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MCM Test 2 > Functions and Dysfunctions of Protein Processing > Flashcards

Functions and Dysfunctions of Protein Processing Flashcards

1
Q

What is the genetic code?

A

the genetic code is a set of rules that allows us to convert the nucleotides of a gene–> the AA of a protein with the help of an mRNA

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2
Q

How do we read nucleotides of mRNA to make the protein?

A

We read nucleotides in sets of 3, called codons.

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3
Q

What do codons code for?

A

Codons can code for amino acids or a stop codon that will end translation

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4
Q

How many codons are there?

A

There are a total of 64 codons.

61 codons code for amino acids
3 codons code for stop codons, and not AA

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5
Q

What does it mean that our code is degenerate?

A

Saying that our code is degenerate means that we are calling it redundant.

Thus, more than 1 codon can code for 1 amino acid.

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6
Q

Is out genetic code STANDARD?

A

yes

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7
Q

Is our genetic code UNIVERSAL?

A

no

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8
Q

2 other features of our genetic code

A
  1. Non-punctuated (without commas)

2. Non-overlapping (some exceptions)

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9
Q

What is a mutation?

A

A mutation is a PERMENANT, HERITABLE change in our DNA sequence

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10
Q

What can be the result of a point mutation?

A 
A point mutation that affects 
a base pair
or 
an open reading frame
can result in a different AA being inserted into our protein.
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11
Q

What are the 4 types of point mutations?

A
  1. Silent mutation: change in codon results in the same AA. Thus, it has no affect on the protein
  2. Missense mutation: change in the codon results in a different AA being inserted into the protein.
    If the AA is of same type= no affect on protein
    If the AA is of different type= very bad
  3. Nonsense mutation–> change in the codon results in a stop codon being inserted
    Result: protein is degraded or truncated
  4. Frameshit mutation–> when the number of deleted AA is not a multiple of three, causing a change in the reading frame and a change in the AA inserted
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12
Q

What are the results of a nonsense mutation?

A
  1. Protein is degraded

2. Protein is truncated

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13
Q

Sickle cell anemia is an example of what type of mutation?

A

Missense mutation
GAG–> GTG

Glu–> Valine ( a hydrophobic AA)

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14
Q

What is the codon changed in sickle cell?

A

GAG–>GTG

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15
Q

What is the AA changed to in Sickle cell?

A

Glu–>Val

Hydrophillic AA–> hydrophobic

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16
Q

What is the result of the missense mutation in sickle cell anema?

A

HbA will aggregate and form rod like structures, causing the cells to sickle. Thus, RBCs will have problems carrying O2 and clog capillaries

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17
Q

__________________ can lead a partially non-functioning dystrophin gene.

A
  1. Large in-frame deletion

2. OOF (out-of-frame) deletion

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18
Q

How do we develop Duchenne Muscular Dystrophy?

What is it?

A
  1. OOF deletion results in little, to no expression of the dystrophin gene.

DMD is a severe form that leads to muscle wasting.

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19
Q

What is Becker Muscular Dystrophy and how do you get it?

A

Becker is a MILDER form of DMD. Muscle is replaced with fat and fibroid and CK levels are elevated.

It occurs due to large-in frame deletions of the dystrophin gene, resulting in a truncated form.

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20
Q

Following modifications to mRNA, it is exported to the ________ for translation

A

cytoplasm

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21
Q

Features of eukaryotic mRNA

A
  1. 7’methylguanosine 5’ cap
  2. Coding region filled with codon
  3. Poly (A) tail
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22
Q

How does the codon find the AA?

A

tRNA. tRNA is an adaptor. It has a site for the codon and a site for the AA to attach to the tRNA.

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23
Q

Structure of tRNA

A
  1. Cloverleaf structure
  2. 2 regions of unpaired nucleotides:
    A. anticodon region
    B. 3’ CCA terminal region
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24
Q

What is an aminoacyl tRNA?

A

An aminoacyl tRNA is the activated tRNA with the AA already attached.

