Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

molecular biology > ethan hack material > Flashcards

ethan hack material Flashcards

1
Q

when end is RNA constructed from

A

5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

which end of an amino acid is positively charged and which is negatively charged

A

amine group (NH2) is positvely charged, carboxyl group (COOH) is negatively charged

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

name the 3 stop codons

A

UAG UAA UGA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what part of tRNA binds to the AA and the codon

A

anticodon binds to mRNA’s codon, 3’ end binds to AA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what type of 2D and 3D structure does tRNA have

A

cloverleaf (2D) and L shaped (3D)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is the name of the enzyme that bonds AA’s to tRNA

A

aminoacyl-tRNA synthase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

name a modified base that may be on the third position of a tRNA’s anticodon allowing it to bind to more than one codon

A

inosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what is the location of translation

A

ribosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what are ribosomes made up of

A

protein and RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

name the 3 binding sites on a ribosome and which sub unit are they one

A

Polypeptide and Anticodon, exit

small subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

describe the initiation part of translation

A

1) first aminoacyl-tRNA binds to the P site of the small sub unit
2) codon-anticodon binding occours
3) large subunit binds
4) second aminoacyl-tRNA binds to the A site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

discuss polycistronic DNA

A

multiple genes transcribed in a single mRNA molecule, like is done in prokaryotes from an operon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

discuss prokaryotic RNA polymerase’s 2 forms

A

core enzyme; 5 subunits
holo enzyme; 6 subunits; also has a sigma factor
only the holo enzyme form can recognise the promotor region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

how does prokaryotic RNA polymerase know where transcription stops

A

a ‘transcription termination sequence’ exists; mRNA folds into a stemp-loop structure which destabilises the mRNA-DNA interaction causing RNA to dissociate from the gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

how do prokaryotic and eukaryotic ribosomes know which codon is the first amino acid to match to an AA

A

prokaryotes; the shine-delgarno sequence of mRNA (close to start codon) binds to ribosomal RNA and acts as the ribosome binding site

eukaryotic; the ribosome binds to the begininning of mRNA and moves to the first AUG of mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what is the shine- dalgarno sequence

A

AGGAGG. a sequence on prokaryotic mRNA which binds to the ribosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

discuss lactose structure

A

disaccaride consisting of 1 glucose and 1 galactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

discuss what the genes lacI, lacZ, lacY, lacA and lacI are expressed as and the function of the expressed products

A

lacA; beta-galactosidase transetylase; unknown function

lacI; repressor protein, binds to the operator region and stops transcription when lactose is absent

lacZ; beta-galactosidase; hydrolyses lactose

lacY; lactose permease; transports lactose into the e coli cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

discuss the 4 domains (polypeptides) of a a repressor protein

A

n terminal; binds to the DNA (operator region)
hinge region; holds N terminal in correct orientation
allolactose binding region
C terminal; used for two repressors to interact to form a dimer, which is needed for the repressor to bind to the DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

discuss how allolactose interacts with repressor protein domain

A

allolactose binds to the allolactose binding region, and causes a conformational shape change which moves the hinge region; N terminal doesnt bind to DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

why does binding of the repressor binding stop RNA polymerase action

A

operator and promotor sites overlap; binding of repressor protein means RNA polymerase cant bind

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

how many operator regions exist per operon. discuss these operators

A

3; one original operator and 2 auxillary operators. the auxillary operators are downstream of lacZ
binidng of repressor to 2 operators decreases transcription much more than binding of one repressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what does i- mean

