Gene Expression Definitions Flashcards
(100 cards)
1
Q
3’ splice site
A
2
Q
5’ Cap
A
7-methylguanosine unusually linked to another 5’ end of the mRNA by a triphosphate linkage. promotes effective future processing and splicing of the strand
3
Q
5’ splice site
A
4
Q
5’ Untranslated Region (UTR)
A
5
Q
Alternative Polyadenylation
A
RNA processing mechanism, that generates distinct 3’ termini on mRNA transcripts. polyA tail is important for nuclear transport, translation, and mRNA stability.
6
Q
Bonds
A
7
Q
C-Terminal Domain Phosphorylation (CTDP)
A
The process for RNA polymerase 2 to be phosphorylated and the addition of a 5’ cap with the use of a capping enzyme so that transcription is not aborted???
8
Q
Capping Enzyme
A
binds to RNA polymerase 2. Responsible for adding 5’ cap to RNA during elongation
9
Q
chromatin
A
tightly wound DNA to fit all genetic material in small volume (a big ball of DNA)
10
Q
chromosomes
A
threadlike structure of nucleic acids which holds genes. X shape
11
Q
Cleavage
A
to cut
12
Q
Cleavage and Polyadenylation Specificity Factor (CPSF)
A
once CPSF reads the AAUAA sequence, it cleaves the pre-mRNA strand and the 3’ end of the strand (meaning there is a hydroxyl group at the end)
13
Q
Diamine Oxidase
A
terminates histamine
14
Q
Elongation
A
Second step of transcription. Addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs.
15
Q
Enhancer
A
activator bound to enhancer to increase rate of transcription
16
Q
Enhancer Binding Proteins
A
17
Q
exons
A
produce functional RNA
18
Q
Genes
A
A distance sequence of nucleotides forming part of a chromosome. A unit of heredity which is transferred from a parent by offspring
19
Q
Genome
A
the complete set of genetic material present in a cell/organism
20
Q
Histamine
A
messaging molecule
21
Q
Histidine
A
Non-toxic form of histamine
22
Q
Histidine Decarboxylase
A
Enzyme that converts histidine to histamine
23
Q
Histone
A
PROTEINS that DNA wraps around have amino acids tails that extend outwards
24
Q
Hydrogen Bonds
A
25
Initiation
First step of transcription. RNA polymerase binds to the promoter (the start of the gene) and then unwinds the DNA helix into single strands so that the template strand can be read in the 3' to 5' direction
26
Initiator Sequence
27
introns
have no function and are spliced off during the processing step
28
Lariat
The cut end then attaches to the conserved branch point region downstream through pairing of guanine and adenine nucleotides from the 5′ end and the branch point, respectively, to form a looped structure known as a lariat
29
Lo-transcriptional capping
occurs during elongation. The 5' cap is added to the pre-mRNA
30
Messenger RNA
31
Nucleosome
32
Nucleosome
A unit of measure. The amount of DNA that can wrap around 8 histones. They serve as a scaffold for formation of higher order chromatin structure as well as for a layer of regulatory control of gene expression
33
Polyadneylation
The process of adding adenines to the 3' end of mRNA in order to make the poly A tail
34
Poly A signal
35
Poly A site
where CPSF cleaves (cuts) mRNA
36
Poly A tail
37
Poly A tail
helps to transport the strand from the nucleus to the cytoplasm, and adds translation efficiency. It also helps to stabilize the strand of mRNA
38
Polyadenylate Polymerase (PAP)
The enzyme that facilitates polyadenylation
39
pre-mRNA (precursor mRNA)
RNA that exists with introns and without the poly A tail
40
Pre-Initiation Complex
Binds to the promoter region and enhancers and composed of 100+ proteins
41
Processing
fourth step of transcription
42
Promoter
43
Purines
have two rings (a 6 carbon ring and a 5 carbon ring): guanine and adenine
44
Pyrimidine
one ring structure (a 6 carbon ring): cytosine, thymine)
45
Regulatory Sequence
46
Ribosomal RNA
47
RNA Polymerase 2
48
Silencer
49
SnRNP
50
SnRNP
51
spliceosome
large complex molecules made up of small nuclear ribonucleoprotein (snRNPs) that remove introns from pre-mRNA. They bind at splicing sites within the pre-mRNA
52
TATA Sequence
53
Termination
Third step of transcription. RNA polymerase 2 reaches terminator sequence and will fall off resulting in pre-mRNA.