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25
Q

How do we activate the tRNA

A

there are 2 steps:

  1. aminoacyl-tRNA synthetase will catalyze [ATP–>AMP], adding it to the COOH end of the AA.
  2. AA can then transfer to the tRNA

We now have a activated tRNA :)

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26
Q

Is there only 1 aminoacyl tRNA synthetase?

A

No. Each AA will have its own aminoacyl tRNA synthetase.

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27
Q

_______________________ serve as the second genetic code.

A

Aminoacyl tRNA synthetase

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28
Q

Will tRNA always bind the correct AA?

A

Yes

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29
Q

Where does protein synthesis occur?

A

Ribosomes

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30
Q

What are ribosomes?

A

large complexes of rRNA and protein

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31
Q

What is the structure of ribosomes?

A

Ribosomes have a large and small subunit. When mRNA is present, the 2 come together to form an active complex.

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32
Q

Eukaryotic ribosome sizes

A

Eukaryotic=EVEN

40/60/80 S

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33
Q

Prokaryotic ribosome sizes

A

prOkaryotic= ODD

30/50/70 S

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34
Q

Antibiotics target _______ ribosomes

A

prokaryotic

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35
Q

Ribosomes Sites

A
  1. A (Acceptor sites)–> site where the mRNA codon is exposed to the aminoacyl tRNA can bind.
    * the initiator met-tRNA will not bind to the A site
  2. P (peptide site)–> where the peptide bond is formed
  3. E (exit)–> where the empty tRNA leaves
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36
Q

At what site does the initator met-tRNA bind?

A

It will bind at the P site

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37
Q

Translation occurs in the _______ direction

A

5’–>3’

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38
Q

Steps of Translation

A

Initiation, Elongation and Termination

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39
Q

Step 1: Initiation

A

Initiation: [mRNA, small ribosomal unit, and initiator tRNA complex] form

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40
Q

Step 2: Elongation

A

Peptide bond is formed between activated AA and methtionine

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41
Q

Step 3: Termination

A

peptide chain is released

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42
Q

When no protein synthesis is occuring, are the 2 ribosomal subunits together or apart?

A

Apart

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43
Q

Initiation: in Detail

A
  1. Pre-initiation complex is formed: [methionyl tRNA, with eIF2 and GTP bound to it] bind to the [P site of the small ribosomal SU]
  2. Other initiation factors are added
  3. ATP is hydrolyzed to ADP as we look for the initial start codon: AUG
  4. When found, GTP hydrolyses to GDP, and the initiation factors will leave
  5. Signals the large ribosomal SU to come in, forming the initiation complex
  6. Aminoacyl tRNA is added to the A site
  7. 1st peptide bond (-CO-NH) forms at the P site
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44
Q

t/f: all mRNA molecules have a signal that defines the beginning of each encoded polypeptide chain

A

TRUE

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45
Q

What is the special initiator tRNA in eukaryotes called?

A

methionyl-tRNA

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46
Q

What are eukaryotic and prokaryotic initiation factors called?

A

Eukaroyotic–> eIF2 (eukaryotic initiation factors)

Prokaryotic–> IF (initiation factors)

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47
Q

Once the first peptide bond is formed, the ribosome subunit translocates to the ______, to push the tRNA with 2AA to the ___ site

A

Right

P-site

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48
Q

How many GTP’s does initiation use?

A

1 in total

GTP is hydrolyzed when we find start codon to trigger the leave of eIFs and the addition of the large ribosomal complex

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49
Q

Elongation factors play a role in _________.

A

proofreading

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50
Q

Elongation: in DETAIL

A
  1. A peptide bond is formed between the aminoacyl tRNA and the methionyl tRNA
  2. Incoming [aminoacyl tRNAs+GTP-bound elongation factor] will bind to their anticodon to the codon region at the A site.
    Loading is assisted by GTP hydrolysis and release of
    the elongation factor
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51
Q

What enzyme catalyzes the formation of the peptide bond?

