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General Biology 1 > Chapter 15, 16, & Selected Topic > Flashcards

Chapter 15, 16, & Selected Topic Flashcards

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1
Q

Gene expression

A

conversion of genotype to phenotype

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2
Q

Why is it important to control gene expression?

A
  1. Gene expression is energetically expensive
    • Eukaryotes: maintain homeostasis
    • Prokaryotes - respond to environmental changes
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3
Q

Regulatory proteins

A

proteins that modulate ability of RNA polymerase to bind to promoter

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4
Q

Positive control

A

Increases frequency of initiation

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5
Q

Negative control

A

Decreases frequency of initiation

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6
Q

Negative control is mediated by _________

A

repressors

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7
Q

Effectors

A

Alter conformation of repressor to enhance or abolish its binding to DNA

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8
Q

Positive control is mediated by _________

A

activators

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9
Q

Lac induction

A

presence of lactose prevents a repressor protein from binding to its regulatory sequence

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10
Q

Trp repression

A

the presence of tryptophan causes a repressor protein to bind to its regulatory sequence

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11
Q

List the three genes that make up the lac operon and what they encode.

A

LacZ - B-galactosidase
LactY - lactose permease
LacA - lactose transacetlyase

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12
Q

Lac repressor

A

Controls initiation of transcription of lac operon

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13
Q

Describe the induction of the lac operon.

A
  • In absence of lactose: lac repressor binds to DNA at operator site -> prevents transcription of operon
  • Lac operon is transcribed (induced) when CAP is bound and when repressor is not bound
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14
Q

Allolactose

A
  • effector that controls DNA binding of repressor
  • produced when lactose is available
  • binds to repressor, altering its conformation so that it no longer can bind to operator
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15
Q

Glucose repression

A

Preferential use of glucose in presence of other sugars (e.g., lactose)

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16
Q

Catabolite activator protein (CAP)

A

activator protein with cAMP as an affector

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17
Q

CAP binds to _______

A

cAMP

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18
Q

The level of cAMP is reduced in the presence of ________

A

glucose

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19
Q

The level of ______ is reduced in the presence of glucose

A

cAMP

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20
Q

The action of CAP is sensitive to ________ levels.

A

glucose

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21
Q

Allolactose allows _________ of the operon.

A

induction

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22
Q

What environmental conditions allow transcription of lac operon to occur?

A

CAP binds + lactose is present

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23
Q

What environmental conditions allow transcription of lac operon not to occur?

A
  1. Glucose is present + repressor binds
  2. CAP + repressor binds
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24
Q

General transcription factors

A

necessary for assembly of transcription apparatus and recruitment of RNA polymerase II to a promoter

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25
Q

Specific transcription factors

A

increase level of transcription

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26
Q

Promoters

A

the binding sites for general transcription factors

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27
Q

_______ are the binding sites for general transcription factors.

A

Promoters

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28
Q

Enhancers

A

Binding sites for specific transcription factors

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29
Q

_________ are the binding sites for specific transcription factors.

A

Enhancers

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30
Q

Coactivators

A

bind to transcription factor

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31
Q

Transcription complex

A
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32
Q

What makes control of transcription in Eukaryotes more complicated than in Prokaryotes?

A
  1. DNA is organized into chromatin - complicates DNA-protein interactions
  2. Transcription and translation are separated physically and temporally
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33
Q

Proto-oncogenes

A

Normal cellular genes that become oncogenic when mutated

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34
Q

Tumor-suppressor genes

A

genes that inhibits cell division

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35
Q

Oncogenes arise from __________

A

proto-oncogenes

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36
Q

What is the most frequently mutated gene in human tumors?

A

tumor-suppressor gene (TP53)

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37
Q

TP53

A

encodes p53 protein

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38
Q

p53 is involved in which cell-division checkpoint?

A

G1/S checkpoint

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39
Q

Explain p53/s contribution to the G1/S checkpoint.

A

In G1/S checkpoint, damaged DNA signals p53 to halt the cell cycle

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40
Q

What are examples of genes in humans that are mutated in germ-line cells?

A

BRCA1/BRCA2

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41
Q

What is the result of mutations in BRCA1/BRCA2 genes in humans?

A

increase a woman’s risk of developing hereditary breast or ovarian cancers

increase a man’s risk of developing hereditary prostate or breast cancers

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42
Q

What percentage of breast cancers involve the duplication of the HER2 gene?

A

10-20%

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43
Q

How many copies of the HER2 gene are typically present in a diploid cell?

A

2

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44
Q

What is the function of the HER2 gene?

A
  • encodes for a receptor protein
  • activates a signal transduction pathway -> resulting in cell proliferation
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45
Q

What is the result of the overexpression of HER2 receptors in cells?

A

Cells grow/divide in an uncontrolled way

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46
Q

What are the control mechanisms of lac operon?

A

Repressor protein, binding CAP site

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47
Q

What are the environmental signals of lac operon?

