Biochemistry Ii: Exam 3

Front 1

Genes that encode proteins necessary for an organism to adapt to a change in environment.

Back 1

Inducible Genes

Front 2

Genes that encode for proteins that cells need in a day to day fashion.

Back 2

Constitutive Genes

Front 3

Regulation of constitutive genes in prokaryotes depends on what?

Back 3

Number of sigma subunits and their affinity for the promoter region.

Front 4

In eukaryotes the GC box identifies the gene as what?

Back 4

Constitutive Gene

Front 5

Regulation of inducible genes depends on what? (3)

Back 5

Protein Factors
Small Molecule Factors
Operator Sites

Front 6

Protein Factors

Back 6

Activators
Repressors

Front 7

Small Molecule Factors

Back 7

Inducers (co-activators)
Co-repressors

Front 8

Operator Sites

Back 8

Enhancers
Silencers

Front 9

Which protein factors binds to enhancer operator site?

Back 9

Activators

Front 10

Which protein factor binds to silencer operator site?

Back 10

Repressors

Front 11

When a gene is normally under negative regulation; this means

Back 11

Transcription of the gene is normally inhibited

Repressor protein is bound to silencer site

Front 12

True or False

Repressor proteins and silencer sites are upstream from the promoter.

Back 12

False

downstream

Front 13

Repressor proteins physically block ________. Preventing transcription.

Back 13

RNA Polymerase

Front 14

Signal molecule that binds to repressor stimulating transcription.

Back 14

Inducer

Front 15

Describe negative regulation mechanism.

Back 15

Co-repressor binds repressor.
Repressor binds silencer site.

Front 16

Gene has to be transcribed very rapidly in order to meet normal conditions.
_________ Regulation

Back 16

Positive Regulation

Front 17

Protein from a gene that is normally under positive regulation is no longer needed. Mechanism?

Back 17

Co-repressor binds activator.
Activator dissociates from enhancer site.

Front 18

Enhancer sites are located
___ stream from the promoter region.

Back 18

Upstream

Front 19

Activators can affect transcription by: (2)

Back 19

Altering the conformation of DNA in the promoter region

Interacting with RNA Pol altering its conformation.
- higher affinity

Front 20

Gene is not normally regulated.
External condition needs it to transcribe. Mechanism

Back 20

Inducer binds activator.
Activator binds enhancer site.

Front 21

The lac operon encodes polycistronic DNA for three enzymes:

Back 21

Beta Galactosidase
Galactoside Permease
Thiogalactoside Transacetylase

Front 22

The lac operon is normally under ______ control.

Back 22

negative control

Front 23

Permits the uptake of galactose into the bacteria.

Back 23

Galactoside Permease

Front 24

What role does beta galactosidase play inside bacteria?

Back 24

Breaks down lactose into glucose and galactose

Front 25

What is the name of the side product formed during the break down of lactose.

Back 25

Allolactose

Front 26

What function does the I gene serve?

Back 26

Transcription of the lac repressor

Front 27

When the lac repressor is synthesized it binds to its silencer sites:

Back 27

O1
O1O2
O1O3

Front 28

The lac operon is a ______ protein, meaning it has 4 subunits.

Back 28

tetrameric

Front 29

O1 is found ______ stream from promoter

Back 29

downstream

Front 30

How does the lac repressor stop transcription?

Back 30

Forms a loop in the DNA downstream of RNA Pol, physically blocking

Front 31

Bacterial DNA binding proteins utilize ________ motifs.

Back 31

Helix-turn-Helix

Front 32

Bases in the major groove of DNA bind to the helix-turn-helix motifs via:

Back 32

Hydrogen bonding
Hydrophobicity

Front 33

The lac repressor binds to DNA via the law of ____ ______. Therefore there will always be a time when it is unbound.

Back 33

mass action

in equilibrium

Front 34

What is the function of allolactose?

Back 34

Inducer that acts to dissociate the lac repressor from its silencer site.

Front 35

______ inducer = 1,6- Allolactose
______ inducer = IPTG

Back 35

Primary

Synthetic

Front 36

What is the proposed function of Thiogalatoside Transacetylase?

Back 36

Thought to start synthesizing a secondary inducer to stimulate transcription.

Front 37

Describe why transcription of the lac operon is slow immediately following a decrease in glucose?

Back 37

RNA Pol has low affinity for the promoter region until it adapts using cyclic amp to induce CRP to bind the enhacer site upstream of the promoter.

Front 38

CRP is also known as ?

Back 38

CAP
Catabolite Gene Activator Protein

Front 39

RNA Pol is bound to the promoter region, CRP protein is bound to enhacer site, but lac repressor is bound to silencer site. Control?

Back 39

Positive and Negative

If repressor leaves - rapid transcription

Front 40

Transcriptional attenuation occurs in the ___ operon.

