Unit3 Flashcards
1
Q
core enzyme
A
The portion of RNA polymerase that catalyzes RNA synthesis.
2
Q
holoenzyme
A
The complete RNA polymerase enzyme, consisting of the core enzyme and a sigma factor.
3
Q
sigma factor
A
A protein that helps RNA polymerase recognize the promoter sequence and initiate transcription.
4
Q
transcription factor
A
A protein that binds to DNA and regulates gene expression.
5
Q
terminator
A
A DNA sequence that signals the end of transcription.
6
Q
promoter
A
A DNA sequence that signals the start of transcription.
7
Q
What components are necessary for transcription to end?
A
A terminator sequence in the DNA and specific RNA sequences that form a hairpin structure.
8
Q
inducible
A
A gene or operon whose expression is increased in response to a specific stimulus.
9
Q
open reading frame (ORF)
A
A sequence of DNA or RNA that can be translated into a protein.
10
Q
monocistronic
A
Describing mRNA that encodes a single protein.
11
Q
polycistronic
A
Describing mRNA that encodes multiple proteins.
12
Q
operon operator
A
A DNA sequence within the operon that binds to a repressor protein, inhibiting transcription.
13
Q
repressor
A
A protein that binds to an operator sequence, inhibiting transcription.
14
Q
inducer
A
A molecule that binds to a repressor protein, causing it to release from the operator and allowing transcription to proceed.
15
Q
constitutive gene expression
A
The continuous expression of a gene or operon.
16
Q
beta-galactosidase
A
An enzyme that breaks down lactose into glucose and galactose.
17
Q
permease
A
A protein that transports lactose into the cell.
18
Q
transacetylase
A
An enzyme involved in the metabolism of lactose.
19
Q
operator
A
A DNA sequence within the operon that binds to a repressor protein, inhibiting transcription.
20
Q
cAMP
A
Cyclic adenosine monophosphate, a second messenger molecule that activates the CAP protein.
21
Q
CAP site
A
A DNA sequence within the promoter region of the lac operon that binds to the CAP-cAMP complex, enhancing transcription.
22
Q
How does the presence of glucose regulate the lac operon?
A
Glucose inhibits the production of cAMP, which reduces the activity of the CAP-cAMP complex. This leads to decreased transcription of the lac operon.
23
Q
trp attenuation
A
A regulatory mechanism in bacteria that controls the expression of genes involved in tryptophan biosynthesis. It involves premature termination of transcription.
24
Q
attenuator
A
A DNA sequence within the leader region of an operon that can form alternative stem-loop structures, affecting transcription termination.
25
tryptophan
An amino acid that serves as a corepressor in the trp operon.
26
repressor
A protein that binds to an operator sequence, inhibiting transcription.
27
2:3 stem loop forms
A stem-loop structure that forms in the leader mRNA when tryptophan levels are high, leading to transcription termination.
28
poly U
A stretch of uracil nucleotides in the leader mRNA that follows the 2:3 stem loop, contributing to the stability of the termination structure.
29
What dictates which stem loops form?
The availability of tryptophan-charged tRNAs and the rate of ribosome movement along the leader mRNA.
30
trp-charged tRNAs
When tryptophan levels are high, there are more trp-charged tRNAs available, which allows the ribosome to move quickly through the leader region, promoting the formation of the 2:3 stem loop and transcription termination.
31
RNA polymerase
The enzyme that synthesizes RNA from a DNA template.
32
reporter assay
An experimental technique used to study gene expression by linking a regulatory sequence of interest to a reporter gene, whose product is easily detectable.
33
transfection
The introduction of foreign genetic material into a cell.
34
cDNA
Complementary DNA, a DNA copy of mRNA.
35
in vitro
Experiments performed outside of a living organism, often in a test tube or petri dish.
36
in vivo
Experiments performed within a living organism.
37
transcriptional regulation
The control of gene expression at the level of transcription.
38
reporter gene
A gene encoding a protein product that is easily detectable, often used in reporter assays.
