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module 2 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

gene

A

entire nucleic acid sequence that is necessary for the synthesis of a useful RNA molecule or a functional polypeptide

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2
Q

distal promotor

A

distant portion of the promoter for a particular gene
region of DNA that may contain additional regulatory elements, often with a weaker influence than the proximal promoter.

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3
Q

proximal promotor

A

upstream of the gene that tends to contain primary regulatory elements
approximately 250 base pairs or nucleotides, nts upstream of the transcription start site

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4
Q

basal transcription factors

A

Required to assemble the transcription complex TFII(N).

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5
Q

regulatory transcription factors

A

regulatory proteins whose function is to activate transcription of DNA by binding to specific DNA sequences

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6
Q

enhancer element

A

elements which enhance transcription by helping transcription factors bind to promoter. Activators bind to enhancers.
upstream or downstream

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7
Q

activator

A

proteins which may alter chromatin structure or interact with the Mediator or other transcription factors.

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8
Q

inducible factor

A

bind to upstream elements that are regulated by an inducer

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9
Q

co-activator

A

only found in eukaryotes, localized in nucleus
may alter chromatin structure or interact with tf

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10
Q

CpG island

A

areas rich in CG repeats. Methylation of cytosine can inhibit gene expression due to enhanced chromatin compaction by methyl binding proteins

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11
Q

methyl binding proteins

A

contain the conserved DNA binding motif methyl-cytosine binding domain
mediating gene silencing via DNA

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12
Q

TATA Box

A

located upstream of start site
has consensus sequence
required for transcription of many genes

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13
Q

TFIID

A

multi protein complex made of TATA binding proteins
bind to DNA and bend

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14
Q

Transcription factor binding elements

A

proteins with DNA binding activity that are involved in the regulation of transcription

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15
Q

TFIIB

A

bind to DNA at TFIID

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16
Q

TFIIH

A

bind to res of preinitiation complex
phosphorylates the COO- terminal of RNA polymerase

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17
Q

RNA Polymerase I

A

Reads Class I genes - rRNA

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18
Q

RNA Polymerase II

A

Reads Class II genes (genes encoding proteins)–produces mRNA)

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19
Q

RNA Polymerase III

A

tRNA, small rRNA, small viral
RNAs

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20
Q

Mediator

A

A multiprotein complex which regulates transcription between activators, coactivators, transcription factors and TFIID.

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21
Q

Silencer

A

interact with repressor proteins which block activator/coactivator from interacting with transcription factors or the initiation complex

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22
Q

insulator

A

act as boundaries between genes to ensure the “correct” gene gets transcribed

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23
Q

wildtype

A

A typical, “normal” form of a given species

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24
Q

mutant

A

Organisms that contain one or more mutations

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25
Q

Intron

A

Noncoding DNA

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26
Q

Exon

A

Coding DNA

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27
Q

PolA tail

A

Polyadenylation
part of mRNA processing

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28
Q

PABP

A

recognizes PolyA tail in assembly of mRNA preinitiation complex

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29
Q

mGuanine cap

A

Guanine methylation
5’ end cap
Recognition of the 5’ mG cap by eIF4E

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30
Q

transcription initiantion/elongation

A

start of transcription in the nucleus
growing nascent mRNA strand

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31
Q

hnRNA

A

heterogeneous nuclear RNA
encompasses various types and sizes of RNAs found in the eukaryotic cell nucleus

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32
Q

mRNA

A

transported to the cytosol for protein synthesis
messenger RNA

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33
Q

Code/sense/codon

A

double-stranded DNA that carries the translatable code in the 5′ to 3′ direction

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34
Q

anti code/antisense/anti-codon

A

template stand

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35
Q

template strand

A

used in its 3’—> 5’ anti-parallel orientation
used to make RNA

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36
Q

HAT/HdAC

A

part of DNA accessibility
Histone acetyltransferase
transfers an acetyl group to a histone protein allowing euchromatin to form

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37
Q

Euchromatin

A

non condensed chromatin

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38
Q

Heterochromatin

A

condensed (transcriptional inactive) chromatin

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39
Q

histone

A

conserved, small basic (Lys & Arg rich) proteins that condense DNA

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40
Q

nucleosome

A

Octamer of 2 of each of the core histones complexed with 146 bp of DNA

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41
Q

zinc finger

A

small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold

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42
Q

helix-loop-helix

A

found in transcription factors which have DNA binding and protein interaction domains.

