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DEN 7101F - Human Structure and Function > Exam 2 10/13 Britton > Flashcards

Exam 2 10/13 Britton Flashcards

1
Q

List 2 gene regulatory mechanisms in which RNA stability is affected

A
  • deadenylation-dependent mRNA decay
  • microRNA (miRNA)
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2
Q

What does deadenylation nuclease (DAN) do?

A
  • Degrades mRNA
  • associates with mRNA 5’ methyl cap and degrades the mRNA in the 3’ to 5’ direction
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3
Q

Deadenyltion nuclease degrades mRNA in the __ to __ direction

A

3’ to 5’

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4
Q

In addition to DAN, the _____ also uses the mRNA 5’ cap and 3’ polyA tail, so there is _____

A

translation initiation apparatus; competition

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5
Q

What are miRNA?

A

small single stranded RNA molecules that negatively regulate gene expression

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6
Q

miRNA have ____ base pairing to how many target mRNA transcripts?

A

perfect/near perfect; one or several (rarely just 1 target)

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7
Q

What happens when miRNA bind to specific sequences in target mRNA?

A
  • promotes cleavage of the target mRNA
  • base pairs with target mRNA to negatively regulate its expression (inhibits protein translation of the target mRNA)
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8
Q

_____ degrades mRNA

A

Deadenylation nuclease

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9
Q

True or false: some miRNA is translated into protein

A

False - they are not translated

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10
Q

What do miRNA gene sequences include?

A
  • mRNA target sequence
  • approximate reverse complement sequence
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11
Q

Steps of miRNA processing following transcription

A
  1. primary mRNA forms hairpin loop structure
  2. pri-miRNA is processed into pre-miRNA (shorter loop structure)
  3. further processing and cleavage (Drosha and Dicer enzymes) to produce mature miRNA
  4. miRNA loaded onto RNA Induced Silencing Complex (RISC), includes Argonaute proteins
  5. Directed towards target mRNA
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12
Q

____ plays a role in osteogenesis

A

miRNA

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13
Q

miRNA plays a role in diseases such as:

A
  • Heart development and disease
  • diabetes
  • cancer
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14
Q

How does miRNA play a role in heart development?

A

Regulation of specific transcription factors important for cardiogenesis

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15
Q

How does miRNA play a role in diabetes?

A
  • lack of miR-375 causes b cells (insulin producing) to die
  • a cells (glucagon producing) increase in mass
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16
Q

miRNA can act as ____ to aid cancer treatment

A

Biomarkers

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17
Q

Translation of mRNA is carried out on:

A

Ribosomes

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18
Q

____ serve as adaptors between the mRNA template and the amino acids incorporated into protein

A

tRNAs

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19
Q

Protein synthesis involved interactions between ____ types of RNA molecules

A

3 (rRNA, tRNA, mRNA)

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20
Q

Ribosomes are known as the:

A

translational apparatus

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21
Q

Where are ribosomes located?

A
  • free floating in the cytosol
  • associated with the ER
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22
Q

Ribosomes consist of ____ subunits

A

2 (large and small)

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23
Q

mRNA is associated with which ribosomal subunit?

A

Small

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24
Q

What does each ribosomal subunit consist of?

A
  • rRNA
  • several ribosomal proteins
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25
Q

Ribosome has ___ binding sites

A

3 tRNA binding sites - A, P, E

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26
Q

What happens at ribosome A site?

A

aminoacyl-tRNA enter at A site

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27
Q

What happens in the P site of ribosome?

A

peptidyl tRNA is bound

(tRNA with growing peptide chain attached)

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28
Q

What happens at E site of ribosome?

A

deacylated tRNA exit at E site

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29
Q

What direction is mRNA translated?

A

5’ to 3’

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30
Q

Codon

A

Groups of 3 nucleotides on mRNA

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31
Q

Initiation codon

A

AUG

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32
Q

____ sets the reading frame for protein translation

A

Initiation codon AUG

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33
Q

How many possible codons are there, and how many code for amino acids?

A

64 total possible; 61 code for amino acids

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34
Q

___ codons are stop codons

A

3

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35
Q

What is meant by degeneracy of the code?

A

Most amino acids are represented by more than one codon (ex. leucine, serine)

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36
Q

During translation, tRNA links the codon on mRNA transcript to a _______

A

specific amino acid

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37
Q

2 key sites on tRNA

A
  • anticodon
  • amino acid attachment site at 3’ end
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38
Q

Complementary base pairing with mRNA occurs at:

A

Anticodon (located on tRNA)

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39
Q

The 3’ end of tRNA is the site of:

A

Attachment of specific amino acids

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40
Q

True or false: there are 64 tRNAs that have distinct anticodons

A

False - Wobble in the 3rd position allows for the anticodon of one tRNA that can bind with several different codons

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41
Q

The genetic code is translated in a ___ step process that uses energy from ____

A

2; ATP

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42
Q

Translation control steps

A
  1. specific amino acid linked to specific tRNA
  2. tRNA (anticodon) binds to mRNA codon by complementary base pairing
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43
Q

Each aminoacyl tRNA synthetase is selective for:

A

Particular amino acid

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44
Q

How is specificity of aa attachment to tRNA controlled?

