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MCAT BIOLOGY FLASHCARDS > MCAT BIO CH. 4 PART 3 > Flashcards

MCAT BIO CH. 4 PART 3 Flashcards

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1
Q

When does termination of elongation in translation occur?

A

When a stop codon appears in the A site

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2
Q

What happens when a stop codon appears in the A site?

A

The A release factor enters the A site

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3
Q

What does the release factor cause to happen?

A

The peptidyl transferase to hydrolyze the bond between the last tRNA dn the completed polypeptide

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4
Q

How many release factors do prokaryotes have?

A

Three release factors

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5
Q

What are the purpose of the first two release factors, RF1and RF2?

A

RF1: Recognize termination codons UAA and UAF
RF2: Recognizes UAA and UGA

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6
Q

What is the purpose of RF3?

A

RF3 is a GTP-binding protein that leads to dissociation of RF1RF2 after peptide release

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7
Q

RF3 recognizes a stop codon T/F

A

False

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8
Q

How is the N-terminal amino acid different from prokaryotes and eukaryotes?

A

Euk: Met
Prok: fMet

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9
Q

What do eukaryotes used during translation instead of the Shine-Dalgarno?

A

There are 5’ UTR sequences in eukaryotes that function in starting translation

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10
Q

What is a common eukaryotes sequences that start translation?

A

Kozak sequence

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11
Q

What does eukaryotic translation begins with?

A

Eukaryotic translation begins with formation of the initiation complex

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12
Q

What complex forms in the beginning on eukaryotic translation?

A

43S pre-initiaion complex forms

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13
Q

What is the 43S pre-initiation complex composed of?

A

Composed of the 40S small ribosomal subunit, Met-tRNAMet and proteins called eIFs

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14
Q

What are eIFs?

A

Eukaryotic initiation factors

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15
Q

What happens once the 43S pre-initiation complex is assembled?

A

Complex recruited to the 5’ capped end of the transcript by an initiation complex of proteins (with eIFs)

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16
Q

What does the initiation complex do to the mRNA?

A

Scans the mRNA from the 5’ end to find the start codon

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17
Q

What happens once the initiation complex finds the start codon on the mRNA?

A

The large ribosomal subunit (60S) is recruited and translation can begin

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18
Q

What eIFs proteins are essential?

A
  1. eIF3

2. eIF4A, eIF4E and eIF4G

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19
Q

What is the purpose of the eIF3 protein?

A

Binds the small ribosomal subunit and prevents it from prematurely associating with the 60S subunit

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20
Q

What is the purpose of eIF4A?

A

A helicase and unwinds mRNA

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21
Q

What is the purpose of eIF4E?

A

Binds to the 5’ cap of the mRNA

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22
Q

What is the purpose of eIF4G?

A

A scaffold protein

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23
Q

What is the importance of the levels of the eIFs proteins?

A

Their levels are a rate-limiting step for translation

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24
Q

Higher amount of the three eIFs proteins means……? A lower amount means…?

A

Higher: Cell can perform more translation
Lower: Decreases translation

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25
Q

The activity of eIF proteins is controlled by what?

A
  1. Post-translational modification such as phosphorylation
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26
Q

What factors do eukaryotes have for the elongation step of translation?

A

eEF-1 and eEF2

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27
Q

What is eEF-1 composed of?

A

Has two subunits

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28
Q

What is the function of both subunits in the eEF-1 eukaryotic prokaryotes?

A
  1. Helps with entropies of an aminoacyl-tRNA into the A site

2. Guanine nucleotide exchange factor that catalyses the release of GDP

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29
Q

What is the function of the eEF-2 eukaryotic prokaryotes?

A

The eukaryotic translocase

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30
Q

What does eukaryotic translation termination include?

A

Two release factors: 1. eRF1 and 2. eRF3

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31
Q

What is the purpose of the eRF1 in eukaryotic translation termination?

A

eRF1 recognizes all three termination codons

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32
Q

What is the purpose of the eRF3 in eukaryotic translation termination?

A

eRF3 is a ribosome-dependent GTPase that helps eRF1 release the completed polypeptide

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33
Q

What is cap-dependent translation?

A

The major role of 5’ mRNA cap recognition for translation

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34
Q

What is cap-independent translation?

A

Eukaryotes can sometimes start translation in the middle of an mRNA molecule

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35
Q

If cap-independent translation means that translation can begin anywhere on the mRNA molecule, what is not required?

