back 78

Cap structure decreases degradation (5' end)
poly A tail provides stability (3' end)

*coding region w/ introns & exons btwn cap and tail

Front 79

Discuss the consequences of mutations in noncoding regions on the gene expression (use thallasemia as example)

Back 79

promoter region mutation, reduces starting point accuracy, leads to lower level of mRNA

Front 80

What do mutations in coding regions result in?

Back 80

-nonsense, frameshift, missense mutations yeild unstable or inactive proteins
-splice-site mutations result in aberrantly spliced mRNA
-3' processing site mutations result in failure to polyadenylate mRNA

Front 81

Characteristics of genetic code (4)

Back 81

1. specificity
2. universality
3. redundancy
4. nonoverlapping and commaless

Front 82

___________ binds to the 30S subunit and distorts its structure, interfering with the initiation of protein synthesis.

Back 82

streptomycin

Front 83

___________ interact w/ small ribosomal subunits, blocking access of the aminoacyl-tRNA to the mRNA-ribosome complex.

Back 83

tetracyclines

Front 84

____________ a component of the 50S ribosomal subunit, transfers the AA from the P site onto the AA at the A site & catalyzes peptide bond formation.

Back 84

peptidyltransferase

Front 85

_______________ inhibits prokaryotic peptidyltransferase. High levels may also inhibit mitochondrial protein synthesis.

Back 85

Chloramphenicol

Front 86

_________ and ________ bind irreversibly to A site on the 50S subunit of the bacterial ribosome, thus inhibiting translocation.

Back 86

clindamycin and erythromycin

Front 87

_________ inactivates the eukaryotic elongation factor, eEF-2, thus preventing translocation.

Back 87

diptheria toxin