A

peptidyl transferase

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52
Q

How many GTPs are used in elongation?

A

2/AA.

1 is used for loading: GTP is bound to the elongation factor
1 powers the translocation of the ribosome

53
Q

Stop codons

A

UAA
UGA
UAG

54
Q

Termination- in detail

A

Translation termination occurs when release factors notice a stop codon.

  1. Release factors bind to the A site
  2. GTP is hydrolyzed
  3. Ester bond is broken between the peptide and tRNA
  4. Complex dissociates
55
Q

Termination requires ____ GTP

A

1 total

56
Q

Polysomes

A

Polysomes are clusters of ribosomes all translating 1 piece of mRNA, producing their own polypeptide

57
Q

Name all of the prokaryotic elongation inhibitors

A
  1. Streptomycin
  2. Tetracycline
    3 and 4. Clindamycin/erthryomycin
  3. Chloramphenicol*
58
Q

Chloramphenicol

A

Inhibits peptidyl transferase in both PROKARYOTES and MITOCHONDRIA

59
Q

Streptomycin
bind:
inhibits:

A

binds: 30s subunit of prokaryotes
inhibits: initiation
how: prevents met-tRNA from being added, thus, preventing the large and small subunit from forming

60
Q

Tetracycline
bind:
inhibits

A

binds: 30s subunit of prokaryotes
inhibits: elongation
how: does not allow aa-tRNA to bind

61
Q

Clindamycin and erthryomycin
bind:
inhibit:

A

bind: 50s subunit of prokaryotes
inhibits: elongation
how: prevents the ribosome from translocating

62
Q

Which two prokaryotic elongation inhibitors bind at the 30s?

A
  1. Streptomycin

2. Tetracycline

63
Q

Which prokaryotic elongation inhibitor binds binds at the 50s?

A
  1. Clindamycin

2. Erythromycin

64
Q

Which prokaryotic elongation inhibitor works on both prokaryotes and mitochondria?

A
  1. Chloramphenicol
65
Q

_______ is used to treat pertussis

A

erthryomycin

66
Q
  1. Shiga toxin
  2. Ricin

bind:
Inhibit:
how:

A

bind: 60 s subunit of eukaryotes
inhibit: elongation by not allowing aa-tRNA to bind

67
Q

Diphtheria toxin

inhibits:
how:

A

inhibits: elongation

by inactivating the EF2-GTP (does not allow aa-tRNA to load onto ribosome)

68
Q

Cycloheximide

inhibits

A

inhibits peptidyl transferase in eukaryotes

69
Q

puromycin

A

eukaroyotes and prokayotes

resembles the 3’ of the aa-tRNA, so it will add to the growing chain and cause early termination

70
Q

Where is peptidyl transferase activity housed?

A

in the large subunits of ribosomes

60s
50s

71
Q

What is chloramphenical for eukaryotes?

A

Cycloheximide

Chloramphenicol is used to inhibit peptidyl transferase in prokaryotes and mitochondria

72
Q

3 steps must occur after protein synthesis

A
  1. Protein sorting: do they go to the cytoplasmic pathway or the secretory pathway
  2. Post-translational modifications
  3. Proteins can be folded or degraded
73
Q

What are the 2 major pathways proteins can enter?

A
  1. Cytoplasmic pathway

2. Secretory pathway

74
Q

Destinations of the cytoplasmic pathway

A
  1. cytoplasm
  2. nucleus
  3. mitochondria
  4. peroxisome
75
Q

Destinations of the secretory pathway

A
  1. rER
  2. lysosome
  3. Plasma membrane
  4. secreted
76
Q

Where are proteins that go through the cytoplasmic pathway translated?

A

Free ribosomes

77
Q

Where are proteins that undergo the secretory pathway translated?

A

1st on free ribosomes

then on bound ribosomes on the rER

78
Q

How do we know which proteins are destined to go through the secretory pathway?

A

Proteins destined to go through the secretory pathway have a ER-targeting signal.