A

allolactose, cAMP

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48
Q

What are the sensors of lac operon?

A

Site on repressor protein, CAP

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49
Q

High glucose ______ cAMP + lactose

A

inhibits

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50
Q

Low/no glucose ________ cAMP + lactose

A

stimulates

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51
Q

CHAPTER 15

Central dogma of biology

A

Information passes from gene (DNA) to an RNA copy of gene

RNA copy directs sequential assembly of a chain of amino acids into a protein

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52
Q

In the central dogma of biology, ____ is transcribed to make ____, which is translated to make a ______.

A

DNA; mRNA; protein

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53
Q

Transcription

A

DNA-to-RNA step

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54
Q

Translation

A

RNA-to-protein step

55
Q

The process of ____ produces an RNA copy of information in DNA.

A

Transcirption

56
Q

What is the difference between a coding and a template strand in Transcription?

A

Template (antisense) strand - DNA strand that is copied

Coding (sense) strand - DNA strand that is not used

57
Q

In what way is the mRNA transcript not identical to the coding strand?

A

The mRNA transcript replaces thymine (T) with uracil (U)

58
Q

mRNA

A

Intermediate form of information in DNA transported out of nucleus to cytoplasm for ribosomal processing

59
Q

tRNA

A

Intermediary adapter molecule between mRNA and aminoa cids

60
Q

What are the functions of tRNA?

A
  1. Interpret informaiton in mRNA
  2. Help position amino acids on ribosome
61
Q

rRNA

A

class of RNA found in ribosomes

62
Q

Codon

A

Sequence of three nucleotides

63
Q

Reading frame

A

Correst succession of nuleotides in triplet codons that specific amino acids on translation

64
Q

What are the three stop codons?

A

UAA, UGA, UAG

65
Q

What is the start codon and what amino acid does it encode?

A

AUG; methionine

66
Q

Degenerate

A

some amino acids are specificed by more than one codon

67
Q

How many possible codons are there?

A

64

68
Q

Transcribe the following mRNA transcript into its amino acid sequence:
5’ - AUGUUUUCCACAGCCUAAUUG

A
69
Q

All organisms (for the most part) share a signle genetic code, what does this imply?

A
70
Q

Describe the RNA polymerase used in Prokaryotic transcription. What does the sigma subunit do?

A

RNA polymerase in prokaryotes exists in two forms :
1. Core polyermase - two identical a subunits, b subunit, b’ subunit
2. Holoenzyme - formed by addition of a sigma subunit to core polyermase

  • Sigma subunit recognizes promoter elements at -35 and -10 and binds to DNA
71
Q

The active site of the core polymerase is formed by ____ and ____ subunits.

A

beta; beta’

72
Q

What is a promoter, and does it become part of the transcript?

A

Forms recognition and binding site for RNA polymerase. No it is not, because the promoter is not transcribed

73
Q

Start site

A

Where transcription actually begins

74
Q

Terminator

A

signals end of transcription

75
Q

Transcription unit

A

region from promoter to terminator

76
Q

Describe the upstream and downstream orientation of transcription.

A

+1 - bases downstream of start site
-1 - bases upstream of start site (e.g., -35 = 35 nt UPSTREAM of start site)

77
Q

Where is the promoter in prokaryotes located?

A

35 nt upstream of start site (-35)

78
Q

What is the first step of prokaryotic transcription?

A

RNA polymerase binds to promoter

79
Q

Transcription bubble

A

region containing RNA polymerase, DNA template, and growing RNA transcript

80
Q

While in the replication bubble, the growing RNA transcript is a ________________________.

A

RNA:DNA hybrid

81
Q

Hairpin

A

Double-stranded stem with a single-stranded loop formed by a self-complementary G-C region that causes RNA polymerase to pause

82
Q

What is the simplest terminator of transcirption in prokaryotes?

A

Series of G-C base-pairs followed by a series of A-T base-pairs

83
Q

In prokaryotes, transcription and translation are ______.

A

coupled

84
Q

Operon

A

cluster of adjacent structural genes transcribed as a unit into a single mRNA molecule (i.e., genes encoding related functions are clustered together)

85
Q

In transcription, new RNA bases are added to what part of the previous nucleotide? (What carbon?)

A
86
Q

List the three RNA polymerases in eukaryotes and what they transcribe?

A
  1. RNA polymerase I - transcribes rRNA
  2. RNA polymerase II - transcribes mRNA
  3. RNA polymase III - transcribes tRNA
87
Q

What is the promoter of RNA polymerase II?

A

TATA box

88
Q

5’ cap

A
  • structed added to 5’ end of mRNA
  • ## methylated GTP is added to 5’ PO4- group
89
Q

3’ poly-A tail

A

series of adenine residues added to 3’ end of mRNA

90
Q

T or F: each polymerase recognizes its own promoter.

A

T

91
Q

What is the role of the 5’ cap?