54
Terminator (on gene)
55
Topology
The way in which constituent parts are interrelated or arranged
56
Transcription Factor 2D (TF2D)
part of the pre-initiation complex. Binds to the TATA box to start everything
57
Transcriptional Control Region (TCR)
58
Transfer RNA
59
Uracil
demethylated form of thymine. Pyrimidine derivative found in RNA
60
Virophage
viruses that affect other viruses
61
Ternary Complex
formed by initiation factors. Made up of eIF2, GTP, tRNA, and Met
62
eIF4E
cap binding protein
63
scanning
64
Translation Termination
eventually the ribosome is going to reach the STOP CODON and fall of the mRNA template, and now we have a complete polypeptide chain ready for modification
65
Translation Elongation
tRNA adds AA tot he growing polypeptide chain. Amino acid first enters the acceptor site, peptide bond formation is catalyzed in the peptidyl site, and it exits through the exit site.
66
Histone acetyltransferase (HATs)
adds an acetyl group, lessens positive charge, and reduces the interaction between the negatively charged backbone of the DNA and the positively charged lysine. The relaxed formation allows for transcription machinery to act on chromatin and for the pre-initiation complex to form. Will increase activity.
67
Histone deacetyltransferase (HDACs)
removes acetyl group from lysine residues, and pulls chromatin back into closed formation. There is a stronger interaction between the negatively charged phosphate backbone and the positively charged lysine residues in the histone tails. Chromatin is now inaccessible to the transcription machinery. will decrease activity.
68
DNA methyltransferases
are the enzymes responsible for methylation.
69
CpG islands
70
Constitutive splicing
every exon is spliced in and every intron is spliced out
71
Lariat
Excised intron as well as the snRNP molecules from 5’ and 3’ splice sites. Also a rope used for lasso or tethering.
72
Alternative Splicing
All introns are spliced out, some exons are spliced in.
73
Translation
The process by which mature mRNA is used to code for proteins. Occurs in the cytosol.
74
Cytosol
One of the liquids found inside cells.
75
Initiation Factor Binding
Process by which eIF1A and eIF3 are added to 40S subunit. First step of the translation process.
76
Ternary Complex
Made up of eIF2, GTP, and tRNA + methionine. When bound to 40S subunit it becomes the 43S PIC.
77
eIF2
Eukaryotic Initiation Factor 2. Part of the ternary complex. Can be made inactive (stopping translation) if a kinase phosphorylates it.
78
GTP
Guanosine triphosphate. eIF2B makes it by adding a phosphate to GDP that is bound to eIF2.
79
Methionine
An amino acid. Non essential. Part of the ternary complex.
80
43S PIC
43S pre-initiation complex. Made up of 40S subunit and the ternary complex.
81
Ternary
Three
82
eIF4E
The cap binding protein. “5’ caps best friend.” The 43S PIC + eIF4A + eIF4G bind to this to start translation.
83
eIF4A
Also known as helocase
84
eIF4G
Binds to 43S subunit. Eukaryotic initiation factor 4G
85
Hydrolysis
Opposite of condensation. Breaking down using water.
86
48S PIC
48S pre-initiation complex. Made up of 43S PIC + eIF4A (helocase) + eIF4E (cap-binding protein) + eIF4G
87
Exit site
Where The tRNA molecule detaches from the AA and exits the ribosome.
88
Peptidyl Site
Where the amino acids form peptide bonds (making a polypeptide). Is the second site of translational elongation.
89
Acceptor Site
A location on the ribosome where a tRNA molecule carrying the appropriate AA enters the ribosome. Is the first site of translational elongation.
90
Transcriptional Regulation
Regulating the process of DNA to RNA. Usually happens by altering the rate at which transcription of a gene can occur.
91
Histone Modification
Adding or removing acetyl groups from histone tales to alter how tightly would the DNA double helix is, therefore affecting rate of transcription.
92
Histone
A protein found in DNA. DNA is wrapped around it, eight of them exist in each nucleosome. They have a tail that is positively charged.
93
Histone Tail
Positively charged tail on Histone protein. Sometimes referred to as a “thread”. Made up of the AA lysine. Interacts w the phosphate backbone.
94
Phosphate backbone.
Negatively charged. Sometimes referred to as the “spine”. Made of phosphate and altering nucleotides.
95
Histone Acetyltransferase
Abbreviated HAT. An enzyme that increases the rate of transcription by adding acetyl groups to Histone tails.
96
Histone deacetyltransferase
Abbreviated HDAT. An enzyme that removes acetyl groups from Histone tails. Decreases the rate of transcription.
97
Acetyl
A functional group that can be added to Histone tails.
98
DNA methylation
A method of transcription control where methyl groups are added to nucleotides (cytosine).
99
CpG dinucleotides.
Cytosine nucleotide followed by a guanine nucleotide.
100
CpG island
Genomic regions that have a high concentration of CpG dinucleotides. 70% of genes contain CpG islands. Is the prime location where DNA methylation occurs, repressing transcription.