N-terminus has 15-60 Lys or Arg basic AA (+++ charges)
C terminus has 10-15 hydrophobic residues

79
Q

Do proteins destined for the cytoplasmic pathway have a translocation signal?

A

No

80
Q

Do proteins destined for the cytoplasm have a translocation signal?

A

No, they just stay there.

81
Q

How do we know which proteins want to go to the MT?

A

they have a N-terminal hydrophobic alpha helix.

TOM and TIM are the guards. They will allow the protein into the outer and inner membrane of the mT, as long as they can show ID: a N-terminal HYDROPHOBIC alpha helix

82
Q

How are mT proteins protected as they go through TOM and TIM?

A

mT proteins are not folded (they’re nakes). They are protected by chaperones (heat shock protein 70: HSP70).

83
Q

How do mT proteins interact with chaperones?

A

Their N-terminal hydrophobic alpha helix will interact with chaperone (HSP 70)

84
Q

mT need ____________ as they go through TOM and TIM

A

chaperones

85
Q

What is an example of a chaperone?

A

Heat shock protein 70.

HSP70

86
Q

Proteins destined to go to the nucleus

A

Have 4 continuous basic AA residues (Lysine, Arginine)

KKKRK

87
Q

how do proteins destined to go to nucleus enter?

A
  1. small ones can enter through small pores

2. large ones must have a nuclear localization signal

88
Q

Proteins destined for the peroxisome

A

C-terminal SKL sequence

89
Q

how do we know which proteins are destined for the secretory pathway

A

They will have a ER targeting signal. This ER targeting signal will have:

a N-terminal that is made up 15-60 basic AA (lysine and Arg) so vvvv +++++++ charged
a C-terminal that has 10-15 hydrophobic residues

90
Q

How does the secretory protein go from being translated on a free ribosome–> bound ribosomes

A

If protein is destined for secretory pathway

  1. A signal recognition particle (SRP) will notice the ER-targeting signal.
  2. SRP will go and bind to the [ribsome+mRNA/polypeptide complex] and stop translation.
  3. it will then bring it over to the SRP receptor on the ER membrane,
  4. Translocation resume and protein is fed into the ER lumen using a protein translocator
  5. Enzymes inside the lumen will then cut the signal and release the protein.
91
Q

Secretory protein pathway:

A
  1. translated on free ribosome in cytosol
  2. translated on bound ribosome on the ER
  3. –> ER lumen
  4. For those that do not STAY in the ER lumen
  5. –> golgi apparatus wil lthen sort the proteins out
    a. Lysosome ( mannose-6-phosphate sequence)
    b. Membrane- (apolar rich N terminal with a stop-transfer sequence)
    c. Secreted- tryptophan rich domain
92
Q

Proteins destined for the ER lumen will have what signal

A

C-terminal KDEL sequence

lysine, aspartic acid, glutamic acid, leucine

93
Q

Proteins destined for the lysosome will have what signal

A

mannose-6-phosphate sequence

94
Q

proteins destined for the membrane will have what signal

A

apolar rich N-terminal with a stop transfer sequence

95
Q

Proteins destined for secreted will have what signal

A

tryptophan rich domain

96
Q

C-terminal KDEL sequence

A

secretory pathway protein wanting to stay in the ER

lysine, aspartic acid, glutamic acid, leucine

97
Q

C terminal SKL sequence

A

cytoplasmic pathway protein that wants to go to the peroxisome

98
Q

mannose-6-phosphate signal

A

secretory pathway protein that wants to go to the lysosome

99
Q

N-terminal hydrophobic alpha helix

A

cytoplasmic protein that needs to go to the mitocondria

100
Q

KKKRK sequence

A

cytoplasmic protein that needs to go to the nucleus

4 continuous basic AA residues (Lys or Arg)

101
Q

I-cell disease

A

I-cell disease is lysosomal storage disease. Proteins that are intended to be destined for the lysosome do not have the mannose-6-phosphate sequence. As a result, we have a high amount of lysosomal enzymes in the plasma.