A

translation, RNA stability, and further processing

92
Q

The 3’ poly-A tail in eukaryotes is similar to which structure in prokaryotes?

A

Hairpin loop

93
Q

Introns

A
94
Q

Exons

A
95
Q

pre-mRNA splicing

A
96
Q

Spliceosome

A
97
Q

Alternative splicing

A

A single transcript cna be spliced into different mRNAs by using different sets of exons

98
Q

Aminoacyl-tRNA synthetases

A

enzyme that attaches amino acids to correct tRNA during tRNA charging reaction

99
Q

Describe the two functional ends of tRNA.

A
  1. Acceptor stem - 3’ end of mRNA; porton where amino aids attach to
  2. Anticodon loop - contains anticodon seuqence that can form base-pairs with codons in mRNA
100
Q

Charging reaction

A

reaction by which aminoacyl-tRNA synthesase attaches a specific amino acid to the correct tRNA

101
Q

T or F: charging reaction is exergonic.

A

F: endergonic

102
Q

Does the charging reaction require ATP?

A

Yes

103
Q

Charged tRNA

A

tRNA joined to an amino acid

104
Q

Where does translation occur?

A

Ribosomes

105
Q

T or F: There is one aminoacyl-tRNA synthetase for ALL 20 amino acids

A

F: There is one aminoacyl-tRNA synthetase for EACH 20 amino acids

106
Q

Describe the three binding sites in bacterial ribosomes.

A
  1. A (aminoacyl) site - binds to tRNA carrying next amino acid to be added
  2. P (peptidyl) site - binds to tRNA attached to growing polypeptide chain
  3. E (exit) site - binds to tRNA carring preivous amino acid added
107
Q

tRNAs move through the three binding sites during the process of _______.

A

Elongation

108
Q

Wat does peptidyl transferase do and where is it located?

A

enzyme that catalyzes formation of peptide bonds; resides in large subunit

109
Q

What is the structure of the initation complex in prokaryotes?

A
  1. initiator tRNA charged with N-formylmethione (chemically modified methionine)
  2. small ribosomal subunit
  3. mRNA strand
110
Q

Ribosom-binding sequence (RBS)

A

Conserved sequence in 5’ end of mRNA complementary to 3’ end of small subunit rRNA

111
Q

T or F: RBSs are in both prokaryotes and eukaryotes.

A

F: only in prokaryotes

112
Q

What is difference between eularyotic and prokaryotic initation

A

Prokaryotes: initating amino acid - N-formylmehionine
Eukaryotes: initating amino acids - methionine

113
Q

Elongation factor (EF-Tu)

A

binds to charged tRNA and GTP

114
Q

Describe the details of the elongation cycle in translation.

A
  1. tRNA comes to ribosome bound to EF-Tu and GTP. After arrival, GTP is hydrolzyed, and EF-Tu and GDP dissociate from ribosome
  2. Peptidly transferase catalyzes the formation of peptide bonds between amino acid in A site and growing chain in P site
  3. Ribosome translocation - tRNA moves from A site to P site
115
Q

Wobble pairing

A

a single tRNA can read more than one codon in mRNA

116
Q

Release factors

A

proteins that release newly made polypeptide chain from ribosome

117
Q

What two places can translation occur in eukaryotes?

A

Cytoplasm or RER

118
Q

Siganl recogntion particle (SRP)

A

cytoplasmic complex of proteins that recognizes and binds a signal sequence of polypeptide

119
Q

Changing a single base in a nucleotide sequence can result in devastating changes to the __________.

A

Phenotype

120
Q

What are the three types of point mutations?

A
  1. Missense mutations
  2. Nonsense mutations
  3. frameshit mutations
121
Q

Point mutation

A

mutation that alters a single base

122
Q

Missense (nonsynonymous) mutation

A
123
Q

Nonsense mutation

A

mutation that changes a codon that encodes an amino acid to a stop codon

124
Q

What is the outcome of a nonsense mutation?

A

Stop codon will cause translation to terminate prematurely

125
Q

Frameshift mutation

A

mutation in which a base is added to or deleted from the DNA sequence; alters reading frame

126
Q

Explain how the impact of frameshift mutations depend on where it occurs in the gene.

A

A framshift mutation early in the gene causes a greater change in sequence; all amino acids after mutation are affected

127
Q

Deletion

A

mutation in which a portion of a chromosome is lost

128
Q

Duplication

A

mutation in which a portion of a chromosome is duplicated

129
Q

Cri-du-chat syndrome

A

deletion on chromosome 5

130
Q

Inversion

A

Translocation

131
Q

Indel

A

gain or loss of 1-50 bp

132
Q

Translocation

A

one chromosome is broken and becomes part of another

133
Q

Recpirocal translocation

A

Both chromosomes are broken and exchange material (i.e., material in a chromosome is transferred between chromsomes)

134
Q

In what way can mutations be beneficial to an organism/species?

A

Mutations provide a source of variation for evolution to act on

General Biology 1 (13 decks)

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