Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCAT Biochem > Biochem #7 > Flashcards

Biochem #7 Flashcards

You may prefer our related Brainscape-certified flashcards:
MCAT flashcards
1
Q

what leads to the diverse array of cells in the body?

A

Different cells express different genes which leads to the diverse array of cells in the body. This is despite the fact that all DNA has the possibility to express all genes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

central dogma of molecular biology

A

major steps in the transfer of information from DNA to proteins.
o DNA replication occurs in the 5-3 direction, as does mRNA synthesis and ribosomal translation. Protein is produced in the N (amino) to C (carboxy) direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

from ribosomes, protein is produce in the ____ direction

A

N to C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

gene

A

unit of DNA that encodes a specific protein or RNA molecule, and through transcription and translation the gene can be expressed.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

DNA coding strand

A

identical to the mRNA (except T for U)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

DNA template strand

A

complementary and antiparallel to the mRNA.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

messenger RNA

A

carries the information specifying the amino acid sequence of the protein to the ribosome.
 Transcribed via RNA polymerase enzymes.
• Done in the nucleus
 Undergoes post transcriptional modifications before it leaves the nucleus sometimes.
 Codons: 3 nucleotide segments on the mRNA that are read by the ribosome.
 Monocistronic: each mRNA molecule translates to only one protein product (eukaryotes)
 Polycistronic: starting translation at different locates in the mRNA can result in different proteins.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

monocistronic and polycistronic

A

Monocistronic: each mRNA molecule translates to only one protein product (eukaryotes)

Polycistronic: starting translation at different locations in the mRNA can result in different proteins.

bacterial RNA is generally polycistronic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

transfer RNA

A

responsible for converting the language of nucleic acids to the language of amino acids and peptides.
 Contains a folded strand of mRNA with an anticodon that pairs with the proper codon on the mRNA in the ribosome
 Charged or activated with a specific amino acid that pertains to the anticodon/codon pair.
• Attached to the 3’ OH end of the tRNA, CCA nucleotide sequence here.
 Aminoacyl-tRNA synthetase: activates the tRNA with the correct amino acid. Specific for the specific amino acid.
• Uses two high energy ATP bonds, which are used to supply the energy to create the peptide bond during translation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

charged or activated tRNA

A

activated with a specific amino acid that pertains to the anticodon/codon pair.
• Attached to the 3’ OH end of the tRNA, CCA nucleotide sequence here.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Aminoacyl-tRNA synthetase

A

activates the tRNA with the correct amino acid. Specific synthetase for the specific amino acid.
• Uses two high energy ATP bonds to add the tRNA to the amino acid. This high energy bond is then used to supply the energy needed for the peptide bond formed during translation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

ribosomal RNA

A

synthesized in the nucleolus and function as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm.
 Many rRNA molecules function as ribozymes: enzymes made of RNA molecules instead of peptides.
• Helps in the formation of peptide bonds and also splicing out its own introns in the nucleus.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How many codons are there?

A

64

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what are the stop codons

A

UAA, UAG, UGA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what are the start codons

A

AUG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what does the start codon code for?

A

met

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

degeneracy

A

more than one codon can specify a single amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

wobble position

A

the variable 3rd base in a codon.
• Evolutionary advantage to protect against mutations because mutations in the wobble position tend to be silent or degenerate.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

point mutation

A

mutation occurs and it affects one of the nucleotides in a codon.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

expressed mutations

A

if the mutation is in a certain point, then it can affect the primary amino acid sequence of a protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

missense mutations

A

a mutation where one amino acid substitutes for another

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

nonsense mutation

A

a mutation where the codon now encodes for a premature stop codon (truncation mutation)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

reading frame

A

the three nucleotides of a codon and the order they are read

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

frameshift mutation

A

occurs when some number of nucleotides are added to or deleted from the mRNA sequence.
• Can be very detrimental, resulting in changes to the amino acid sequence or premature truncation of the protein.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

are mutations in introns a big deal?

A

no not if they are cleaved out

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

introns vs exons

A

exons are expressed while introns are cleaved out

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

transcription

A

the creation of mRNA from DNA template is transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

transcription

A

the creation of mRNA from DNA template is transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

describe initiation of transcription

A

Helicase and topoisomerase are involved in unwinding the dsDNA and preventing formation of supercoils.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

template strand

A

antisense strand

the strand that the mRNA is synthesized from.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

RNA is synthesized by a DNA-dependent RNA polymerase. Scans the DNA looking for _____

A

promoter region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

another name for the promoter region in eukaryotes is _____

A

TATA box (usually falls around -25)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

transcription factors

A

help the RNA polymerase locate and bind to this promoter region.
o Does not require a primer to start

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

whart are the roles of RNA pol I, II, and III in eukaryotes?

