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bio 2 > midterm - quiz 2 - lectures 7,8,9 > Flashcards

midterm - quiz 2 - lectures 7,8,9 Flashcards

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1
Q

T OR F: each gene has information for one protein

A

TRUE - one gene one protein hypothesis

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2
Q

what is gene expression

A

cellular process in which the info held in the DNA sequence of a gene is used for making final product (polypeptide chain)

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3
Q

rRNA tRNA and other RNA genes encode…

A

info for making RNA molecules that are not translated into proteins

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4
Q

what is a gene (parts)

A

protein encoding gene
promoter
transcription unit 5’ -> 3’ , UTR, coding region
terminator

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5
Q

what is a promoter

A

transcription start site

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6
Q

what is a transcription unit

A

sequence for mRNA

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7
Q

what is UTR

A

untranslated region
protection - regulation

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8
Q

what is termination sequence

A

transcription stop site

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9
Q

Gene expression occurs in 2 steps, name and brief description

A

1 - transcription: synthesis of mRNA using template DNA strand
2 - translation: synthesis of proteins using mRNA as template

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10
Q

in prokaryotes transcription…

A

and translation are couples and occur together in cytoplasm

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11
Q

in eukaryotes transcription…

A

occurs first in nucleus and translation occurs second in cytoplasm after mRNA export (through nuclear pores)

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12
Q

in prokaryotes describe chromatin, genes, promoters, transcription and translation, mRNA

A

chromatin - none
genes - operons, promoter - multiple genes
promoters - no TATA box
t&t - simultaneous
mRNA - polycistronic, multiple coding regions per mRNA, no splicing (no introns), no processing

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13
Q

in eukaryotes describe chromatin, genes, promoters, transcription and translation, mRNA

A

chromatin - euchromatin vs heterochromatin
genes - one promoter per gene
promoters - TATA box present, TBP TATA binding protein
t&t - separate (nucleus/cytoplasm)
mRNA - monocistronic, 1 mRNA = 1 coding region, splicing removal of introns, processing

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14
Q

name components of transcription

A

RNA polymerase and general transcription factors
DNA template strand
ribonucleotides (NTPs)
mRNA (product of transcription)

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15
Q

name 3 main steps of transcription

A

initiation
elongation
termination

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16
Q

where does promoter lie in transcription

A

upstream of start site and coding region of gene

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17
Q

describe transcription initiation

A

RNA polymerase binding to promoter
in eukaryotes - TATA box TBP is key to recognition of promoter and recruitment and binding of RNA polymerase II (transcribes protein coding genes)

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18
Q

describe transcription elongation

A

mRNA synthesis 5’->3’
mRNA sequence is complementary and antiparallel to that of template strand

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19
Q

describe transcription termination

A

release of mRNA and RNA polymerase
in eukaryotes - a polyadenylation signal and site are involved

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20
Q

similarities between transcription and DNA replication

A

energy requited NTP/dNTP
formation of bubble (unidirectional vs bidirectional movement)
synthesis is always 5’->3’

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21
Q

differences of RNA polymerase (transcription) vs DNA polymerase (DNA rep) (6)

A

Initiation at promoter
no primer needed - RNA polymerase has helicase activity
bubble does not grow
one template used -> hybrid parent strands reanneal and RNA is realease
no proof reading
stops at terminator

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22
Q

name components of translation

A

mRNA: holds codons
ribosomal subunits (small and large)
rRNA
charged tRNA
pool of amino acids

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23
Q

describe rRNA

A

scaffold of ribsosomal subunits and peptidyl transferase catalytic activity (ribozyme)

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24
Q

describe charged tRNA (gen / 4)

A

clover, L shaped
anticodon - second loop
amino acid attachment site 3’ end
brings amino acid into position of growing polypeptide chain

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25
Q

name 3 steps of translation

A

initiation
elongation
termination

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26
Q

describe translation initiation (5 steps)

A

1 - binding of small subunit and translation initiation factors to 5’ UTR, in eukaryotes requires 5’ CAP
2 - scanning for start AUG codon
3 - pairing of anticodon of initiatior tRNA with start codon
4 - GTP hydrolysis
5 - binding of large subunit

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27
Q

describe translation elongation

A

synthesis of protein amino to carboxy terminus

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28
Q

describe translation termination

A

occurs when ribosome reaches stop codon
release factor recognizes codons and causes dissociation of the polypeptide chain from last tRNA molecule
small and large subunits dissociate from mRNA

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29
Q

name 4 steps of translation elongation

A

1 - charge tRNA binds to A site
2 - peptide bond formation, rRNA catalyst
3 - translocation, ribosome moves along mRNA
4 - exit of uncharged tRNA