39
eukaryotic
Organisms whose cells contain a nucleus and other membrane-bound organelles.
40
prokaryotic
Organisms whose cells lack a nucleus and other membrane-bound organelles.
41
RNA polymerase
An enzyme that synthesizes RNA molecules from a DNA template.
42
gene
A segment of DNA that encodes a specific protein or RNA molecule.
43
nucleus
A membrane-bound organelle in eukaryotic cells that contains the genetic material.
44
mRNA
Messenger RNA, a type of RNA that carries genetic information from DNA to ribosomes for protein synthesis.
45
cytoplasm
The fluid-filled region of a cell that surrounds the nucleus and contains organelles.
46
nucleosomes
Basic units of chromatin, consisting of DNA wrapped around histone proteins.
47
chromatin
The complex of DNA and proteins that makes up chromosomes.
48
RNA polymerase II
The main RNA polymerase responsible for transcribing protein-coding genes in eukaryotes.
49
tRNA
Transfer RNA, a type of RNA that carries amino acids to the ribosome for protein synthesis.
50
sigma factor
A protein that binds to RNA polymerase and helps it recognize promoter sequences in bacteria.
51
holoenzyme
A complex of proteins, including RNA polymerase and sigma factor, that initiates transcription in bacteria.
52
transcription factors
Proteins that bind to DNA and regulate the rate of transcription.
53
5' capping
The addition of a modified guanine nucleotide to the 5' end of mRNA.
54
3' poly-A tail addition
The addition of a string of adenine nucleotides to the 3' end of mRNA.
55
splicing
The removal of introns and the joining of exons in pre-mRNA.
56
alternative splicing
A process that allows different protein isoforms to be produced from a single gene.
57
regulatory region
A DNA sequence that controls the expression of a gene.
58
promoter
A DNA sequence that signals the start of transcription.
59
enhancer
A DNA sequence that can increase the rate of transcription.
60
operator
A DNA sequence that can bind to a repressor protein, inhibiting transcription.
61
bacteria
Single-celled prokaryotic organisms.
62
protein
A large molecule composed of amino acids.
63
luciferase
An enzyme that produces light.
64
luminometer
A device used to measure luminescence.
65
green fluorescent protein
A protein that emits green light when exposed to blue light.
66
beta-galactosidase
An enzyme that breaks down lactose.
67
ribosomes
Cellular structures responsible for protein synthesis.
68
tRNA
Transfer RNA, a type of RNA that carries amino acids to the ribosome for protein synthesis.
69
translational control
The regulation of gene expression at the level of translation.
70
Northern blot
A technique used to detect specific RNA molecules.
71
in situ hybridization
A technique used to detect specific RNA or DNA sequences in cells or tissues.
72
transfection
The introduction of foreign genetic material into a cell.
73
basal transcription
The minimum level of transcription required for gene expression.
74
core promoter
The DNA sequence that is directly recognized by RNA polymerase II.
75
TATA box
A DNA sequence found in many eukaryotic promoters.
76
initiator sequence
A DNA sequence that can function as a core promoter element in the absence of a TATA box.
77
primer extension
A technique used to determine the transcription start site of a gene.
78
RNA polymerase II basal transcription complex
A complex of proteins that assembles at the core promoter and initiates transcription.
79
general transcription factors
Proteins that bind to the core promoter and help RNA polymerase II initiate transcription.
80
primer extension assay
A technique used to determine the transcription start site of a gene.
81
TATA-Binding Protein (TBP)
A protein that binds to the TATA box and recruits other transcription factors.
82
pyrimidine
A nitrogenous base, such as cytosine or thymine, that contains a single ring.
83
downstream promoter element
A DNA sequence located downstream of the core promoter that can influence transcription.
84
reverse transcriptase
An enzyme that synthesizes DNA from an RNA template.
85
helicase
An enzyme that unwinds DNA.
86
kinase
An enzyme that adds phosphate groups to proteins.