A

 RNA pol I: located in the nucleolus and synthesizes rRNA
 RNA pol II: located in the nucleus and synthesizes hnRNA (pre-processed RNA) and small nuclear RNA (snRNA)
 RNA pol III: located in the nucleus and synthesizes tRNA and some rRNA.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

RNA pol travels in the ____ which allows transcribed mRNA in the ____

A

3 to 5 direction

5 to 3 direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Does RNA pol proofread its work?

A

No

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

coding strand

A

sense strand

DNA that is not used as a template during transcription, same as mRNA except mRNA has U’s for T’s.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

what do the numbers mean on the gene with regard to transcription?

A

 +1: the first base transcribed
 Negative numbers: to the left of the start of transcription where the promoter is.
 Positive numbers: downstream of the gene
 0: does not exist

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

what does the number 0 on the gene for transcription mean?

A

it does not exist

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

hnRNA to mRNA from ____

A

post-transcriptional modifications

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

after transcription, in the nucleus, ____ are spliced, and ____ are ligated

A

introns

exons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

lariat

A

introns that are released after being spliced

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

alternative splicing

A

when the primary transcript of hnRNA is spliced together in different ways to produce multiple variants of proteins encoded by the same original gene.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

discuss the 5’ cap

A

Is added during transcription and is recognized by the ribosome as the binding site. It also protects the mRNA from degradation in the cytoplasm.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

3’ poly A tail

A
  • Added to the 3’ end of the mRNA transcript and protects the message against rapid degradation.
  • Assists with export of the mature mRNA from the nucleus.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

nuclear pores

A

used by the mRNA to exit the nucleus.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

translation

A

converting the mRNA transcript into a functional protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

what is the ribosome composed of

A

proteins and rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

the small and large subunits of the ribosome only come together during ____

A

protein synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

what is the difference between eukaryotic and prokaryotic translation initiation?

A

For eukaryotes, mRNA has to be transferred to the cytoplasm before translation begins but in prokaryotes it begins before the mRNA is even complete yet.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

what are the factors involved in the 3 steps of translation?

A

initiation factors (IF), elongation factors (EF), and termination release factors (RF)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

describe translation initiation

A

 Prokaryotes: small subunit binds to the Shine Dalgarno sequence in the 5’ untranslated region, Initial amino acid is fMet
 Eukaryotes: small subunit binds to the 5’ cap structure, Initial amino acid is methionine
 The charged initiator tRNA binds to the AUG start codon in the P site of the ribosome.

53
Q

describe translation elongation

A

handing down the peptide chain from each tRNA to the next (only the amino acid on top is being handed down while the uncharge tRNA is eventually kicked)

3 step cycle that is repeated for every AA after the initial methionine is added
 1. A site: holds the incoming aminoacyl tRNA complex. Next to be added, determined by mRNA codon in A site
 2. P site: holds the tRNA that carries the growing polypeptide chain
• Peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site, which requires peptidyl transferase (part of the large subunit). GTP is used for energy during the formation of this bond.
 3. E site: the uncharged tRNA pauses here before exiting the ribosome. Unbinds from mRNA and is now ready to be charged again.
 Elongation Factors: recruit charged tRNA and GTP.
 Signal sequences can also be present on the proteins that help them get sent to a certain place.

54
Q

describe translation termination

A

 Reach stop codon in the A site, release factor binds to the stop codon, termination factors help to hydrolyze the completed polypeptide chain from the final tRNA and the polypeptide chain is released from the tRNA in the P site.

55
Q

order of APE in ribosome describe

A

EPA pretty much and mRNA is read 5 to 3

56
Q

chaperones

A

posttranslational

assist the protein in its folding process

57
Q

what are two different things that must happen for some proteins to become active following translation?

A

o Some proteins must be cleaved to become active while others must come together to form their quaternary structure before they are active.

58
Q

phosphorylation

A

addition of phosphate group by kinases.

59
Q

carboxylation

A

addition of carboxylic acid groups, usually act as calcium binding sites.

60
Q

glycosylation

A

addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination.

61
Q

prenylation

A

addition of lipid groups to certain membrane-bound enzymes.

62
Q

operon

A

a cluster of genes transcribed as a single mRNA; all relate to each other.
o Very common in prokaryotic cells
o Ex: trp operon in E. coli (negative repressible system)
 Turned off when there is too much tryptophan in the system.