102
Q

Post-translational processing: Protein folding

A

After translation, proteins must fold into their native confirmation. Small proteins can do this by themselves. But large proteins need help.

  1. Chaperones (like HSP70) will protect proteins and help them form into their native 3 strcutures
  2. Chaperonins, on the other hand, have barrel-like compartments and help proteins fold using ATP.
103
Q

Without chaperones or chaperonins, what would happen to proteins?

A

They would be exposed and aggregate.

104
Q

PTM: Proteolytic cleavage

A

some proteins need to be cleaved to be activated

105
Q

PTM: covalent modification via glycoslyation

A

Glycosylation–> the addition of sugars to proteins.

Can occur in an O-linked form or N-linked form

O-links are formed with -OH groups of serine/threonine residues
N-links are formed with [amide groups] of Asparagine (Asn)

106
Q

how are o-links formed?

A

-OH groups of serine/threonine residues

107
Q

How are n links formed?

A

-amide groups of Asparagine (Asn)

108
Q

PTM: Covalent modification via phosphorylation

A

Ester bond is formed between an [OH] group and an AA

via serine/threonine and tyrosine kinases

109
Q

Too much glycosylation can cause _________

A

cataracts

110
Q

PTM: Covalent modification via disulfide bond

Where are disulfide bonds formed?
How?

A

disulfide bonds are formed in the ER lumen between thiol (-SH) groups of 2 cysteine residues.

111
Q

Are disulfide bonds intramoleculear or inter? How do they affect the protein

A

disulfide bonds can be intra or inter-molecular and can help to stabilize the protein.

112
Q

How are disulfide bonds made?

A

Disulfide bonds are made with the help of

DISULFIDE ISOMERASES

113
Q

Proteins are usually acetylated on _____ residues

A

lysine

114
Q

Histone acetylation is important for ________

A

gene expression

115
Q

Are histone modifications heritable?

A

YESSSSSS. Epigenetics study heritable changes in gene expression where the DNA sequence is not altered.

116
Q

_____ is the most abundant structural protein in vertebrates

A

Collagen

117
Q

What is so crazy about collagen?

A

it undergoes alot of PTM

118
Q

PTM in collagen

A
  1. Lysine residues are modified –> 5’hydroxylysines
  2. Glycolsylated by adding galactose and glucose
  3. Ascorbic acid is needed for [lysyl and prolyl hydroxylases]
119
Q

Defects in the lysyl hydroxylase in collagen can do what?

A

Cause Ehlers Danlos Syndrome- flexible joints, blood vesse;s and intestines and uterus may rupture

120
Q

Alzheimers disease is due to

A
  1. Amyloid precursor proteins (APP) are broken down and form beta-amyloid. Beta amyloid will aggregate and form plaques extracellalary.
  2. Hyperphosphorylation of tau will form neurofibrillary tangles
    occurs intracellulary
121
Q

What is the common denominator in SPORADIC FORM of alzheimers?

familial form?

A

brain aging

Familial forms–> mutations in APP and tau

122
Q

What causes parkinsons

A

Alpha-synuclein (AS) will aggregate and create Lewy bodies in the dopaminergic neurons in the substantia nigra.

As a result, DA is decreased and causes neuronal death.

123
Q

Familial form of Parkinsons are caused by

Familial form of Alzheimers are caused by

A

Parkinsons–> mutations in alpha-synuclein, which causes lewy bodies

Alzheimers–> APP degradation–> beta-amyloid plaques and hyperphosphorylation of tau

124
Q

what is the common denominator in the sporadic form of parkinsons

A

brain aging

125
Q

Huntingtons disease sx

A

loss of movement and cognitive functions

126
Q

Mutation in hunginton

A

expansion of CAG repeats and polyglutamine repeats

127
Q

What fucks up in Huntington?

A

cells in the BASAL GANGLIA selectively die.

128
Q

Creutzfield- Jacob

A

misfolded prions infect healthy prions and cause them to misfold

129
Q

TSE

A

CD is a transmissible spongiform encephalopathy

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