87
TFIID
A general transcription factor that contains TBP.
88
TFIIA
A general transcription factor that stabilizes the binding of TFIID to DNA.
89
TFIIB
A general transcription factor that recruits RNA polymerase II to the promoter.
90
TFIIF
A general transcription factor that helps RNA polymerase II bind to the promoter and initiate transcription.
91
TFIIE
A general transcription factor that helps recruit TFIIH to the promoter.
92
TFIIH
A general transcription factor that unwinds DNA and phosphorylates RNA polymerase II.
93
RNA polymerase II C-terminal domain (CTD)
A domain on RNA polymerase II that is phosphorylated during transcription initiation and elongation.
94
amino acid
The building blocks of proteins.
95
helix-turn-helix
A common DNA-binding motif found in many transcription factors.
96
zinc fingers
A DNA-binding motif that uses zinc ions to coordinate protein structure.
97
leucine zippers
A DNA-binding motif that uses leucine residues to form a dimerization interface.
98
helix-loop-helix
A DNA-binding motif that uses two alpha helices separated by a loop.
99
peptide chain
A chain of amino acids linked together by peptide bonds.
100
holotrimer
A protein complex composed of three subunits.
101
DNA binding domain
A protein domain that recognizes and binds to specific DNA sequences.
102
Enhancer
A regulatory DNA sequence that can be located far from the gene it regulates and can increase gene expression.
103
Activation domain
A protein domain that interacts with other proteins (e.g., co-activators) to stimulate transcription.
104
Regulatory promoter
A promoter that contains binding sites for transcription factors that regulate gene expression.
105
Activator
A transcription factor that binds to an enhancer or regulatory promoter to increase gene expression.
106
Co-activator
A protein that interacts with an activator to enhance its ability to stimulate transcription.
107
Mediator complex
A large protein complex that bridges the interaction between transcription factors and RNA polymerase II, facilitating the initiation of transcription.
108
Promoter deletions
A technique used to identify the core promoter elements by progressively deleting regions of the promoter and measuring the effect on gene expression.
109
Linker scanning mutagenesis
A technique used to identify regulatory elements within a DNA sequence by systematically replacing short stretches of DNA with a linker sequence and measuring the effect on gene expression.
110
Heterochromatin
Tightly packed form of chromatin that is transcriptionally inactive.
111
Euchromatin
Loosely packed form of chromatin that is transcriptionally active.
112
Chromatin Remodeling
Process of altering chromatin structure to regulate gene expression.
113
Nucleosome Modification
Chemical modifications of histones within nucleosomes to affect gene expression.
114
Acetylation
Addition of an acetyl group to a histone, typically leading to increased gene expression.
115
Methylation
Addition of a methyl group to a histone or DNA, typically leading to decreased gene expression.
116
Epigenetics
Study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence.
117
Fusion Protein
Protein created by combining two or more genes or protein fragments.
118
Yeast-Two Hybrid Assay
Technique used to identify protein-protein interactions.
119
Hyperacetylation
Increased level of acetylation on histones, associated with increased gene expression.
120
Hypoacetylation
Decreased level of acetylation on histones, associated with decreased gene expression.
121
Chimeric Proteins
Proteins composed of parts from different sources, often used in research and biotechnology.
122
RNA Splicing
Process of removing introns from pre-mRNA and joining exons together to form mature mRNA.
123
Alternative Splicing
Process of producing different mRNA transcripts from a single gene by splicing exons in different combinations.
124
Oligo(dT) Column
Column chromatography technique used to isolate mRNA from a mixture of nucleic acids.
125
Capping
Addition of a modified guanine nucleotide to the 5' end of pre-mRNA to protect it from degradation and enhance translation efficiency.
126
Polyadenylation
Addition of a poly(A) tail to the 3' end of pre-mRNA to protect it from degradation and enhance translation efficiency.
127
mRNA Processing
Series of modifications made to pre-mRNA to produce mature mRNA, including capping, polyadenylation, and splicing.