Back 40

trp Operon

Front 41

trp operon encodes __ proteins that combine to subunits to give all of the enzymes necessary to synthesize ______

Back 41

5

Tryptophan

Front 42

What happens when tryptophan is in high concentration?

Back 42

Acts as a co-repressor to the trp repressor allowing it to bind to the silencer site.

Front 43

The trp operon is regulated by varying levels of tryptophan in the cell by ______ _______

Back 43

transcription attenuation

Front 44

What is found in the trp operon?

Back 44

trpE
Start codon AUG
Leader Peptide
mRNA
Stop Codon UAA

Front 45

What is the significance of two codons in the trp operon?

Back 45

As mRNA on the leader peptide is converted into protein, depending on concentration of tryptophan in the cell, transcription will continue through entire operon or undergo rho-dependent termination prior to doing so.

Front 46

RNAP I transcribes genes for large ______ molecules

Back 46

rRNA

Front 47

RNAP II transcribes genes for _____ (which encodes proteins)

Back 47

mRNA

Front 48

RNAP III transcribes genes____, ____ and other small RNA molecules

Back 48

tRNA, snRNA

Front 49

____carries amino acids to the translation complex and is very stable.

Back 49

tRNA

Front 50

RNAP II contains ___ ____ ____ ____ ____ ____ called the initiation complex with other
enhancers and mediators.

Back 50

TFIID
TFIIE
TFIIA
TFIIB
TFIIH
TFIIF

Front 51

The σ subunit used in prokaryotic RNAP is replaced by _____ for inducible genes
(RNAP II = mRNA).

Back 51

TFIID

Front 52

True or False

RNAP II can recognize the GC box

Back 52

False

RNAP I + III

Front 53

Constitutive genes contain _____ boxes that function like prokaryotic promoters.

Back 53

GC

Front 54

True or False

GTFs are usually required for constitutive genes.

Back 54

False

Front 55

Inducible genes contain _____ boxes that function like promoters.

Back 55

TATA

Front 56

GTFs are required for the initiation of transcription of ______ genes.

Back 56

Inducible

Front 57

The _______ is analogous to the
prokaryotic NusA which binds after the σ subunit leaves.

Back 57

The elongator

Accelerates transcription

Front 58

Once RNAP synthesizes an end consensus sequence, an ________ binds to the consensus sequence and
breaks the synthesized RNA into two pieces:

Back 58

endonuclease

Front 59

What is the purpose of the 5'-end capping and Poly-A tail?

Back 59

Protect eukaryotic mRNA from exonucleases, increasing stability over time.

Front 60

The _________ adds a chain of adenosines on the 3’ end of the mRNA which
can be removed by exonucleases without changing the structure of the actual mRNA

Back 60

Poly-A tail

Front 61

___________ prevents nucleases from recognizing the mRNA

Back 61

5’-end capping

Front 62

Optional step in the protection of mRNA that prevents autohydrolysis involves?

Back 62

2'-O-methyltransferase

Front 63

4 proteins involved in formation of the 3' Poly-A tail:

Back 63

CPSF
Endonuclease
PAP
PABP

Front 64

_____ are untranslated regions of a gene.
Transcribed but not translated

Back 64

Introns

Front 65

_____ are translated regions of a gene.
Transcribed and translated.
Hold the genetic code for a protein

Back 65

Exons

Front 66

______ are removed and _____
are spliced together to get the
right mRNA to be translated into a
functional protein.

Back 66

Introns

Exons

Front 67

Small nuclear RNAs bond to proteins form a structure called _________ which associate to form a spliceosome.

Back 67

small nuclear ribonucleoproteins
snRNP

Front 68

The actual spliceosome has __
proteins and __ snRNAs.

Back 68

45 proteins

5 snRNA's

Front 69

The spliceosome places ______ on the intron near the 5' splice site to form a phosphodiester bond breaking the mRNA.

Back 69

adenylate

Front 70

The lasso-shaped intron is otherwise known as a ______

Back 70

lariat

Front 71

The spliceosome makes deliberate errors and through this planned ______ ________
we get many functional variants for one gene.

Back 71

alternative splicing

Front 72

_______ _________ determines sex in fruit flies.

Back 72

Alternative splicing

Front 73

Rifamycin B is a natural product and ________ is synthetic
• Both are specific for prokaryotic RNAP and act by
preventing RNA ________ downstream of the
promoter.

Back 73

Rifampicin

elongation

Front 74

What is the function of aminoacyl-tRNA synthetases?

Back 74

Generate charged tRNA

Front 75

A ________ mutation is usually mediated by a single base substitution in the anticodon of a tRNA.