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30
Q

what is A site

A

pockets in large ribosomal subunits
amino acyl
binding of incoming charged tRNA

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31
Q

what is P site

A

peptidyl
binding site for tRNA holding nascent - growing polypeptide chain

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32
Q

what is E site

A

exit for uncharged tRNA

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33
Q

why is energy needed during elongation

A

peptide bond formation (by rRNA)
translocation of ribosome relative to mRNA

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34
Q

describe difference between charged tRNA and uncharged tRNA

A

charged tRNA = bound with aa, amino acyl + tRNA but doesnt have neg or pos charge
uncharged tRNA = tRNA with no aa

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35
Q

describe mRNA codons

A

universal - all organisms use same genetic code
redundant - amino acid can be specified by more than one codon
not all mutations are expressed and produce defective protein
but not ambiguous - one codon never specifies more than one aa

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36
Q

what does accuracy of translation depend on

A

specific pairing between anticodon (tRNA) and codon (mRNA)
specific attachement of an aa to a corresponding tRNA by amino acyl tRNA synthase

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37
Q

T OR F transcription and translation dont require energy

A

F - ARE energy requiring

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38
Q

describe mRNA processing and splicing (gen)

A

post-transcriptional modifications
nucleus
pre-mRNA
Sn-RNA - spliceosome (ribonucleoprotein complex)
ONLY IN EUKARYOTES

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39
Q

describe processing

A

addition of 5’ CAP (modified guanine) and 3’ poly A tail
serve to protect mRNA from degradation and required for export and efficient translation initiation

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40
Q

describe splicing

A

removal of introns and rejoining of exons, spliceosome

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41
Q

describe spliceosome

A

protein + SnRNA
ribonucleoprotein complex made of protein SNRNPS (proteins + SnRNA (catalyzes splicing = ribozyme))

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42
Q

describe introns

A

presence of introns provides an additional regulatory step in overall control of gene expression
introns allow for alternative splicing (more proteins per gene)

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43
Q

describe mutations

A

changes in nucleotide sequence of DNA and/or mRNA of a gene

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44
Q

name types of mutations

A

substitution
silent
missense
nonsense
insertion/deletion in exons (frameshift)

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45
Q

describe substitution mutations

A

can be silent, missense or nonsense

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46
Q

describe silent

A

change of last redundant nucleotide of a codon - doesn’t change aa sequence

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47
Q

describe missense

A

change in sequence of a single or multiple codon - changes aa of protein
extensive = causes frameshift and causes loss of function or altered function

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48
Q

describe nonsense

A

change in sequence of codon to stop codon = premature termination of translation - truncated non functional protein

49
Q

describe insertion/deletion in exons (frameshift)

A

extensive missense with frameshift = within an exon - elongated and non functional protein
immediate nonsense with frameshift = stop codon - truncated and non functional protein

50
Q

what happens if there is a mutation in intron or silent mutation

A

no effect on amino acid sequence of corresponding protein

51
Q

what are exons and introns

A

eukaryotic coding sequences - exons
introns - non coding regions of DNA

52
Q

describe signal peptide

A

20 amino acids at N terminus of nascent polypeptide chain is recognized by SRP and brought to translocation complex, where translation resumes and polypeptide is gradually translocated into ER lumen
signal peptide is cleaved once protein has been completely synthesized and translocated into ER lumen

53
Q

are secreted proteins the predicted size

A

NO - 20 amino acids shorter than predicted by gene sequence

54
Q

what is endomembrane system

A

RER
golgi
vesicle
plasma membrane

55
Q

what are constitutive genes

A

always expressed
encode house keeping genes (ribosomal, general t&t genes, basal metabolic genes, sustain basal activity of cell)

56
Q

what are structural proteins needed for

A

maintaining cell shape
actin and microtubules

57
Q

why are RNA molecules essential

A

for translation
rRNA tRNA

58
Q

what are regulated genes

A

induced (turned on) or repressed (turned off)
when change in internal or external cellular environment happens

59
Q

describe response to environment

A

Homeostasis
growth and development of body plan and organs
cell specific genes: expressed only in specific cells and tissues

60
Q

where does regulation of gene expression occur

A

at level of transcription initiation

61
Q

what is positive control

A

gene expression is induced
increase rate of transcription initiation (binding of RNA polymerase to promoter)
greater levels mRNA = greater levels of corresponding protein

62
Q

what is negative control

A

gene expression is repressed
blocking transcription (repressor bound to DNA control element)
lower levels mRNA = lower levels of corresponding protein

63
Q

describe repressible genes in prokaryotic regulation of gene expresion

A

on -> turned off (repressible operons)
code for enzymes of anabolic pathways synthesizing essential products (aa, nt)
exL trp: tryptophan aa synthesis