A

Doesn’t require the 5’ cap of the mRNA

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36
Q

In order to be able to start translation anywhere on the eukaryotic mRNA, what must be included in the transcription?

A

Internal ribosome entry site

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37
Q

What is the internal ribosome entry site (IRES)?

A

Specialized nucleotide sequence

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38
Q

What is the purpose of IRES in most cells?

A

Code for proteins that help the cell deal with stress or help activate apoptosis

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39
Q

What does the IRES makes sure?

A

Makes sure the cell can make essential proteins when under sub-optimal growth conditions

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40
Q

What happens when a cell is under stress?

A

Cells under stress generally inhibit translation (via inhibiting translation initiation)

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41
Q

What does cap-independent translation allow based on cell stress?

A

Allows the cell to make proteins wending so is crucial for survival or programmed cell death

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42
Q

Activation of translation using an IREs requires what that is different?

A

Requires different proteins than normal initiation

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43
Q

What are the six ways gene expression can be controlled

A
  1. Transcriptional control
  2. RNA processing control
  3. RNA transport and localization control
  4. mRNA degradation control
  5. Translation control
  6. Protein activity control
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44
Q

What is the principle site gene expression control in both eukaryotes and prokaryotes?

A

Transcription

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45
Q

What is epigenetic?

A

Change gene expression due to heritable or have a long term effect, not due to DNA sequence

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46
Q

What are the three most studied areas in epigenetic?

A
  1. DNA methylation
  2. Chromatin re-modelling
  3. DNA interference
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47
Q

What are the four ways we can control gene expression at the DNA level?

A
  1. DNA Methylation and Chromatin Remodeling
  2. Gene dose
  3. Imprinting
  4. Chromosome inactivation
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48
Q

How can the DNA of eukaryotic and prokaryotic cells be modified?

A

Covalently modified by adding a methyl group

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49
Q

What do bacteria do to DNA after DNA synthesis and why is it important?

A

Bacteria methylate new DNA shortly after synthesis, and the brief delay is useful in mismatch repair pathway

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50
Q

How can methylation control one expression in prokaryotes?

A

By promoting or inhibiting transcription

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51
Q

What does DNA methylation do to gene expression in eukaryotic cells?

A

Turns off eukaryotic gene expression

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52
Q

What are the two ways gene expression is turned off by methylation in eukaryotes?

A
  1. Blocking

2. Change DNA

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53
Q

Based on methylation turning off gene expression in eukaryotes, what is the “blocking” reasoning of how it turns it off?

A

Methylation physically blocks the gene from transcriptional proteins

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54
Q

Based on methylation turning off gene expression in eukaryotes, what is the “blocking” reasoning of how it turns it off?

A

Methylation physically blocks the gene from transcriptional proteins

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55
Q

Based on methylation turning off gene expression in eukaryotes, what is the “Change DNA” reasoning of how it turns it off?

A

Certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change the winding of DNA around histones

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56
Q

What is the gene dose way of increasing gene expression?

A

Increase the copy of number of gene by amplification

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57
Q

When increasing the number of gene copy, why does that increase gene expression?

A

Allows a cell to make large quantities of the corresponding protein

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58
Q

What is genomic imprinting?

A

When only one allele of a gene is expressed

59
Q

What is imprinting considered?

A

An epigenetic process

60
Q

Silencing of certain gene involves….?

A

DNA methylation, histone modifications and binding of long ncRNAs

61
Q

When epigenetic marks are there, how long does it stay for genomic imprinting?

A

Established in the germ-line and maintained throughout life

62
Q

At which stage does X-inactivation occur?

A

At the blastocyst stage of early development

63
Q

What is X-inactivation?

A

Each cell in the inner cell mass randomly inactivates an. X chromosome and the decision is irreversible

64
Q

How is the X inactivated?

A

Condensed, packaged in heterochromatin and high levels of DNA methylation

65
Q

What is a simple mechanism of transcriptional regulation that is also problematic?

A

Some promoters are simply stronger than others and don’t respond to changing conditions in the cell

66
Q

What is anabolism? What is catabolism?

A

Anabolism: Biosynthesis
Catabolism: Degradative metabolism

67
Q

What does repressible means?

A

Anabolic enzymes inhibited in the presence of excess amounts of products

68
Q

What does inducible enzymes mean?

A

Catabolic enzymes who transcription can be stimulation by the abundance of a substrate

69
Q

What are the two examples of repressible and inducible enzymes?

A
  1. Lac Operon

2. Trp Operon

70
Q

The lac operon is….?