A

mutated lacI gene; mutated repressor protein which cant bind to the operon; transcription os constitutive (constant)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

is the lacI gene part of the lac operon

A

no

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
discuss Oc (lap operon)
operator region is mutated; repressor cant bind; constitutive
26
discuss evidence for the lac operon mechanism name the 3 scientists who worked on this
Jacob, Lwoff and Monod looked at mutants with altered gene expression the way that mutated beta-galactosidase (lacY) is screened for is by giving colonies the arteficial substrate X-gal, which is converted to blue product. those colonies which arent blue have a mutated gene and should be studied
27
when do lac operon mutation diagrams become complicated
when the cells are engineered to be diploid, cis and trans acting mutations now exist. trans mutation effect expression of genes in other DNA molecules to the one where mutation occoured
28
why is the lac promotor a weak promotor; what is the name of a mutated promotor which isint weak, and why isint it weak
the -10 and -35 sequences are non standard PlacUV5; -10 and -35 sequences are close to the consensus sequence
29
discuss of the importance of glucose concentrations being low in terms of lac operon regulation
when glucose concentration is low, cAMP concentrations are high; cAMP activates a CAP protein which binds to DNA's -35 region, bends DNA 90 degrees. RNA polymerase binds to CAP with one of its sub units; increased binding to promoter occours if CAP is present
30
catabolic operons are switched (ON/OFF) when metabolite is present Biosynthetic operons are switched (ON/OFF) when supply of product is low
ON | ON
31
discuss what the trp operon has genes for. | discuss how the operon's expression is switched off
tryptophan AA repressor only works when high concentrations of tryptophan exists, which binds to the repressor and allows it to bind to the DNA
32
# define quorum sensing discuss the bobtail squid being bioluminescent discuss pathogenic bacteria
regulating gene expression in response to cell population density symbiotic bacteria in the squids light organ are responsible for the light these cells synthesise AHL (luxI gene), which diffuses out of the cell if the cell density of bacteria is high enough then the concentration of AHL incrases, bacteria take it up, it binds to the LuxR gene, which activates transcription of the lux operon; light emmision when invading a host, bacteria only produce degradative enzymes if the density of cells is high enough
33
discuss structure of a chromosome
DNA associated with histone proteins telomeres (repetitive DNA) exist at the end of DNA, proteins attach to the telomeres a nucleosome is a unit of DNA wrapped around a histone protein
34
why are DNA and histones bound so tightly
DNA is negatively charged, histones are positively charged
35
how many polypeptides does a histone protein consists of
8 (H2A, H2B, h3, H4 are all present twice)
36
discuss how many bp's and genes are possessed by; yeast, plants, invertbebrates and vertebrates
bp; 12 mbp, 125mbp, 100 mbp, 3300 mbp genes; 6000, 25000, 10000, 24000
37
define an intron and estimate how much of the human genome is makes up
a sequence of DNA that is transcribed but then removed from mRNA by splicing 20%
38
discuss how much of the human genome is made up of repetitive DNA discuss simple sequence repeats and transposons discuss the two types of transposons
50% simple sequence repeats; two nucleotides repeated 5% guman genome helps organise chromosome structure transposons; DNA that is duplicated and then moves to a new site form via an RNA intermediate (require reverse transcriptase) slow to move; often cause mutations leading to DNA repair or apoptosis LINE's; long interspaced elements (6000bp) code for enzymes needed for transposition (reverse transcriptase) 20% human genome SINE's; short interspaced elements (200bp) 15% human genome; must be more frequent than LINE's Alu elements are a type of SINE, which rely on LINE elements for transposition
39
discuss % composition of human genome
``` introns 20% simple repeats 5% LINE's 20% SINE's 20% exons; 2% ```
40
discuss the 3 ways RNA is processed | discuss how intron removal occours
1) 7-methyl cap at 5' end 2)cleavage of 3' end and addition of Poly(A) tail 3) removal of introns via splicing splicosome (made up of snRNP's) perform this a) splicosome binds to the 5' end of intron and cuts it b) lariat (loop) formed as the 5' end is bonded to the 2' of the other end of the intron c)spliceosome binded to and cuts the 3' end d) exons are joined