63
Q

inducible operon systems

A

the system is normally off but can be induced to be on

 The repressor is bonded tightly to the operator system and acts as a roadblock.
 Negative control mechanism.
 Allows genes to only be produced when they are needed.
 Inducer binds to the repressor and allows the RNA polymerase to function.
 Ex: lac operon (negative inducible system)
• Induced by the presence of lactose
• It is also activated by catabolite activator protein (CAP) which acts through a positive control mechanism

64
Q

describe the lac operon

A

negative inducible system

normally off but can be induced to turn on in the presence of lactose.

65
Q

describe the trp operon

A

negative repressible system

normally on but can be bound to to turn off

66
Q

describe the order along the genome of regulator, structural, operator, promoter

A

regulator, promoter, operator, structural

67
Q

repressible systems

A

the system is usually on but can be made to turn off
 Allow constant production of protein product. The repressor made by the regulator gene is inactive until it binds to a corepressor  then binds to the operator site to stop future transcription.
 Sometimes negative feedback of the protein product that shuts it off.

68
Q

jacob-monod model

A

prokaryotes
used to describe the structure and function of operons.
o In this model, operons contain structural genes, an operator site, a promoter site, and a regulator gene.
o Structural gene: codes for the protein of interest.
o Operator site: a nontranscribable region of DNA that is capable of binding a repressor protein
o Promoter site: similar in function to promoters in eukaryotes
o Regulator gene: codes for a repressor protein

69
Q

transcription factors

A

transcription-activating proteins that search the DNA looking for specific DNA-binding motifs. Two domains:
o DNA-binding domain: binds to a specific nucleotide sequence in the promoter region or to a DNA response element (a sequence of DNA that binds only to specific transcription factors) to help in the recruitment of transcriptional machinery.
o Activation domain: allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylases, which function in the remodeling of chromatin structure.

70
Q

gene amplification

A

: amplification of transcription of a particular gene due to signals
o Enhancers: consists of response elements that allow for the control of one gene’s expression by multiple signals.  many txn factors can bind to one enhancer.
 Might be distance between the promoter and the enhancer so the DNA must bend to bring them together.
 By using enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels.

71
Q

enhancers

A

consists of response elements that allow for the control of one gene’s expression by multiple signals.  many txn factors can bind to one enhancer.
 Might be distance between the promoter and the enhancer so the DNA must bend to bring them together.
 By using enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels.

72
Q

gene duplication

A

allows for more copies of the gene in the genome. Mass transcription of the gene product.

73
Q

histone acetylation

A

 Transcription factors that bind to the DNA can recruit other coactivators such as histone acetylases.
 Acetylation of histone proteins decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA, opening the chromatin structure.

74
Q

histone deacetylase

A

proteins that function to remove acetyl groups from histones, which closes the chromatin conformation and decreases gene expression levels in the cell.

75
Q

DNA Methylation: DNA methylases

A

add methyl groups to cytosine and adenine nucleotides, which silences genes.
 Methylation occurs during development to silence genes that no longer need to be expressed.

76
Q

mRNA is produced in what direction?

A

mRNA is produced in the 5’ to 3’ direction, adding onto the 3’ end.

77
Q

which end of the tRNA is the amino acid added to?

A

the 3’ end after a CCA sequence

78
Q

are all aminoacyl tRNA synthetases the same?

A

No, each type of amino acid is activated by a different one

79
Q

how many ATPs does it cost to charge a tRNA molecule?

A

2

80
Q

what type of RNA is synthesized in the nucleolus?

A

rRNA

81
Q

each codon specifies _____ amino acids but many codons can specify ____

A

only

the same amino acid

82
Q

what is the name of the enzyme used to charge tRNA with their correct amino acid?

A

aminoacyl-tRNA synthetase

83
Q

are there tRNA molecules that recognize the stop codons?

A

no, when these codons come up it just leads to the release of the protein from the ribosome.

84
Q

what are the benefits of the wobble position in the genetic code?

A

it allows for mutations to occur and not have an effect on the protein product.

85
Q

what are mutations in the wobble position called?

A

degenerate or silent

86
Q

missense vs. nonsense mutation

A

missense: one amino acid subtitutes for another
nonsense: the codon produced by the point mutation now encodes for a premature stop codon

87
Q

what is another word for a nonsense mutation?

A

truncation mutation

88
Q

where does a silent mutation occur?

A

occurs in a wobble position, introns, or noncoding DNA.

89
Q

what are the roles of helicase and topisomerase during transcription?

A

they play the same roles as in replication

topoisomerase: prevents supercoiling
helicase: unwinds the DNA

90
Q

what is another name for the DNA template strand?

A

the antisense strand

91
Q

what is the difference between RNA polymerase and DNA polymerase in terms of starting?

A

RNA polymerase does not need a primer to begin

92
Q

Does RNA polymerase proofread its work?

A

no

93
Q

what is mRNA called before posttranscriptional modifications?