A

Inducible since the enzyme it codes for are part of lactose catabolism

71
Q

The Trp Operon is….?

A

Repressible since the enzyme it codes for mediate tryptophan biosynthesis or anabolism

72
Q

What are the components of an operon?

A

Coding sequence for enzymes and upstream regulator sequences (control sites)

73
Q

What can operons also include but don’t usually?

A

Regulatory proteins such as repressors or activators

74
Q

What are the five letters that explain the components of the Lac Operon?

A
  1. P region
  2. O region
  3. Z gene
  4. Y gene
  5. A gene
75
Q

What is the purpose of the P region in the Lac Operon?

A

The promoter site on DNA to which RNA polymerase binds to initiate transcription of Y, Z and A genes

76
Q

What is the purpose of the O region in the Lac Operon?

A

The operator site to which the Lac repressor binds

77
Q

What is the purpose of the Z gene in the Lac Operon?

A

Codes for the enzyme β-galactosidase

78
Q

What is the purpose of β-galactosidase?

A

Cleaves lactose into glucose and galactose

79
Q

What is the purpose of the Y gene in the Lac Operon?

A

Codes for permease

80
Q

What is the purpose of permease?

A

A protein which transports lactose into the cel

81
Q

What is the default for repressible systems? What is the default for inducible systems?

A

On, Off

82
Q

What is the purpose of the A gene in the Lac Operon?

A

Codes for transacetylase

83
Q

What is the purpose of transacetylase?

A

Enzyme that transfers acetyl group from acetyl-CoA to β-galactosidase

84
Q

Is the A gene required for lactose metabolism?

A

No

85
Q

Based on the regulation of the lac operon, which genes have their own promoters?

A
  1. Crp gene

2. I gene

86
Q

What is the purpose of the crp gene in lac operon? Where is it located?

A
  1. Codes for a catabolic activator protein (CAP) and helps couple the lac operon to glucose levels in the cell
  2. Located at a distant site
87
Q

What is the purpose of the I gene in the Lac Operon? Where is it located?

A

Codes for Lac repressor protein; located at a distant site

88
Q

The protein product of the crp and I gene control what?

A

Control gene expression of Z, Y and A

89
Q

What does bacterial cells use as an energy source preferably?

A

Glucose

90
Q

What happens in the bacteria cell in the presence of glucose?

A

Lac operon will be off or expressed at low amounts

91
Q

What mediates the lac operon being off in the presence of glucose?

A

CAP and repressor proteins

92
Q

What does the glucose level control in the lac operon?

A

Glucose levels control protein called adenyl cyclase

93
Q

What is the purpose of adenyl cyclase in the lac operon?

A

Adenyl cyclase converts ATP to cyclic AMP (cAMP)

94
Q

In high glucose levels, how is cAMP and adenyl cyclase?

A

Adenyl cyclase: Inactivated

cAMP: Levels are very low

95
Q

In low glucose levels, how is cAMP and adenyl cyclase?

A

Adenyl cyclase: Activated

cAMP: levels are high

96
Q

What happens at low glucose levels that aid in activating RNA polymerase?

A

CAP binds cAMP and complex binds the promoter of the lac operon

97
Q

What does the repressor protein bind to when coded by the __ gene?

A

Binds to the operator when coded by the I gene

98
Q

What does the lac repressor protein prevent from binding?

A

Prevents RNA poly from binding the promoter and transcribing Z, Y and A genes and blocking transcription of operon when lactose is absent

99
Q

What can lactose do to the lac repressor protein?

A

Allosteric bind; change conformational and falls off DNA as it can no longer bind

100
Q

What does high transcription of Z, Y and A gene occur?

A

When glucose is absent and lactose is present; digest lactose to produce glucose

101
Q

When high levels of cAMP bind to Cap, what does that cause?

A

Helps activate RNA polymerase activity at the lac operon

102
Q

What happens when lots of lactose start to go scarce?

A

Isn’t enough to bind to the repressor and most of the repressor proteins return to their original state

103
Q

How many enzymes do bacteria use to make tryptophan from chromatic acid?

A

Five

104
Q

What is the repressor protein to production of tryptophan?

A

trpR gene

105
Q

What does the trpR gene product do?

A

Repressor binds to Trp and complex binds to operator, turning off transcription

106
Q

What happens when no Trp is present?

A

Repressor protein cannot bind the operator

107
Q

What happens when repressor protein cannot bind to the operator since Trp is not present?