A

Proofreading reactions will hydrolyze any incorrectly formed aa-tRNAs

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45
Q

Translation occurs in 3 stages which are:

A
  • initiation
  • elongation
  • termination
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46
Q

What happens during initiation of translation?

A
  • synthesis of the first peptide bond of protein
  • ribosome needs to bind to mRNA to form initiation complex (1st AUG-tRNA)
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47
Q

What happens during elongation of translation?

A

chain is extended by the sequential addition of amino acids

48
Q

What happens during termination of translation?

A
  • aa addition is stopped
  • completed protein is released and dissociates from the mRNA
49
Q

_____ is optimal for translation initiation

A

Kozak sequence

50
Q

What can block translation initiation?

A
  • translation repressor proteins can hide the Kozak sequence
  • miRNA
51
Q

What is the Kozak sequence?

A

A/G-X-X-A-U-G-G
First AUG codon from 5’ cap site on mRNA
Start codon

52
Q

What is the function of eukaryotic initiatior factors (eIF)?

A

Control mRNA translation
eIF-2/4

53
Q

If mRNA is _____, eIF-4 will associate with mRNA transcript at _____

A

correctly processed; 5’ cap and 3’ polyA tail

54
Q

Once eIF-4 associated with mRNA, what happens?

A

mRNA can be correctly positioned in the small ribosomal subunit

55
Q

eIF-2 binds to:

A

initiator tRNA molecule

56
Q

Translation initiation: The ____ is brought to the small ribosomal subunit in association with ____

A

initiator-tRNA; eIF-2

57
Q

True or false: The initiation tRNA can only bind when the small ribosomal subunit is not attached

A

False - if large is not attached

58
Q

The initiator-tRNA scans the mRNA transcript looking for:

A

Kozak sequence (AUG start codon)

59
Q

eIF2/4 must ____ to allow the large ribosomal subunit to bind and begin translation

A

dissociate

60
Q

What causes eIF proteins to dissociate?

A

GTP-eIF2 is hydrolyzed to form GDP, causing dissociation

61
Q

How is eIF-2 activity controlled?

A
  • association with guanine nucleotide exchange factor eIF-2B
  • should be phosphorylated
62
Q

Phosphorylated eIF-2 is active or inactive? Would protein synthesis be faster or slower?

A

Inactive and sequesters eIF-2B as an inactive complex

Protein synthesis is slowed

63
Q

If eIF-2 is phosphorylated ____ cannot participate in GDP to GTP exchange

A

eIF-2B

64
Q

Steps of translation initiation associated with eIF-2

A
  1. initiatior-tRNA brought to small ribosomal subunit in association with eIF-2 (GTP bound)
  2. initiatior-tRNA scans mRNA transcript in search for Kozak sequence (AUG start codon)
  3. eIF-2 GTP is hydrolyzed to form GDP, allowing eIF-2 (and 4) to dissociate
  4. Large ribosomal subunit can bind and begin translation
65
Q

Steps of translation elongation phase

regarding each binding site

A
  1. aa-tRNA binds to vacant A site (enters)
  2. new peptide bond formed at P site
  3. mRNA moves 3 nucleotide positions through the ribosomal subunit to the E site
  4. tRNA is used up and ejected
66
Q

EF-1 and EF-2

A
  • Elongation factors
  • facilitate peptide chain elongation during protein synthesis
67
Q

Function of EFs (elongation factors)

A
  • control the accuracy of translation (and proofreading)
  • drive the elongation phase of translation forward to make it faster
68
Q

EF-1 transports aa-tRNAs into the ___. After peptide bond formation, EF-2 mediates ____

A

A site; ribosome translocation and resetting

69
Q

EF-1 and EF-2 are associated with what source of energy?

A

GTP/hydrolysis to GDP

70
Q

EF-1 and EF-2 use the hydrolysis of GTP to GDP to:

A
  • displace any incorrectly base-paired tRNA
  • reset the ribosome
  • eject the spent tRNA
71
Q

Post-translational control of gene expression refers to the control of:

A

Protein activity, stability, localization, and interacting partner molecules

72
Q

Proteins can be modified to make them:

A

Functionally active/inactive

73
Q

True or false: There are both reversible and irreversible events of protein modifications

A

True

74
Q

Proteolysis is reversible or irreversible?