128
Spliceosome
A large complex of proteins and RNA molecules that removes introns from pre-mRNA.
129
Self-splicing
The ability of some RNA molecules to catalyze their own splicing without the need for additional proteins.
130
Transesterification
A chemical reaction that involves the exchange of an ester group between two molecules. In splicing, it involves the breaking and forming of phosphodiester bonds.
131
Branchpoint
A specific nucleotide sequence within an intron that is essential for the splicing reaction.
132
snRNA (small nuclear RNA)
A class of small RNA molecules that form part of the spliceosome and play a crucial role in splicing.
133
snRNP (small nuclear ribonucleoprotein)
A complex of snRNA and proteins that functions as a unit in the spliceosome.
134
Intron lariat
A loop-shaped structure formed during splicing, containing the excised intron.
135
U6
A specific snRNA that plays a critical role in catalysis during splicing.
136
U2
A specific snRNA that recognizes the branchpoint sequence and helps to form the spliceosome.
137
U1
A specific snRNA that recognizes the 5' splice site of an intron.
138
U5
A specific snRNA that interacts with both the 5' and 3' splice sites, bringing them together for splicing.
139
UTR (Untranslated Region)
A region of mRNA that is transcribed but not translated into protein. UTRs can influence mRNA stability, localization, and translation efficiency.
140
Polyadenylation signal
A specific sequence of nucleotides in mRNA that signals the addition of a poly(A) tail.
141
Polyadenylation site
The site in the mRNA where the poly(A) tail is added.
142
RNA interference (RNAi)
A biological process in which RNA molecules inhibit gene expression by targeting mRNA for degradation or translational repression.
143
miRNA (microRNA)
A small non-coding RNA molecule that regulates gene expression by binding to the 3' UTR of target mRNAs.
144
shRNA (short hairpin RNA)
An artificial RNA molecule with a hairpin structure that can be processed by cellular machinery to produce siRNA.
145
siRNA (small interfering RNA)
A small double-stranded RNA molecule that triggers RNA interference by targeting specific mRNA sequences for degradation.
146
Guide strand
The strand of siRNA or miRNA that directs the RNA-induced silencing complex (RISC) to the target mRNA.
147
DICER
An enzyme that cleaves double-stranded RNA into small interfering RNA (siRNA) or microRNA (miRNA).
148
R2D2
A protein that assists DICER in processing double-stranded RNA.
149
Argonaute
A protein that is a key component of the RNA-induced silencing complex (RISC).
150
RISC (RNA-induced silencing complex)
A protein complex that binds to siRNA or miRNA and cleaves target mRNA or represses translation.
151
Transfer RNA (tRNA)
A type of RNA molecule that transfers amino acids to the ribosome during protein synthesis. It has a specific anticodon that recognizes a codon on mRNA.
152
Ribosomal RNA (rRNA)
A type of RNA molecule that forms the structural and catalytic core of the ribosome, the cellular machinery responsible for protein synthesis.
153
Peptidyl transferase
An enzymatic activity of the ribosome that catalyzes the formation of peptide bonds between amino acids during protein synthesis. 1
154
Charged tRNA
A tRNA molecule that is covalently linked to an amino acid.
155
RNA processing
A series of modifications that RNA molecules undergo after transcription to produce mature, functional RNA molecules.
156
Codon
A sequence of three nucleotides in mRNA that codes for a specific amino acid or a stop signal.
157
Anticodon
A sequence of three nucleotides in tRNA that is complementary to a codon in mRNA.
158
pre-rRNA
A precursor RNA molecule that is processed to form mature ribosomal RNA.
159
snoRNA (small nucleolar RNA)
A small RNA molecule that guides the modification of other RNAs, such as rRNA and tRNA.
160
snoRNP (small nucleolar ribonucleoprotein)
A complex of snoRNA and proteins that carries out RNA modification.
161
Ribozyme
An RNA molecule that can catalyze chemical reactions, such as peptide bond formation in the ribosome.