41
define alternative splicing, discuss what % of human genome has this performed on them, and discuss an example of gene
a single gene can code for more than one protein if different exons are used; proteins usually have related but not identical function 60% tropomyosin has 8 different mRNA's
42
discuss pseudogenes. how many does the human genome have
genes that evolve by duplication but then mutate and lose their function 20,000
43
difference the principle of synteny
the idea that the order of genes within a chromosome is conserved over evolutionary time
44
comapre yeast and human genomes
yeast a more compact genome (more genes relative to genome size) yeast have less repetitive DNA yeast average gene size is much smaller much of yeast genome is open reading frame (start to stop codon); little space between genes yeast genes usually have no introns, and if they do have an intron they only have one
45
define euchromatin and heterochromatin and which type is accessable for transcription and which type of formation DNA is in for mitosis/meiosis
euchromatin (nucleosomes spread out and not tightly packed) heterochromatin (nucleosomes are condensed and closely packed together) euchromatin is required for transcription; the only packaging present is into nucleosomes during cell division, DNA is in the heterochromatin form
46
discuss 2 methods of opening up chromatin for transcription is ATP required
1) histone chemical modification; acetyl groups are added to the the lysin AA's of the protein, causing the histone to lose its positive charge so the DNA-histone and histone-histone interaction decreases 2) chromatin remodelling is done by chromatin remodelling complexe enzyme (remodeler) to make DNA more accessible a) move nucleosomes b) remove histone protein c) unwarap DNA from protein ATP required
47
name the 3 types of eukaryotic RNA polymerase and what they transcribe approx how many subunits do these enzymes have
RNA Pol 1; transcribes genes for rRNA (found in nucleolus) RNA Pol 2; transcribes protein coding genes. is involved in RNA processing too RNA Pol 3; transcribes genes for tRNA and snRNP's all have more than 10 sub units
48
discuss the name of the sequence where eukaryotic transcription begins, discuss sequence length and how far away from from transcription starting point it is
TATA 8 bp long (TATAAAXX) 25 bp upstream of transcription start point
49
discuss the translation's 3 stages
initiation elongation termination
50
how does ribosome know where to begin translation (there are lots of AUG codons in mRNA)
for prokaryotes, the ribosome binds to the Shine-Dalgarno sequence of mRNA (AGGAGG) for eukaryotes, the ribosome binds to the beggininng of mRNA and moves to the first AUG in the mRNA
51
discuss the 2 elongation factors required for translation; their roles and their different names in prokaroytes/eukaryotes
EF-Tu (EF-1 in eukaryotes) carries aminoacyl-tRNA to the amino acid EF-G (EF-2) binds to the A site of the small sub unit and moves the ribosome relative to the mRNA (resets it) Both hydrolyse GTP for energy
52
discuss how eukaryotic transcription is initiated
``` over 50 polypeptides required activator proteins chromatin remodelling proteins TFIID (TBP); bend DNA 70 degress RNA POL 2 binds elongation factor p-TEFb phosphorylates the carboxy terminal domain of RNApol2 which allows transcription to resume after it has been paused ```
53
discuss what sequences are present in eukaryotes if no TATA box is present
BRE (30 upstream) DPE (30 downstream) TBP is still required
54
discuss genes with no TATA box and no other sequences to define where transcription starts
these genes code for housekeeping proteins; (needed in small amounts). transcription doesnt start at a specific base but dispersed initiation occours every 50bp along the sequence
55
define cis-regulatory element
a DNA sequence in a gene, which transcription factors bind to which regulates the rate of gene expression 10bp consensus sequence
56
what are the two mechanisms by which a transcription factor works
alters chromatin structure | interacts with the transcription complex to change how RNA pol 2 binds to the promotor
57
define core promotor, proximal promtor and enhancer
the core promotor is the region of DNA that RNA polymerase binds to proximal promotors are the region next to the core promotor that contains Cis-regulatory elements enhancer, cis regulatory element very far from the core promotor
58
discuss what the metallothionein gene is expressed as and the fucntion of that protein discuss 2 of the response elements that increase expression as well as the associated TF