A

Irreversible

75
Q

Post translational modifications are reversible or irreversible?

A

Reversible

76
Q

A protein’s ____ depends on its shape

A

Function

77
Q

During protein folding, what structures usually form first?

A
  • alpha helix
  • beta sheet

secondary protein structure

78
Q

Example of protein with quaternary structure

A

Hemoglobin

79
Q

Alpha helices and beta sheets within a protein can interact to form:

A

Tertiary structure

80
Q

Proteins fold into ____ shapes which include forming _____ to bind a particular molecule

A

Functional; pockets

Lock and key

81
Q

Failures in protein ___ causes several known diseases

A

folding

82
Q

Cystic fibrosis and sickle cell anemia are associated with

A

Mutations that cause protein misfolding

83
Q

Accumulation of mis-folded proteins play a large role in _____ diseases such as:

A

Neurological; Alzheimer’s, Parkinson’s, Lou Gehrig’s disease (ALS), Huntington

84
Q

Disulfide bridge

A

Linking of sulfur residues between two cysteine aa’s

85
Q

Preproinsulin

A

Precursor of insulin, has A and B chain joined by intervening C chain

86
Q

How is preproinsulin modified to form insulin?

A
  • C chain removed by cleavage
  • A and B chains connected by disulfide bonds
87
Q

Examples of post translational modifications

A
  • methyl
  • acetyl
  • hydroxyl
  • phosphate
  • ubiquitin
  • lipids
  • carbohydrates
88
Q

Where do post translational modifications occur?

A
  • cytoplasm
  • nucleus
  • Golgi
89
Q

Proteins can be activated or deactivated through the activity of

A

Kinases and phosphatases

90
Q

Phosphorylation can happen on amino acids which have a ___ residue, which are

A

hydroxyl; serine, threonine, tyrosine

91
Q

Ubiquitination

A

Regulated degradation mechanism to control protein levels; adding ubiquitin is a PTM

92
Q

Ubiquitin is found in

A

Most tissues

93
Q

Ubiquitination steps (3)

A
  1. Activation via ubiquitin-activating enzymes (E1)
  2. Conjugation by ubiquitin-conjugating enzymes (E2)
  3. Ligations by ubiquitin ligases (E3)

Amino Can’t Live

94
Q

Ubiquitination marks proteins for _____ via _____

A

Degradation via proteosome

95
Q

Degradation of cyclins, TFs, protein kinases occurs through:

A

Ubiquitination

96
Q

Rough ER has ribosomes on

A

cytosolic surface

97
Q

In post-translational transport, where does translation occur?

A

In ribosomes in cytosol

98
Q

In post-translational transport, once a protein is made, it is transported to

A

Its functional cellular location (nucleus, mitochondria, peroxisomes, etc)

99
Q

In co-translational transport, ribosomes with mRNA attached are targeted to the ___, where translation occurs in association with the

A

ER; ER

100
Q

Ribosomes are targeted to the RER by a ____ at the ____-terminal of the translated protein

A

signal sequence; N-terminal

101
Q

What is a signal sequence

A

short stretch of amino acids, interacts with SRP (signal recognition particle)

102
Q

If a protein does not have a signal sequence, where does it go?

A

In the cytosol and translated there

103
Q

Proteins with a signal sequence move from the RER to:

A

Golgi, then secretory vesicles, plasma membrane, lysosome

104
Q

What is the signal hypothesis?

A
  1. signal sequence synthesized and binds to SRP
  2. SRP binds to receptor on RER
  3. Protein synthesized into ER
  4. Signal is removed when the growing peptide enters the ER

Protein synthesis is complete

105
Q

Constitutive secretion

A

proteins secreted from a cell continuously regardless of external factors or signals

106
Q

Regulated secretion

A

Proteins secreted from a cell when a specific signal is detected by the cell (insulin secretion)

107
Q

The ____ is the major site for the modification and packaging of proteins

A

Golgi

108
Q

Different coat proteins select different _____ and determine different _____

A

protein cargo; transport between ER, Golgi, organelles, cell membrane

109
Q

Coat proteins examples

A

Clathrin
COP1
COPII

110
Q

Once a coated vesicle finds a target membrane, they

A

Fuse; exocytosis

111
Q

SNARE stands for

A

Soluble NSF Attachment protein Receptors

112
Q

v-SNAREs

A

vesicle membrane SNAREs

113
Q

t-SNAREs

A

target membrane snares

114
Q

Complementary ______ proteins form stable complexes to allow for fusion

A

v-SNAREs and t-SNAREs

115
Q

True or false: each complementary set of v-SNAREs and t-SNAREs is associated with a particular organelle involved in the secretory pathway

A

True - example neurotransmitter release

DEN 7101F - Human Structure and Function (23 decks)

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