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43
Q

leucine zip

A

important sequence motif facilitating protein–protein interactions
sequence-specific DNA-binding proteins that regulate transcription

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44
Q

monocistronic

A

one promotor
one gene
eukaryotes

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45
Q

polycistronic

A

one promotor
many proteins
prokaryotes

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46
Q

epigenetic

A

Heritable gene regulation that does not involve
changes in the DNA code

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47
Q

structural gene

A

gene that codes for the amino acid sequence of a protein (such as an enzyme) or for a ribosomal RNA or transfer RNA

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48
Q

ubiquitin

A

histone modification
small regulatory protein that regulates turnover of proteins

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49
Q

acylation

A

post-translational modification of proteins via the attachment of functional groups through acyl linkages

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50
Q

sumoylation

A

covalent attachment of SUMO family f proteins to lysine of a specific target via enzymatic cascade

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51
Q

microRNA

A

controls gene expression mainly by binding with messenger RNA (mRNA) in the cell cytoplasm

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52
Q

half-life

A

time at which the amount of message produced has been reduced to one half the starting value

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53
Q

Hoagland & Zmaecnick

A

proposed that The code was transcribed from DNA onto RNA

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54
Q

Gamow

A

proposed that In order to make 20 different amino acids from 4 different nucleotides would require that a minimum of 3 nucleotides must be present since 42 = 16 and 43 = 64

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55
Q

redundant

A

a different sequence may specify the same amino acid, e.g. serine is coded by 6 different
codons

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56
Q

wobble base

A

the first 2 nucleotides of the codon and anticodon interact tightly, the 3rd is looser

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57
Q

non-standard nucleotide

A

wobbles base references this on tRNA
tRNA 5’ base is paired to the codon 3’ base.
Referred to as the degenerate base.

58
Q

shine/Delgarno

A

sequence signals recognition of start site by ribosome (16 S of the 30 S Subunit)

59
Q

Kozac sequence

A

AUG

60
Q

formyl-methione

A

initiation of protein synthesis from bacterial and organellar genes

61
Q

30S, 50S, 70S

A

70s is final complex for prokaryotes
30s&50S subunit

62
Q

40S
60S
80S

A

eukaryotes
40s and 60s subunits

63
Q

IFS 1

A

binds with IFS 3 and both bind to 30s subunit

64
Q

IFS 2

A

binds with fmet containing anticodon, once binding occurs IF3 released

65
Q

IFS 3

A

fidelity function in the initiation of translation, inducing the dissociation of fMet-tRNAfMet from 30S initiation complexes containing a non-canonical initiation triplet in place of a canonical initiation triplet

66
Q

elF4E

A

Recognition of the 5’ mG cap

67
Q

elF4G

A

cap-binding protein which, in synergy with proteins such as the helicase eIF4A and the scaffolding protein eIF4G, binds to mRNA, allowing the recruitment of ribosomes and translation initiation

68
Q

elf4A

A

unwinds during Assembly of the mRNA Preinitiation Complex

69
Q

amino-acyl “a-site”

A

Anticodon of tRNA binds to mRNA codon
turns into p site

70
Q

peptidyl transferase “p-site”

A

turns into e site

71
Q

exit channel “e-site”

A

Release and exit of the deacylated tRNA from E and reloading new acylated- tRNA at the “A” site

72
Q

ribosome

A

site of peptide bond synthesis; made of rRNA and Protein

73
Q

EF-tu

A

escorts next t-RNA to Aminoacyl Domain

74
Q

EF-G

A

energy release drives the movement of the Ribosome complex to the next codon
changes gtp to gdp

75
Q

release factors

A

proteins used in the place of tRNA.

76
Q

reading frame

A

correct identification and translocation at
each codon

77
Q

frame shift

A

insertion or deletion of nucleotide bases in numbers that are not multiples of three

78
Q

biosynthesis

A

refers to the making of proteins and their modifications through the ER and Golgi.

79
Q

trafficking

A

refers to the targeting and transport of proteins to specific cellular organelles.

80
Q

signal peptidase

A

enzyme which cleaves the signal peptide from the growing nascent peptide chain.

81
Q

disulfide isomerase

A

enzyme that catalyzes the formation and shuffling of disulfide bonds. Needed for unfolding

82
Q

proteasome

A

specialized structures that degrade misfolded proteins

83
Q

glycosyltransferase

A

enzymes that add an oligosaccharide chain to a protein

84
Q

SER

A

synthesises many lipids such as cholesterol, and other molecules such as steroids and hormones for use inside the cell and for export outside of the cell

85
Q

RER

A

The N-terminal of the nascent polypeptide
encodes a signal peptide which directs the
Ribosome to the RER

86
Q

signal sequence

A

on the N-terminal

87
Q

signal recognition particle

A

binds to the recognition sequence.

88
Q

SRP receptor

A

SRP binds to
GTP binds to after SRP bind to SRP receptor, causes release of SRP

89
Q

translocon

A

term for the protein channel where
the ribosome attaches and inserts nascent strand

90
Q

integral protein

A

different functional characteristics based upon
structural insertion in the membrane

91
Q

binding protein

A

help chaperon the new peptide into the ER lumen.

