Chapter 15, 16, & Selected Topic Flashcards
(134 cards)
1
Q
Gene expression
A
conversion of genotype to phenotype
2
Q
Why is it important to control gene expression?
A
- Gene expression is energetically expensive
- Eukaryotes: maintain homeostasis
- Prokaryotes - respond to environmental changes
3
Q
Regulatory proteins
A
proteins that modulate ability of RNA polymerase to bind to promoter
4
Q
Positive control
A
Increases frequency of initiation
5
Q
Negative control
A
Decreases frequency of initiation
6
Q
Negative control is mediated by _________
A
repressors
7
Q
Effectors
A
Alter conformation of repressor to enhance or abolish its binding to DNA
8
Q
Positive control is mediated by _________
A
activators
9
Q
Lac induction
A
presence of lactose prevents a repressor protein from binding to its regulatory sequence
10
Q
Trp repression
A
the presence of tryptophan causes a repressor protein to bind to its regulatory sequence
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
12
Q
Lac repressor
A
Controls initiation of transcription of lac operon
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
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
15
Q
Glucose repression
A
Preferential use of glucose in presence of other sugars (e.g., lactose)
16
Q
Catabolite activator protein (CAP)
A
activator protein with cAMP as an affector
17
Q
CAP binds to _______
A
cAMP
18
Q
The level of cAMP is reduced in the presence of ________
A
glucose
19
Q
The level of ______ is reduced in the presence of glucose
A
cAMP
20
Q
The action of CAP is sensitive to ________ levels.
A
glucose
21
Q
Allolactose allows _________ of the operon.
A
induction
22
Q
What environmental conditions allow transcription of lac operon to occur?
A
CAP binds + lactose is present
23
Q
What environmental conditions allow transcription of lac operon not to occur?
A
- Glucose is present + repressor binds
- CAP + repressor binds
24
Q
General transcription factors
A
necessary for assembly of transcription apparatus and recruitment of RNA polymerase II to a promoter
25
Specific transcription factors
increase level of transcription
26
Promoters
the binding sites for general transcription factors
27
_______ are the binding sites for general transcription factors.
Promoters
28
Enhancers
Binding sites for specific transcription factors
29
_________ are the binding sites for specific transcription factors.
Enhancers
30
Coactivators
bind to transcription factor
31
Transcription complex
32
What makes control of transcription in Eukaryotes more complicated than in Prokaryotes?
1. DNA is organized into chromatin - complicates DNA-protein interactions
2. Transcription and translation are separated physically and temporally
33
Proto-oncogenes
Normal cellular genes that become oncogenic when mutated
34
Tumor-suppressor genes
genes that inhibits cell division
35
Oncogenes arise from __________
proto-oncogenes
36
What is the most frequently mutated gene in human tumors?
tumor-suppressor gene (TP53)
37
TP53
encodes p53 protein
38
p53 is involved in which cell-division checkpoint?
G1/S checkpoint
39
Explain p53/s contribution to the G1/S checkpoint.
In G1/S checkpoint, damaged DNA signals p53 to halt the cell cycle
40
What are examples of genes in humans that are mutated in germ-line cells?
BRCA1/BRCA2
41
What is the result of mutations in BRCA1/BRCA2 genes in humans?
increase a woman's risk of developing hereditary breast or ovarian cancers
increase a man's risk of developing hereditary prostate or breast cancers
42
What percentage of breast cancers involve the duplication of the HER2 gene?
10-20%
43
How many copies of the HER2 gene are typically present in a diploid cell?
2
44
What is the function of the HER2 gene?
- encodes for a receptor protein
- activates a signal transduction pathway -> resulting in cell proliferation
45
What is the result of the overexpression of HER2 receptors in cells?
Cells grow/divide in an uncontrolled way
46
What are the control mechanisms of lac operon?
Repressor protein, binding CAP site
47
What are the environmental signals of lac operon?
allolactose, cAMP
48
What are the sensors of lac operon?
Site on repressor protein, CAP
49
High glucose ______ cAMP + lactose
inhibits
50
Low/no glucose ________ cAMP + lactose
stimulates
51
# CHAPTER 15
Central dogma of biology
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
52
In the central dogma of biology, ____ is transcribed to make ____, which is translated to make a ______.
DNA; mRNA; protein
53
Transcription
DNA-to-RNA step
54
Translation
RNA-to-protein step
55
The process of ____ produces an RNA copy of information in DNA.
Transcirption
56
What is the difference between a coding and a template strand in Transcription?
Template (antisense) strand - DNA strand that is copied
Coding (sense) strand - DNA strand that is not used
57
In what way is the mRNA transcript not identical to the coding strand?
The mRNA transcript replaces thymine (T) with uracil (U)
58
mRNA
Intermediate form of information in DNA transported out of nucleus to cytoplasm for ribosomal processing
59
tRNA
Intermediary adapter molecule between mRNA and aminoa cids
60
What are the functions of tRNA?
1. Interpret informaiton in mRNA
2. Help position amino acids on ribosome
61
rRNA
class of RNA found in ribosomes
62
Codon
Sequence of three nucleotides
63
Reading frame
Correst succession of nuleotides in triplet codons that specific amino acids on translation
64
What are the three stop codons?
UAA, UGA, UAG
65
What is the start codon and what amino acid does it encode?
AUG; methionine
66
Degenerate
some amino acids are specificed by more than one codon
67
How many possible codons are there?
64
68
Transcribe the following mRNA transcript into its amino acid sequence:
5' - AUGUUUUCCACAGCCUAAUUG
69
All organisms (for the most part) share a signle genetic code, what does this imply?
70
Describe the RNA polymerase used in Prokaryotic transcription. What does the sigma subunit do?