A

RNA poly can transcribe the give genes and give gene products allows the making of Trp

108
Q

What is Trp an example of?

A

Anabolic repressible transcription

109
Q

What is usually conserved in protein coding genes?

A
  1. Upstream control elements
  2. Promoter with binding sites for basal transcription complex and RNA poly II
  3. TATA box at -25
110
Q

What is the TATA box?

A

A highly conserved DNA recognition sequence for the TATA box binding protein (TBP)

111
Q

What does the binding the TBP allow, based on the TATA box?

A

Initiates transcription complex assembly at the promoter

112
Q

Where are activator proteins located?

A

Bound by enhancer sequences in DNA

113
Q

Which cell has gene repressor proteins?

A

Eukaryotes

114
Q

What do gene repressor proteins do?

A

Inhibit transcription

115
Q

What do transcription factor have that is extremely important?

A

Transcription factors have DNA binding domain and are crucial in transcription regulation

116
Q

What can transcription factors bind to?

A

Bind to promoters or other regulatory sequences

117
Q

The binding of transcriptional machinery to DNA is controlled by?

A

Extracellular signals

118
Q

What are the three most common methods of transcriptional regulation in eukaryotes?

A
  1. RNA Translocation
  2. mRNA Surveillance
  3. RNA Interference
119
Q

What is RNA Translocation, based on methods of transcriptional regulation in eukaryotes?

A

mRNA transcripts aren’t translated into proteins until they are localized properly in the cell

120
Q

What is mRNA Surveillance, based on methods of transcriptional regulation in eukaryotes?

A

Cells monitor mRNA molecules to ensure that only high-quality mRNA transcripts are read by ribosome

121
Q

What is RNA Interference (RNAi) based on methods of transcriptional regulation in eukaryotes?

A

A way to silence gene expression after a transcript has been made; amount of transcripts in the cell decreases

122
Q

What is RNAi mediated by?

A

miRNA and siRNA (Section 4.7)

123
Q

What are the three types of post-transcriptional modification?

A
  1. Protein Folding
  2. Covalent Modification
  3. Processing
124
Q

What are chaperons?

A

Function in assembly or folding of other macromolecular structures

125
Q

If the protein is folded correctly, it is said to be in its…

A

Native conformation

126
Q

For covalent modification during post-translational modification, adding a hydrophobic group would aid in what?

A

Facilitate membrane localization

127
Q

What does it mean when a protein is acetylated?

A

Addition of an acetyl group (-C(O)CH3) usually at the N terminus of a protein or at a lysine

128
Q

What does it mean when a protein is formylated?

A

Addition of a formyl group (-C(O)H)

129
Q

What does it mean when a protein is alkylated? What AAs is it usually done to?

A

Addition of an alkyl group; usually done to lysine or arginine

130
Q

What does it mean when a protein is glycosylated?

A

Addition of a glycosyl group; substitute for of a cyclic saccharide

131
Q

What does it mean when a protein is phosphorylated?

A

Addition of a phosphate group (PO) to serine, threonine, tyrosine, or histidine amino acid

132
Q

What does it mean when a protein is sulphated?

A

Addition of a sulphate group (SO4^-2) to a tyrosine

133
Q

What can proteins do to other proteins that is considered a covalent modification?

A

Can link to other proteins

134
Q

What do many proteins require in order to become mature or functional?

A

Cleavage

135
Q

What are zymogens or proenzymes? What is their purpose?

A

Enzyme precursors; used when the mature protein may be dangerous to the organism

136
Q

What is a well-known example of post-translation processing?

A

Insulin

137
Q

What is insulin made from?

A

A prohormone - preproinsulin

138
Q

What is preproinsulin?

A

The primary translation product of the human INS gene

139
Q

What needs to be removed to have proinsulin formed?

A

N-terminus signal peptide is removed and sulphide bonds form, in the endoplasmic reticulum

140
Q

How many cleavage events are necessary to process proinsulin?

A

Three

141
Q

What are the events cleaved to process proinsulin?

A
  1. C peptide is removed

2. Dipeptide fragments

142
Q

How is the C peptide removed to process proinsulin?

A

Removed by a family of enzymes called pro protein coneytases

143
Q

How is the Dipeptide fragments removed to process proinsulin?

A

Removed from the C-terminus of the B chain peptide by carboxypeptidase

144
Q

Where do the cleavage events occur, based on the cleavage events to process insulin?

A

Secretory vesicle

MCAT BIOLOGY FLASHCARDS (23 decks)

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