64
Q

describe inducible genes in prokaryotic regulation of gene expression

A

off -> turned on (inducible operons)
codes for enzymes of catabolic pathways breaking down non essential carbon sources for energy
ex: lac: lactose breakdown

65
Q

describe regulation at the level of transcription initiation in prokaryotic regulation of gene expression

A

negative control - active repressor that binds to operator and stops transcription
lac or trp operon
positive control - catabolite activator protein CAP binds to promoter and increases transcription
lac or any operon involved in utilization of non essential carbon sources

66
Q

describe operons

A

only in bacteria
group of genes of the same function under control of same and single promoter

67
Q

describe polycistronic mRNA

A

single mRNA with multiple coding regions for multiple proteins

68
Q

describe repressible operons

A

any synthesis operon
repressible genes - on get turned off
ex: trp operon encodes enzymes involved in synthesis of amino acid tryptophan

69
Q

describe inducible operons

A

any catabolism of alternative sugars operon
inducible genes - off but get turned on
ex: lac operon encodes enzyme involved in uptake and breakdown of lactose to glucose and galactose

70
Q

state essential carbon sources

A

glucose

71
Q

state alternative sugars

A

lactose
sucrose
arabinose
maltose

72
Q

describe tryptophan synthesis

A

anabolic pathway
default on
repressed by high levels tryptophan
rapid regulation of enzyme activity - feedback inhibition
slow but longer lasting regulation of enzyme production (level of transcription initiation, repressor protein, co repressor tryptophan)

73
Q

describe trp operon default state

A

default on
low levels tryptophan
repressor inactive

74
Q

describe trp operon repressed

A

operon off
Tryptophan levels high
Tryptophan co repressor binds to allosteric site of repressor
repressor is active and binds to operator blocking RNA polymerase from binding to promoter
Transcription is blocked
no protein products

75
Q

describe default state lac operon

A

default off
lactose absent
repressor active
binds to operator and blocks RNA polymerase from binding to promoter
no transcription

76
Q

describe induced state lac operon

A

low/moderate levels
lactose present
glucose high
allolactose binds to allosteric site of repressor
repressor inactive
transcription occurs but CAP inactive
low levels of transcription

77
Q

describe overexpression lac operon

A

lactose is present
glucose absent
repressor is inactive
CAP active
MAX transcription

78
Q

describe CAP

A

catabolite activator protein
universal activator protein in bacteria, induces expression of many operons involved in breakdown of carbon sources

79
Q

what happens when CAP is active

A

cAMP levels are high when glucose is scarce or absent
cAMP binds to CAP to activate it

80
Q

what happens when CAP inactive

A

cAMP levels are low when glucose is present

81
Q

describe lac genes (3)

A

lac I = not part of lac operon, codes for an active repressor
lac Z = codes for B galactosidase, enzymes cleave lactose disaccharide
lac Y = codes for permease, transporter for lactose

82
Q

control of chromatin is…

A

pretranscriptional control

83
Q

describe euchromatin

A

loose DNA with nucleosomes
genes can be expressed or induced
DNA demethylation - removal of CH3 from nitrogenous base of C
histone tail acetylation = acetyl groups -COOH3 are added to lysine of histone protein tails
histone proteins = wrapped with DNA in nucleosomes

84
Q

describe acetylation of histone tails (associations)

A

euchromatin loose DNA
promoters accessible (rna pol binds to
promoter)
transcription occurs
gene induction

85
Q

describe heterochromatin

A

compact DNA - looped domains - metaphase chromosome
genes are auto repressed
DNA methylation - addition of methyl
may be linked with increased histone deacetylation

86
Q

describe deacetylation of histone tails (associations)

A

heterochromatin (compact DNA)
promotes hidden (rna pol doesn’t bind)
no transcription
gene repression

87
Q

describe control of transcription initiation - binding of RNA polymerase to promoter

A

promoters are more complex
subtle fine tune adjustments in gene expression

88
Q

what does basal minimal promoter consist of (control of transcription initiation)

A

TATA box (25nt from transcription initiation site)
DNA sequence for binding RNA polymerase and general transcription factors

89
Q

what are control elements (control of transcription initiation)

A

regulatory elements (RE) or switched
upstream of minimal promoter
enhancers and silencers
NON CODING

90
Q

activators are…

A

specific transcription factors - proteins that bind to - enhancer control elements

91
Q

repressors are…

A

specific transcription factors - proteins that bind to - silencer control elements

92
Q

regulatory elements and their…

A

respective DNA binding proteins control assembly of an active RNA polymerase and associated general transcription factors to the promoter

93
Q

describe modes of action of activators and repressors

A

activators = proteins that bind to enhancers
promote binding of RNA pol and DNA control elements to promoter VIA recruitment of mediator proteins
activate general transcription factors and RNA pol
repressors = proteins that bind to silencers
block action of activators by binding on or near enhancers

94
Q

describe coexpression of genes with similar functions in eukaryotes

A

genes have identical control elements upstream of their promoters respond to same activators and repressors
subject to similar regulation
ex = steroid responsive genes and heat shock genes

95
Q

describe cell type specific expression in eukaryotes

A

all cells in organism have same set of genes
specific combos of transcription factors are present (active) in different cell types, only subsets of genes are on or off
ex = liver cell expressed albumin gene and lens cell expressed crystalline gene

96
Q

describe cell communication

A

asses environments and maintain homeostasis
important during growth and development to activate right sequence of genes

97
Q

describe local and long distance signaling

A

direct contact (gap junctions/planodesmata, cell-cell recognition)
local signalling =
paracrine signalling
synaptic signalling
long distance signalling (endocrine and hormonal)

98
Q

name 3 steps of communication

A

reception
signal transduction
cellular response

99
Q

describe reception gen

A

binding of signalling molecule usually hormone to receptor protein of the target cell
signalling molecule acts as ligand bc it interacts with specific site of receptor

100
Q

describe signal transduction gen

A

transmission of signal by activation of cascade of events involving relay molecules and proteins
initial signal transformer to another

101
Q

describe cellular response gen

A

target cell responds by changing cytoskeleton or by activating metabolic enzyme -cytoplasmic or by activating expression of specific genes in response to signal - n

102
Q

name 2 types of receptors

A

embedded in plasma membrane
intracellular

103
Q

describe receptors embedded in pm

A

contain site for binding of signalling molecule on surface of cell
ex: G protein coupled receptor, tyrosine kinase receptors)

104
Q

describe intracellular receptors

A

require signalling molecule enters cytoplasm by crossing membrane first
once bound with signaling molecule receptors translocate to nucleus where they act as transcription factors in activation of specific genes
ex= steroid receptors

105
Q

how many steps does signal transduction have

A

6

106
Q

describe a in signal transduction

A

activation of a series of steps involving relay molecules and proteins
called a cascade or domino effect

107
Q

describe b in signal transduction

A

transformation of initial signal into a different form
involves activator by phosphorylation of relay molecules

108
Q

describe c in signal transduction

A

rapid transmission bc relay molecules are already in place just need to be activated

109
Q

describe d in signal transduction

A

amplification bc one signaling molecule can lead to activation of millions of target proteins

110
Q

describe e in signal transduction

A

fine tuning bc several steps are involved that can be regulated
signal transduction pathway can be used in different cell types to provide specific outcome

111
Q

describe f in signal transduction

A

termination bc steps can be inhibited
involves de phosphorylation of relay molecules by protein phosphatases

112
Q

name 3 ex of signal transduction pathways

A

phosphorylation/ de phosphorylation cascades involving protein kinases and protein phophatases
second messengers = non proteins, small molecules or ions (cAMP ca2+ or IP3)
combo of both are observed

113
Q

describe epinephrine stimulation

A

leads to breakdown of glycogen to glucose by glycogen phosphorylase
1 - reception = binding of epinephrine to a G protein coupled receptor
2 - signal transduction = activation of adenylyl cyclase (formation of cAMP, activation of PKA and phosphorylation cascade)
3 - cellular response = phosphorylation of glycogen phosphrylase (hydrolysis of glycogen to glucose)
4 - termination (de phosphorylation with PP, phosphodiestherase, GDP - G protein inactive, detached hormone epinephrine)

114
Q

describe cellular response

A

varied depending on signaling molecule and type of target cell receiving signal
- nuclear response = activation of specific genes
- cytoplasmic response - activation of specific enzymes or proteins or change in cellular shape

115
Q

describe steroid communication (cellular response)

A

activated cellular receptors act as transcription factors that bind to specific enhancers (slower but longer lasting response)
- reception = intracellular receptor for steroid hormone
- transduction = translocation of hormone receptor complex from cytoplasm to nucleus
- cellular response = nuclear, activation of transcription settled responsive genes (binds to RE enhancer)

116
Q

describe insulin

A

leads to import of glucose in target cells such as liver and muscle
activated bc insulin causes the glucose transporters to be expressed at pm
promotes storage of glucose as glycogen by leading to activation of glycogen synthase

117
Q

describe growth factor stimulation of cell cycle

A

tyrosine receptor
Ras-G protein proto-oncogene - protein kinase cascade
nuclear response = activation of cell cycle
hyperactive Ras - oncoprotein

118
Q

describe UV induced DNA damage and inhibition of cell cycle

A

no receptor per se (DNA damage)
protein kinase cascade
activation of p53 transcription factor - tumour suppressor protein
nuclear response - expression of cell cycle inhibitor p21
inactive p53 - inactive tumour suppressor protein

bio 2 (6 decks)

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