Back 75

Nonsense

Front 76

________ means that more than one codon can specify the same amino acid.

Back 76

Degenerate

Front 77

________ contain several different proteases that degrade proteins.

Back 77

Proteasomes

Front 78

Which nucleotide found in the wobble position could lead to a non-functional or incorrect protein?

Back 78

Inosine

Front 79

In bacteria, the peptidyl transferase activity that catalyzes peptide bond formation is found in

Back 79

23S ribosomal RNA

Front 80

The _____________ sequence is a translation initiation signal in bacteria mRNAs that guides the __S ribosome to the initiating (5′) AUG of the mRNA

Back 80

Shine-Dalgarno

30S

Front 81

EF-G can bind the A site of the ribosome because its structure resembles

Back 81

EF-Tu / tRNA complex

Front 82

Upon termination of polypeptide synthesis the ribosome dissociates into

Back 82

30S + 50S subunits

Front 83

True or False

Translation and transcription are coupled only in prokaryotes

Back 83

True

Front 84

Proofreading occurs in the __ ____ of the ribosome.

Back 84

A site

Front 85

True or False

Transcriptional attenuation is common to prokayotes and eukaryotes.

Back 85

False

Front 86

Antineoplastics such as Actinomycin D are __________ agents.

Back 86

Intercalating

Front 87

_______ alter the conformation of RNAP II preventing it from moving along the template.

Back 87

Toxins

Front 88

The sequences of nucleotides that identify the positions of amino acids in the primary
structure of a protein are known as the

Back 88

genetic code.

Front 89

AUG =

Back 89

Start

Front 90

UAA
UAG
UGA

Back 90

Stop Codons

Front 91

Stop and look over the structure of tRNA.

Back 91

Okay

Front 92

______ _____ is an enzyme that covalently attaches an amino acid to
its corresponding tRNA molecule
• Creates ________ ____

Back 92

Aminoacyl-tRNA synthetase

aminoacyl tRNA

Front 93

The 3’ end of tRNA has a highly conserved sequence of
nucleotides:

Back 93

ACC

Front 94

True or False

Each amino acid has its own aminoacyl synthetase

Back 94

True

Front 95

There are __ amino acids
There are __ codons
There are __ tRNAs (some tRNAs bind >1 codon)

Back 95

20

61

32

Front 96

_______ is often found at
the 5’ wobble position
• I can form H bonds with A,
C, or U

Back 96

• Inosinate

Front 97

Ribosomes are composed of both _____ and _____.

Back 97

rRNA

Protein

Front 98

____ rRNA (establishes the reading
frame in prokaryotic translation)

Back 98

16S

Front 99

____ rRNA (catalyzes the formation
of the peptide bond)

Back 99

23S

Front 100

The following histone modifications weaken DNA-histone bond

Back 100

• Trimethylation of Lys
• Acetylation of Lys
• Phosphorylation of Ser/Thr
• Ubiquitination of Lys

Front 101

_________ are sequences of nucleotides in DNA that define the boundaries of
transcriptionally functional DNA
– They may act by preventing methylation of key histone residues

Back 101

Insulators

Front 102

____ methylation is reversible

Back 102

DNA

Front 103

Methylation of DNA on cytosine by ____ __________ turns off eukaryotic gene expression

Back 103

DNA Methyltransferases

Front 104

____ ________ is a process in which double-stranded RNA triggers the fragmentation of
complimentary mRNA and thereby prevents gene expression by preventing translation.

Back 104

RNA interference

Front 105

Similar to the situation in plants,
in eukaryotes a _____ _____
cuts microRNA into short
interfering RNA (siRNA) which
is still double stranded

Back 105

dicer enzyme

Front 106

_____ binds siRNA and causes the two strands of the siRNA to separate

Back 106

RISC

Front 107

Epigenetically RISC promotes DNA _________.

Back 107

methylation

Front 108

These proteins act as intermediaries between the transcription activators and the GTF-RNAP II complex.

Back 108

Co-activator Protein Complexes

Front 109

The principle co-activator protein complex is called the _______

Back 109

mediator

Front 110

Mediator complex binds to ___ domain of RNAP II and stimulates phosphorylation by ____

Back 110

CTD

TFIIH

Front 111

True or False

Methylation of DNA is reversible

Back 111

True

Front 112

Three main classes of regulatory RNA:

Back 112

siRNA
miRNA
piRNA

Front 113

pri-miRNA is endonucleased by ____ into pre-miRNA which is processed by ______ into miRNA

Back 113

Drosha

Dicer

Front 114

Eukaryotic Transcription:

TBP recruits _____ which places active site at +1 start site. Indicates binding for _____. ___ and ___ act as helicase to unwinds DNA, _____ phosphorylates ___ domain of RNAP II which breaks away from promoter then elongator binds.

Back 114

TFIIB

RNAP II

TFIIH + TFIIE

TFIIH

CTD