the metalliothionein gene is expressed as a metallothionnein proteiin which binds toxic damaging metals as well as metals that are needed, like Zn2+ when Zn2+ is present, it binds to an activator protein which then binds to the MRE response element when glucocorticoid is present, it binds to the glucocorticoid receptior which is activator which binds to the GRE
59
where is the beta globin gene found and what is the TF for this gene
the beta globin gene is found in erthroid cells (RBC precursor) and is activated when the gata-1 TF binds
60
explain a mechanism by which steroid hormones regulate transcription
the steroid hormone diffuses into the cell, binds to an activator protein and changes how it interacts with the cis regulatory element
61
what is most important secondary messenger of peptide hormones
cAMP
62
what is the name of the group of TF's which bind to steroid hormones
ligand responsive transcription factors (LRTF)
63
what type of steroid hormone glucocorticoids and what is one improtant glucocorticoid hormone
adrenal steroid (released by the adrenal gland) cortisol
64
what two situations is cortisol released in what physiological effects does it have (does it it inhibit or promote)
starvation/intensive exercise blood sugar increase by activation of genes needed for gluconeogenesis (liver cells) inhibit
65
when glucocorticoid is not present, what stops the protein it effects having impacts on transcription
Hsp90 chaperone protein holds the glucocorticoid receptor in the cytoplasm. cortisol binds to the protein and causes hsp90 to dissociate allowing the protein to enter the nucleus
66
why does removal of hsp90 chaperone allow for the cortisol recepetor cell to enter the nucleus
its nuclear localisation signal has been unmasked
67
what is the mechanism by which cortisol receptor alters transcription
the recpeptor remodels the chromatin which allows other TF's to bind
68
name other groups of steroid hormones apart from adrenal steroids
thyroid hormones, steroid sex hormones, vitamin D, retinoic acid
69
why do certain cells not respond to hormones
they dont have the receptor
70
define somtie
a cluster of undifferentiated cells which form next to the notochord in vertebrate embryos
71
discuss the two steps of muscle development
somite neighbouring cells signal for somite cells to transcribe MyoD and Myof5 genes, which cause the somites to convert into myoblasts myoblasts transcribe myogenin which causes the myoblasts to fuse and form a multinucleate muscle cell (myotubule)
72
define myoblast
undifferentiated cells which are precursors for muscle cells
73
whats the name of a mature muscle cell
myotubule
74
name the 3 genes needed for muscle development
MyoD and Myof5 (for somite to myoblast conversion) and myogenin (for myoblast to myotubule differentiation)
75
discuss evidence for the muscle development process
knocking out myoD and Myof5 means myoblasts dont form knocking out Myogenin means myotubules done form
76
discuss how cells can be induced to become other cells discuss 3 examples (cell that is induced, cell it can become, transcription factors, applications)
if different transcription factors are expressed, then different target genes are expressed so proteins for other cell types now exist ``` 1) fibroblast>muscle cells myogening, Myof5, MyoD 2) fibroblast>iinduced pluripotent cells oct4, sox2, Klf4, Myo these cells can give rise to many cells ``` 3)pancreatic exocrine cells>inset of Langerhans beta cells Pdx1, Ngn3, MafA cure diabetes
77
name two ways to alter gene expression apart from transcription discuss an example of both
altering translating mRNA for ferratin (iron storage protein) is only trnaslated when iron concentration is high altering mRNA stability trasferrin, (transfer protein used to take up iron when cell concentration is too low) mRNA is made more stable due to signalling for this low concentration
78
explain what a zinc finger protein is and an exmaple of one
proteins that consists of loops/helixes of amino acids. protein is stabilised by zinc ions steroid hormone receptors (TF's)
79
what the region of a zinc finger which binds to DNA
recognition helix
80
discuss the need for glucose as a regulator of the lac operon
the lac operon is weak due to non standard -10 and -35 regions in the promotor; glucose concentrations need to be low so that cAMP concentrations are high; cAMP binds to a catabolite activator protein (CAP) which binds to DNA's -35 region, bends DNA and helps RNA polymerase bind

molecular biology (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions