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BIOSCI 107 > CSF (week 4) > Flashcards

CSF (week 4) Flashcards

1
Q

what is TBP

A

a TATA binding protein, an important initiation factor in thr promoter region, which is usually ~25 NT upstream from area of transcription starting.

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2
Q

when is a a transcription initiation complex formed

A

when all transcription factors are present at the promoter and RNA polymerase II is bound to DNA, allowing transcription to begin

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3
Q

template strand is read from _’ to _’ direction?

A

3’ to 5’

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4
Q

the RNA strand made in transcription is made in _’ to _’ direction? is a copy of what?

A

5’ to 3’. copy of coding strand.

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5
Q

in elongation, DNA is unwound by ______, how many nucleotides at a time?

A

helicase enzyme activity, 10-20 nts

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6
Q

how are adjacent NTs held together?

A

phosphodiester bonds

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7
Q

what in the terminagtor signals the end of transcription

A

polyadenylation signal (lots of A nucleotides)

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8
Q

how are RNA and DNA nucleotides held in place during transcription?

A

weak hydrogen bonds

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9
Q

what is the order of mRNA processing?

A

capping, tailing, splicing

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10
Q

what does capping consist of

A

a modified guanine nucleotide cap is added to the 5’ end

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11
Q

what is a spliceosome made of

A

proteins and small RNAs (called sRNA)

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12
Q

what is a UTR

A

untranslated region. RNA sequences at the 3’ and 5’ end of mRNA that are in the exon, therefore transcribed, but not translated into protein.

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13
Q

what does splicing consist of and where

A

at the spliceosome in the nucleus, introns are removed from the RNA and exons are joined together to form mature mRNA

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14
Q

what is important about alternative splicing

A

it allows for complexity, as one section of mRNA could be spliced many different ways, therefore one DNA/pre mRNA sequence could code for many different protein products.

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15
Q

what does tailing consist of

A

a poly-A (series of adenine nucleotides) tail is added to the 3’ end of the RNA

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16
Q

two types of bonds involved in translation

A

hydrogen bonding of the tRNA anti-codons to mRNA codons, peptide bonding between adjacent peptides as they are brought to the PP chain by tRNA

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17
Q

name and describe the purpose for each ‘site’ in a ribosome

A

A - site for next tRNA to be read to dock
P - site for currently read tRNA
E - exit site for read tRNA

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18
Q

describe the initiation step of translation

A

small unit of ribosome binds with initiator tRNA with Met amino acid.
this binds to the 5’ capped end of mRNA. small unit scans downstream for AUG start codon. large ribosomal unit binds on top, completing translation initiation complex.

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19
Q

what is the purpose and structure of a poly-A tail

A

it is made up of 50-250 adenine nucleotides. thought to be important for stabilising the fragile RNA, exporting it out of the nucleus for translation, and ribosome binding.

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20
Q

what binds to the ribosome first - tRNA or mRNA?

A

the tRNA anti-codon, always carrying Met amino acid

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21
Q

describe the elongation phase of translation

A

codon recognition, in which complimentary tRNA anti-codons bind mRNA codons bringing AAs with them.
peptide bonding, in which the large ribosomal subunit triggers peptide bonds to form between AAs.
translocation, in which tRNA shuffles/moves down sites, releasing the read tRNA from the E site.

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22
Q

what energy is required for translation

A

GTP energy

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23
Q

what stage of translation doesn’t require GTP

A

peptide bonding within the elongation phase

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24
Q

describe the termination phase of translation

A

ribosome reaches a stop codon.
a release factor binds to the A site, causing the bond between peptide and tRNA in P-site to be hydrolysed.
finished PP chain is released.
remaining components at ribosome dissociate.

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25
what happens to used ribosomal units?
they are reused
26
why is gene expression controlled?
to achieve the right things in the right place at the right time - temporal and spatial control.
27
what are characteristics and examples of house-keeping genes
housekeeping genes are transcribed at a fairly frequent and consistent rate, as they're needed constantly. they tend to have longer half-lives. e.g tubulin and TBP
28
what aspect of an amino acid differentiates it and determines its function?
the R' side chain
29
what type of bond are polypeptide bonds?
strong covalent bonds
30
what are the C and N terminus
N = upstream amino end = 5' end C = downstream carboxyl end = 3' end
31
where would a protein be translated if it is destined to be in a vesicle?
ate a fixed ribosome in the RER, as vesicle = endomembrane system
32
describe how a protein would be directed to the RER if it needs to be translated there?
a signal peptide on the N terminus will be bound by an SRP floating in the cytosol. this directs the mRNA to the RER, and docks to an SRP receptor protein in the RER membrane translation of PP chain is completed into the RER
33
where do all proteins begin translation?
free ribosomes in the cytosol
34
what are post-translational modifications, where do they take place?
modifications to a folded protein that are necessary to allow it to function/activate it. occur usually in golgi or cytosol, at area appropriate to where they will function, e.g phosphorylation in the cytosol.
35
what might a post-translational modification do
- activate a protein - affect its interactaction w other molecules - determine protein location
36
what are isoforms
different proteins that come from the same gene due to alternative splicing
37
control points for gene expression
1. transcription factors/transcription actually occurring 2. mRNA processing 3. exit via nuclear pores is regulated 4. translation and lifespan of mRNA is regulated
38
where do 5' and 3' names come from
5' refers to the 5th carbon on ribose sugar which binds to phosphate group. 3' refers to the 3rd carbon which binds to hydroxyl group of new nucleotide.
39
what happens in G1 phase
cellular activities, organelles are duplicated for division
40
what happens in S phase
DNA is replicated
41
what does a signal-cleaving enzyme do
cut off the signal peptide on a polypeptide chain after it has been directed to the RER
42
what happens in G2 phase
preparation for division, e.g gathering of reactants, production of related proteins, replication of centrosomes.
43
what phases does interphase consist of
G1, S, G2 (all except M)
44
what is a germline cell, what doesn't occur at them?
gametic cells and the stem cells they develop form. no mitosis.
45
what is a tetrad
2 homologous duplicated chromosomes (of sister chromatids)
46
what happens in prophase (meiosis and mitosis!)
chromosomes condense, spindle fibres form, nuclear envelope disintegrates (in late prophase). synapsis and crossing over in meoisis I.
47
what is checked at G1 checkpoint? what is following action?
is cell undamaged does it have correct size and nutrition are appropriate signals present. no -> go to G0. yes -> continue.
48
what is checked at M checkpoint?
if all chromosomes are attached to spindle fibres
49
what happens in metaphase (meiosis and mitosis!)
chromosomes line up at central plate, spindle fibres attach to centromeres. independent assortment in meiosis I
50
how many chromosomes line up in metaphase of each of meiosis I, meiosis II, mitosis?
meiosis I: 23 tetrads line up (homologous duplicated chromosomes next to each other) meiosis II: 23 chromosomes line up (duplicated, i.e consist of 2 chromatids) mitosis: 46 chromosomes lie up (duplicated)
51
what is G0?
a resting active state of no further division. can be a temporary or permanent state, neurons for example stay here forever.
52
what happens in telephase
nuclear envelopes reform around each new set of DNA
53
what happens in anaphase (meiosis and mitosis!)
spindle fibres pull apart: sister chromatids (in mitosis and meiosis II) homologous pairs of chromatids (in meiosis I)
54
what do different spindle fibres do in anaphase?
some shorten pulling the chromatids, ad some lengthen to push apart/separate the two cells for division
55
what are spindles fibres made of?
microtubules
56
what is crossing over/recombination
homologous chromosomes exchange some genetic material at points called chiasmata after synapsis in meiosis I
57
what are kinetochores
protein complexes at centrosomes for connection of kinetochore (shortening/separating) microtubules
58
what is the cleavage furrow
contractile indentation allowing cells to separate in telophase/cytokinesis
59
what are the three sources of variation in gametes/humans?
1. crossing over 2. independent assortment 3. fusing of gametes
60
a mutation on which end of the DNA strand is more likely to have effect?
3' end of DNA, therefore 5' end of mRNA
61
what is a reason that mutations may not have an effect?
because we have two copies of DNA for each gene, 1 from each parent. if only one is mutated, the non-mutated gene products produced may be sufficient for function.
62
what area of the body would a mutation in a somatic cell affect?
the individual cell at first, and eventuallya broader local effect as all cells dividing from mutated cell will have the mutated DNA.
63
what type of mutation can cause a frameshift, why is this significant?
insertions/deletions. every codon/AA downstream of the mutation is affected.
64
when would a 'truncated protein' arise, what types of mutations could cause it?
if translation was stopped (early stop codon coded for) early due to a mutation. - nonsense substitution - frameshift - mutation affecting ribosome, spliceosome, etc.
65
what is sickle cell anemia, what are its consequences?
recessive inherited disorder that causes abnormally shaped red blood cells which are inflexible and weak. leads to blockages in capillaries and reduced blood/oxygen supply.
66
when would an indel not cause a frameshift?
if 3 (or multiple of 3) bases were inserted/ deleted.
67
why is G2 checkpoint so important?
because it can stop a damaged cell from dividing
68
explain an MPF and its components
maturation promoting factor. initiates mitosis in G2 checkpoint. consists of a cyclin and CDK. cyclins are proteins fluctuating in concentration as needed throughout the cell cycle. CDKs are cyclin dependent kinases, which are activated when bound to a cyclin and relaint on their concentration being high enough.
69
how does an MPF initiate mitosis
phosphorylates other proteins initiating mitosis
70
which components of an MPF are reused or not reused
cyclin ISN'T reused, is degraded and remade each cycle. CDKs are reused, can be activated and deactivated as needed.
71
'stop' molecules normally:
keep cell proliferation in check.
72
'go' molecules normally:
stimulate cell proliferation.
73
what could happen if a mutation arose in a stop/go molecule?
G2 checkpoint won't work -> cell cycle proceeds where it shouldn't -> uncontrolled cell growth -> tumor
74
two manners of mutation acquisition, and respective outreach:
genetic - inherited from parents, or de novo, meaning mutation in egg/zygote. affects all cells, as all cells arise from fused gametes. acquired - somatic cell during life is mutated due to exposure to mutagens. affect local cells, as only ones arising from the mutated cell will have the mutated DNA.
75
what is a proto-oncogene
a go gene which stimulates cell division. if mutated, could cause cancer/become an oncogene.
76
what is Ras, how does it function, how could it cause cancer
it is a GTPase enzyme involved in cell signalling to trigger cell division. if mutated, could over-activate signalling pathway, overactivate transcription factor causing overexpression of proteins which cause uncontrolled cell division.
77
what is a tumor suppressor gene
a type of stop molecule which normally keep cell proliferation in check, but if mutated could fail to stop uncontrolled cell growth, therefore cause cancer
78
what is gene p53, what does it do, how could it cause cancer
a tumor suppressor gene that controls growth of damaged cells by repairing damaged DNA, or halting cycle and signalling apoptosis if DNA is damaged beyond repair. if mutated p53 gene, p53 protein is also mutated, therefore there is no control over damaged cells replicating.
79
does cancer result from one mutation; why or why not.
no. typically requires a compounding series of mutations to create a malignant cell.
80
what is the name of the molecule that reloads amino acids to tRNA in the cytoplasm?
aminoacyl-tRNA synthetase
81
what is apoptosis
programmed cell death
82
how does huntingdons disease arise
several trinucleotide insertions coding for additional glutanamine amino acids, which affect protein folding. the more triplets inserted, the earlier huntingdons onsets.

BIOSCI 107 (10 decks)

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