92
Q

heat shock protein

A

refold the protein (ATP) and targeting sequence is cleaved from protein, aka binding protein

93
Q

carrier

A

pass trait to offspring

94
Q

chaperone

A

proteins that guide proteins along the proper pathways for folding

95
Q

stop-transfer anchor sequence

A

signals the channel to stop importing into the ER and to translocate the peptide through the channel proteins into the membrane

96
Q

signal-anchor sequence

A

initiate the translocation of the following polypeptide segments

97
Q

clathrin

A

A fibrous lattice protein made of triskelion that forms on the cytosolic face of the membrane pulls the membrane into pits to form vesicles

98
Q

oligosaccaryl transferase

A

atalyzes the addition of glycans to selected Asn residues within nascent polypeptides in the lumen of the endoplasmic reticulum.

99
Q

N- glycosidic bond

A

asparagine

100
Q

O- glycosidic bond

A

threonine or serine

101
Q

COP-I

A

Recovers Retrograde Transport

102
Q

COP II

A

Delivers Anteriograde Transport

103
Q

Glycosylphosphotidyl inositol

A

posttranslational modification of proteins with a glycolipid and is used ubiquitously in eukaryotes and most likely in some Archaea

104
Q

GPI anchor

A

acting as receptors, transporters, and adhesion molecules

105
Q

transamidase

A

enzymes that add the protein to a lipid

106
Q

anterio transport

A

vesicles released from trans-Golgi Recticulum for export to membrane

107
Q

retrograde transport

A

Vesicles from the RER transported to
the cis-Golgi Recticulum - Network

108
Q

cis RER/Golgi

A

protein travels from here to trans to excrete

109
Q

trans RER/Golgi

A

receiver that collects from the cis Golgi only its most refined fraction for later distribution to specific locations throughout the cell

110
Q

M6P

A

transporting proteins from the Golgi complex and cell surface to the lysosome

111
Q

M6P receptor

A

bind to M6P-containing lysosomal acid hydrolases and transport them from the Golgi to the endosomal–lysosomal system

112
Q

lysosome storage disease

A

malfunction of the lysosome mechanism
Enzyme wont break down material
Problem with export after breakdown

113
Q

t-snares

A

mediate vesicle fusion
associated with nerve terminal membranes

114
Q

complexin

A

acts as both an inhibitor and a facilitator of synaptic vesicle fusion and neurotransmitter release

115
Q

syntaxin

A

essential component of the presynaptic exocytotic fusion machinery in the brain and interacts with several other proteins

116
Q

fusion-pore opening

A

cells fuse lipid bilayers and target proteins from one cellular compartment to the next in membrane trafficking

117
Q

endosome

A

vesicles formed from endocytosis which contain recycled proteins, and foreign materials like bacteria which will be degraded

118
Q

receptor mediated endocytosis

A

means to import macromolecules from the extracellular fluid

119
Q

receptor mediated exocytosis

A

specific for substances recognized by a cell-surface receptor
secretion of large molecules

120
Q

triskelion

A

clathrin forms triskelion shape
involved in coating membranes that are endocytosed from the plasma membrane and those that move between the trans-Golgi network and endosomes

121
Q

nuclear pore complex

A

Proteins which form a basket-like complex which extends into cytoplasm and nucleoplasm

122
Q

importin

A

proteins which direct proteins into the nucleus

123
Q

exportin

A

proteins that direct RNA out as complexes with
protein

124
Q

ran-GTP

A

support formation of complexes containing an export receptor and cargos such as RNAs, RNPs or proteins that are destined for export

125
Q

ran-GDP

A

binds either GTP or GDP and shuttles between the nucleus and cytoplasm

126
Q

RCC1

A

Regulates Nuclear Envelope Formation, Spindle Formation and Nuclear Transport

127
Q

Ran GDP binding protein

A

molecular switch, converting between the active GTP-bound and inactive GDP-bound conformations.

128
Q

NLS

A

Amino acid sequences which direct a protein to import into the nucleus.

129
Q

NES

A

Amino acid sequences which direct a protein out of the nucleus

130
Q

Ran-GAP

A

causes their local release and assembly into nuclear pore complexes, the fusion of vesicles to form a double membrane, and the restarting of nuclear transport.

131
Q

Ran-GEF

A

modulating nuclear import and export of proteins

132
Q

matrix stimulating factor

A

recognizes the sequence and binds (ATP dependent) or Heat Shock Protein (HSP) delivers

133
Q

matrix targeting sequence

A

short peptide, about 15–70 amino acids long, bearing positively charged basic residues, that directs the transport of a protein to the mitochondria.

134
Q

Tom receptor

A

required for the import of proteins into the organelle

135
Q

Tom channel

A

allows movement of proteins through this barrier and into the intermembrane space of the mitochondrion

136
Q

intermembrane space targetting

A

nucleotide phosphorylation

137
Q

sequence

A

primary structure of a biological macromolecule

138
Q

Tic receptor

A

mediates the import of the vast majority of nuclear-encoded plastid proteins from the cytoplasm

139
Q

Hsp60

A

maintains protein homeostasis.

140
Q

Pex5

A

peroxisome associating factor

141
Q

CHAP

A

chaperone, HSP

142
Q

DTM

A

Docking/translocating Machinery

cell biology (5 decks)

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