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
The active site of the core polymerase is formed by ____ and ____ subunits.
beta; beta'
72
What is a promoter, and does it become part of the transcript?
Forms recognition and binding site for RNA polymerase. No it is not, because the promoter is not transcribed
73
Start site
Where transcription actually begins
74
Terminator
signals end of transcription
75
Transcription unit
region from promoter to terminator
76
Describe the upstream and downstream orientation of transcription.
+1 - bases downstream of start site
-1 - bases upstream of start site (e.g., -35 = 35 nt UPSTREAM of start site)
77
Where is the promoter in prokaryotes located?
35 nt upstream of start site (-35)
78
What is the first step of prokaryotic transcription?
RNA polymerase binds to promoter
79
Transcription bubble
region containing RNA polymerase, DNA template, and growing RNA transcript
80
While in the replication bubble, the growing RNA transcript is a ________________________.
RNA:DNA hybrid
81
Hairpin
Double-stranded stem with a single-stranded loop formed by a self-complementary G-C region that causes RNA polymerase to pause
82
What is the simplest terminator of transcirption in prokaryotes?
Series of G-C base-pairs followed by a series of A-T base-pairs
83
In prokaryotes, transcription and translation are ______.
coupled
84
Operon
cluster of adjacent structural genes transcribed as a unit into a single mRNA molecule (i.e., genes encoding related functions are clustered together)
85
In transcription, new RNA bases are added to what part of the previous nucleotide? (What carbon?)
86
List the three RNA polymerases in eukaryotes and what they transcribe?
1. RNA polymerase I - transcribes rRNA
2. RNA polymerase II - transcribes mRNA
3. RNA polymase III - transcribes tRNA
87
What is the promoter of RNA polymerase II?
TATA box
88
5' cap
- structed added to 5' end of mRNA
- methylated GTP is added to 5' PO4- group
-
89
3' poly-A tail
series of adenine residues added to 3' end of mRNA
90
T or F: each polymerase recognizes its own promoter.
T
91
What is the role of the 5' cap?
translation, RNA stability, and further processing
92
The 3' poly-A tail in eukaryotes is similar to which structure in prokaryotes?
Hairpin loop
93
Introns
94
Exons
95
pre-mRNA splicing
96
Spliceosome
97
Alternative splicing
A single transcript cna be spliced into different mRNAs by using different sets of exons
98
Aminoacyl-tRNA synthetases
enzyme that attaches amino acids to correct tRNA during tRNA charging reaction
99
Describe the two functional ends of tRNA.
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
Charging reaction
reaction by which aminoacyl-tRNA synthesase attaches a specific amino acid to the correct tRNA
101
T or F: charging reaction is exergonic.
F: endergonic
102
Does the charging reaction require ATP?
Yes
103
Charged tRNA
tRNA joined to an amino acid
104
Where does translation occur?
Ribosomes
105
T or F: There is one aminoacyl-tRNA synthetase for ALL 20 amino acids
F: There is one aminoacyl-tRNA synthetase for EACH 20 amino acids
106
Describe the three binding sites in bacterial ribosomes.
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
tRNAs move through the three binding sites during the process of _______.
Elongation
108
Wat does peptidyl transferase do and where is it located?
enzyme that catalyzes formation of peptide bonds; resides in large subunit
109
What is the structure of the initation complex in prokaryotes?
1. initiator tRNA charged with N-formylmethione (chemically modified methionine)
2. small ribosomal subunit
3. mRNA strand
110
Ribosom-binding sequence (RBS)
Conserved sequence in 5' end of mRNA complementary to 3' end of small subunit rRNA
111
T or F: RBSs are in both prokaryotes and eukaryotes.
F: only in prokaryotes
112
What is difference between eularyotic and prokaryotic initation
Prokaryotes: initating amino acid - N-formylmehionine
Eukaryotes: initating amino acids - methionine
113
Elongation factor (EF-Tu)
binds to charged tRNA and GTP
114
Describe the details of the elongation cycle in translation.
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
Wobble pairing
a single tRNA can read more than one codon in mRNA
116
Release factors
proteins that release newly made polypeptide chain from ribosome
117
What two places can translation occur in eukaryotes?
Cytoplasm or RER
118
Siganl recogntion particle (SRP)
cytoplasmic complex of proteins that recognizes and binds a signal sequence of polypeptide
119
Changing a single base in a nucleotide sequence can result in devastating changes to the __________.
Phenotype
120
What are the three types of point mutations?
1. Missense mutations
2. Nonsense mutations
3. frameshit mutations
121
Point mutation
mutation that alters a single base
122
Missense (nonsynonymous) mutation
123
Nonsense mutation
mutation that changes a codon that encodes an amino acid to a stop codon
124
What is the outcome of a nonsense mutation?
Stop codon will cause translation to terminate prematurely
125
Frameshift mutation
mutation in which a base is added to or deleted from the DNA sequence; alters reading frame
126
Explain how the impact of frameshift mutations depend on where it occurs in the gene.
A framshift mutation early in the gene causes a greater change in sequence; all amino acids after mutation are affected
127
Deletion
mutation in which a portion of a chromosome is lost
128
Duplication
mutation in which a portion of a chromosome is duplicated
129
Cri-du-chat syndrome
deletion on chromosome 5
130
Inversion
Translocation
131
Indel
gain or loss of 1-50 bp
132
Translocation
one chromosome is broken and becomes part of another
133
Recpirocal translocation
Both chromosomes are broken and exchange material (i.e., material in a chromosome is transferred between chromsomes)
134
In what way can mutations be beneficial to an organism/species?
Mutations provide a source of variation for evolution to act on