A

heterogenous nuclear RNA (hRNA)

94
Q

in the genetic code chart, the codons represent the ______ strand

A

coding (same except for U for A)

95
Q

what is the name of the complex that accomplishes splicing of hnRNA and what is in it?

A

spliceosome
small nuclear RNA (snRNA)
small nuclear ribonucleoproteins (snRNPs)

96
Q

do introns or exons get spliced?

A

introns

97
Q

what are the formal names of the 5’ cap and polyA tail?

A

5’ cap: 7-methylguanylate triphosphate cap

3’ tail: polyadenosyl tail

98
Q

what is an example of a mutation in noncoding DNA that can effect the final protein?

A

mutation in the splice sites

99
Q

explain the process of splicing

A

removal of introns, joining of exons, uses snRNA and snRNPs in the spliceosome to create a lariat, which is then degraded; exons are ligated together

100
Q

what are the formal names of of the binding sites in the ribosome?

A

A: aminoacyl
P: peptidyl
E: exit

101
Q

what is the difference between eukaryotes ribosome and prokaryotic?

A

eukaryotic: 40S + 60S == 80S
prokaryotic: 30S + 50S == 70S

102
Q

what is the rRNA not transcribed in the nucleolus?

A

5S

103
Q

compare where the small ribosomal subunit binds: eukaryotes vs. prokaryotes

A

eukaryotes: 5’ cap
prokaryotes: shine-dalgarno sequence in the 5’ untranslated region

104
Q

where does the Met tRNA initially bind to the start codon in the ribosome?

A

P site

105
Q

what is the name of the enzyme that creates the peptide bond in the ribosome?

A

peptidyltransferase

106
Q

is there energy required to form each peptide bond in the ribosome?

A

yes, energy from GTP.

107
Q

Are tRNA reused?

A

yes, once they leave the E site of the ribosome then they can be recharged.

108
Q

what do initiation factors do?

A

help the large subunit bind to the smaller subunit

109
Q

what do elongation factors do?

A

recruit aminoacyl-tRNA along with GTP

110
Q

signal sequences on the N-terminal end of the protein do what?

A

dictate that the ribosome move to the rough ER so that the protein can be directly translated into the lumen of the ER (for proteins being excreted or going to the nucleus, cell membrane, or lysosomes.

111
Q

what is the role of release factor?

A

it binds to the stop codon on the mRNA sequence in the A site and recruits a water molecule to be used to hydrolyze the completed polypeptide chain from the P site.

112
Q

what are some examples of posttranslational modifications?

A

correct folding
cleavage events (to form active peptides or cleaving the signal sequence)
subunits come together to form quaternary structure
adding other biomolecules: phosphorylation, carboxylation, glycosylation, prenylation

113
Q

what does a regulator gene code for?

A

repressor

114
Q

where is the promoter site with respect to the operator site and the regulator site

A

promoter - operator - gene that makes protein

115
Q

is the operator site transcribed in prokaryotes?

A

no

116
Q

negative control mechanisms

A

the binding of a protein reduces transcriptional activity

117
Q

positive control mechanisms

A

the binding of a molecule increases transcription of a gene

118
Q

explain the role of the CAP protein in lac operon

A

CAP: catabolite activator protein
activated by cAMP in the presence of lactose (when glucose levels are low). Binds to promoter region of lac operon to increase transcription.

119
Q

what is the role of the corepressor

A

binds to the repressor and activates it in a repressible operon system.

120
Q

what are the two recognizable domains of transcription factors?

A

DNA binding domain

Activation domain

121
Q

where can transcription factors bind?

A

promoter or DNA response element (a sequence of DNA that binds only to specific transcription factors)

122
Q

response element

A

a sequence of DNA that binds only to specific transcription factors

123
Q

cis regulators vs. trans regulators

A

cis: promoter, right next to the gene
trans: transcription factors, they are proteins that must be translated in the cytoplasm and transported back to the nucleus for action.

124
Q

because of the location of enhancers, DNA oftentimes must ____ to bring the enhancer elements closer to the promoter

A

bend

125
Q

are heterochromatin or euchromatin more methylated?

A

heterochromatin are, which plays a factor in heterochromatin DNA being more silenced.

126
Q

____ acetylation and ___ methylation in transcriptional control

A

histone

DNA

127
Q

2 roles of elongation factors

A

bring in incoming tRNA and move growing strand from A to P site while moving ribosome down the mRNA

128
Q

which stages of protein synthesis require energy?

A

all 3 parts, initiation, elongation, and termination.

129
Q

do enhancers bind to multiple promoters?

A

no. specific transcription factors bind to specific DNA sequences (ex: enhancer) and to specific RNA polymerase at a single promoter sequence.

MCAT Biochem (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions