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cell biology > Gene Expression Definitions > Flashcards

Gene Expression Definitions Flashcards

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AP® Biology flashcards
1
Q

3’ splice site

A
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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

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3
Q

5’ splice site

A
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4
Q

5’ Untranslated Region (UTR)

A
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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.

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6
Q

Bonds

A
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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???

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8
Q

Capping Enzyme

A

binds to RNA polymerase 2. Responsible for adding 5’ cap to RNA during elongation

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9
Q

chromatin

A

tightly wound DNA to fit all genetic material in small volume (a big ball of DNA)

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10
Q

chromosomes

A

threadlike structure of nucleic acids which holds genes. X shape

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11
Q

Cleavage

A

to cut

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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)

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13
Q

Diamine Oxidase

A

terminates histamine

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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.

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15
Q

Enhancer

A

activator bound to enhancer to increase rate of transcription

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16
Q

Enhancer Binding Proteins

A
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17
Q

exons

A

produce functional RNA

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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

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19
Q

Genome

A

the complete set of genetic material present in a cell/organism

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20
Q

Histamine

A

messaging molecule

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21
Q

Histidine

A

Non-toxic form of histamine

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22
Q

Histidine Decarboxylase

A

Enzyme that converts histidine to histamine

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23
Q

Histone

A

PROTEINS that DNA wraps around have amino acids tails that extend outwards

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24
Q

Hydrogen Bonds

A
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25
Q

Initiation

A

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

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26
Q

Initiator Sequence

A
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27
Q

introns

A

have no function and are spliced off during the processing step

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28
Q

Lariat

A

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

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29
Q

Lo-transcriptional capping

A

occurs during elongation. The 5’ cap is added to the pre-mRNA

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30
Q

Messenger RNA

A
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31
Q

Nucleosome

A
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32
Q

Nucleosome

A

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

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33
Q

Polyadneylation

A

The process of adding adenines to the 3’ end of mRNA in order to make the poly A tail

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34
Q

Poly A signal

A
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35
Q

Poly A site

A

where CPSF cleaves (cuts) mRNA

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36
Q

Poly A tail

A
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37
Q

Poly A tail

A

helps to transport the strand from the nucleus to the cytoplasm, and adds translation efficiency. It also helps to stabilize the strand of mRNA

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38
Q

Polyadenylate Polymerase (PAP)

A

The enzyme that facilitates polyadenylation

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39
Q

pre-mRNA (precursor mRNA)

A

RNA that exists with introns and without the poly A tail

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40
Q

Pre-Initiation Complex

A

Binds to the promoter region and enhancers and composed of 100+ proteins

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41
Q

Processing

A

fourth step of transcription

42
Q

Promoter

A
43
Q

Purines

A

have two rings (a 6 carbon ring and a 5 carbon ring): guanine and adenine

44
Q

Pyrimidine

A

one ring structure (a 6 carbon ring): cytosine, thymine)

45
Q

Regulatory Sequence

A
46
Q

Ribosomal RNA

A
47
Q

RNA Polymerase 2

A
48
Q

Silencer

A
49
Q

SnRNP

A
50
Q

SnRNP

A
51
Q

spliceosome

A

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
Q

TATA Sequence

A
53
Q

Termination

A

Third step of transcription. RNA polymerase 2 reaches terminator sequence and will fall off resulting in pre-mRNA.

54
Q

Terminator (on gene)

A
55
Q

Topology

A

The way in which constituent parts are interrelated or arranged

56
Q

Transcription Factor 2D (TF2D)

A

part of the pre-initiation complex. Binds to the TATA box to start everything

57
Q

Transcriptional Control Region (TCR)

A
58
Q

Transfer RNA

A
59
Q

Uracil

A

demethylated form of thymine. Pyrimidine derivative found in RNA

60
Q

Virophage

A

viruses that affect other viruses

61
Q

Ternary Complex

A

formed by initiation factors. Made up of eIF2, GTP, tRNA, and Met

62
Q

eIF4E

A

cap binding protein

63
Q

scanning

A
64
Q

Translation Termination

A

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
Q

Translation Elongation

A

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
Q

Histone acetyltransferase (HATs)

A

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
Q

Histone deacetyltransferase (HDACs)

A

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
Q

DNA methyltransferases

A

are the enzymes responsible for methylation.

69
Q

CpG islands

A
70
Q

Constitutive splicing

A

every exon is spliced in and every intron is spliced out

71
Q

Lariat

A

Excised intron as well as the snRNP molecules from 5’ and 3’ splice sites. Also a rope used for lasso or tethering.

72
Q

Alternative Splicing

A

All introns are spliced out, some exons are spliced in.

73
Q

Translation

A

The process by which mature mRNA is used to code for proteins. Occurs in the cytosol.

74
Q

Cytosol

A

One of the liquids found inside cells.

75
Q

Initiation Factor Binding

A

Process by which eIF1A and eIF3 are added to 40S subunit. First step of the translation process.

76
Q

Ternary Complex

A

Made up of eIF2, GTP, and tRNA + methionine. When bound to 40S subunit it becomes the 43S PIC.

77
Q

eIF2

A

Eukaryotic Initiation Factor 2. Part of the ternary complex. Can be made inactive (stopping translation) if a kinase phosphorylates it.

78
Q

GTP

A

Guanosine triphosphate. eIF2B makes it by adding a phosphate to GDP that is bound to eIF2.

79
Q

Methionine

A

An amino acid. Non essential. Part of the ternary complex.

80
Q

43S PIC

A

43S pre-initiation complex. Made up of 40S subunit and the ternary complex.

81
Q

Ternary

A

Three

82
Q

eIF4E

A

The cap binding protein. “5’ caps best friend.” The 43S PIC + eIF4A + eIF4G bind to this to start translation.

83
Q

eIF4A

A

Also known as helocase

84
Q

eIF4G

A

Binds to 43S subunit. Eukaryotic initiation factor 4G

85
Q

Hydrolysis

A

Opposite of condensation. Breaking down using water.

86
Q

48S PIC

A

48S pre-initiation complex. Made up of 43S PIC + eIF4A (helocase) + eIF4E (cap-binding protein) + eIF4G

87
Q

Exit site

A

Where The tRNA molecule detaches from the AA and exits the ribosome.

88
Q

Peptidyl Site

A

Where the amino acids form peptide bonds (making a polypeptide). Is the second site of translational elongation.

89
Q

Acceptor Site

A

A location on the ribosome where a tRNA molecule carrying the appropriate AA enters the ribosome. Is the first site of translational elongation.

90
Q

Transcriptional Regulation

A

Regulating the process of DNA to RNA. Usually happens by altering the rate at which transcription of a gene can occur.

91
Q

Histone Modification

A

Adding or removing acetyl groups from histone tales to alter how tightly would the DNA double helix is, therefore affecting rate of transcription.

92
Q

Histone

A

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
Q

Histone Tail

A

Positively charged tail on Histone protein. Sometimes referred to as a “thread”. Made up of the AA lysine. Interacts w the phosphate backbone.

94
Q

Phosphate backbone.

A

Negatively charged. Sometimes referred to as the “spine”. Made of phosphate and altering nucleotides.

95
Q

Histone Acetyltransferase

A

Abbreviated HAT. An enzyme that increases the rate of transcription by adding acetyl groups to Histone tails.

96
Q

Histone deacetyltransferase

A

Abbreviated HDAT. An enzyme that removes acetyl groups from Histone tails. Decreases the rate of transcription.

97
Q

Acetyl

A

A functional group that can be added to Histone tails.

98
Q

DNA methylation

A

A method of transcription control where methyl groups are added to nucleotides (cytosine).

99
Q

CpG dinucleotides.

A

Cytosine nucleotide followed by a guanine nucleotide.

100
Q

CpG island

A

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.

cell biology (5 decks)

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