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MCAT BIO (BCHM/ORGO/CELL/MICRO) > Molecular Bio > Flashcards

Molecular Bio Flashcards

1
Q

how many distinct / unique chromosomes do humans have?

A

24 (22 autosomes and 2 different sex chromosomes)

in total we have 46 chromosomes

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2
Q

what is intergenic DNA?

A

This is regions of DNA that are non-coding. Therefore they do not create proteins

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3
Q

What are single-nucleotide polymorphism’s?

A

SNP’s (snips) are a form of genetic variation. In our sequence of DNA humans have random mutations that create genetic variability. these are called SNP’s

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4
Q

the genetic code: explain codons and anti-codons.

A

the 3 letter sequence on mRNA is “read” and gives rise to a specific amino acid. Therefore, since the mRNA letters code for an amino acid it is called the codon.

The anti-codon has that specific amino acid attached to it and it is on tRNA.

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5
Q

what are the start and stop codons (note: stop codons are aka nonsense codons)

A

start = AUG which codes for methionine (M)

nonsense = UAG, UAA, and UGA

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6
Q

why is the genetic code said to be degenerate and non- ambiguous?

A

degenerate –> it is error resistant. Since most of the time, if a codon starts with the same 2 letters the third letter doesn’t change the amino acid. (multiple codons make the same AA)

not ambiguous –> for each codon only one specific AA is made

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7
Q

DNA replication

What enzyme forms the open complex in eukaryotes and prokaryotes?

A

eukaryotes - DNA helicase

prokaryotes - DnaB

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8
Q

what is DnaA?

A

a protein that find the ORI (origin of replication) in prokaryotes. It attracts DnaB for the formation of the open complex

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9
Q

what is topoisomerase and SSBP’s?

A

topoisomerase stabilizes the open complex by reducing the super coil created up and down stream of it.

SSBP’s are single stranded binding proteins which protect ssDNA

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10
Q

true or false, DNA polymerase requires a template and a primer to function.

A

true, primases must place a primer on the template parent strand. Additionally, DNA pol can only read 3’ to 5’ (i.e. create DNA in the 5’ to 3’ direction)

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11
Q

prokaryotes have 5 main DNA polymerase enzymes. What is the function of DNA pol 1 and DNA pol 3?

A

DNA pol 3 –> this is responsible for the continuous and rapid 5’ to 3’ elongation of DNA. It also contains 3’-5’ exonuclease for proof reading ability

DNA pol 1 –> this has much slower processivity than DNA pol 3. DNA pol 1’s main job is to use its own 3’ to 5’ exonuclease activity to get chop up Okazaki primers and simultaneously replace them with new DNA (5’ to 3’)

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12
Q

what is the difference between an endonuclease and exonuclease?

A

endonuclease will cut the chain in the middle

exonuclease will cut at terminal sides

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13
Q

DNA pol 3 is the main polymerization enzyme and DNA pol 1 is the main primer replacement enzyme. DNA pol 2 however is also important, what it do?

A

DNA pol 2 is involved in DNA repair pathways!!

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14
Q

what is theta replication?

A

the replication of prokaryotic DNA since this DNA has is circular and has only one ORI region.

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15
Q

what are the three types of point mutations? explain each.

A

a point mutation is when one nucleotide is switched for another.
1. missense mutation –> the switch of nucleotides results in a different amino acid coded for

  1. nonsense mutation –> the switch of nucleotides results in a stop codon (nonsense codon) which causes premature end to translation.
  2. silent mutation –> same amino acid is the result.
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16
Q

what are deletions, insertions, and inversions.

A

all forms of mutations - typically frameshift

deletion + insertion are point shift if 3 nucleotides are added / removed together.

inversion - a segment of DNA is flipped often due to a transposon

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17
Q

what is a translocation mutation?

A

sometimes 2 non-homologous chromosomes can undergo recombination in which they switch parts of their genes.

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18
Q

Transposons are mobile genetic elements. Their basic structure is two inverted repeats surrounding a transposon gene. The transposon gene transcribes/translates for the enzyme transposase which comes back and cuts the transposon at the inverted repeats (in some cases its cut straight out, others its copied then cut out).

What is the IS element, complex transposon, and composite transposon?

A

IS element is the basic structure: 2 inverted repeats flanking a transposon gene

complex transposon –> includes some genes within the two inverted repeats

composite transposon –> contains two transposons with a region in-between

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19
Q

For IS elements and complex transposons, the transposase enzyme can copy and paste them into any other region of the genome. This can be placed in gene promoter regions, in intergenic DNA, or even in coding sequences.

Composite transposons have 2 effects. Explain what occurs if the two transposons run in the same direction vs. opposite directions.

A

same direction –> two transposons will cut out the middle section of DNA which can take one of the transposons with it and re-enter at another site in the genome.

opposite ( –>

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20
Q

what is hemizygosity?

A

haploid expression in a diploid organism.

diploids have 2 copies of each gene, but if one of those copies is unable to every be expressed, the person is hemizygotic for that gene.

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21
Q

Double strand break repair: explain the process of homologous recombination.

A

After DNA replication, there are homologous sister chromatids within the cell. As a result, if one sister chromatid has a DSB, the cell finds the normal homologous sister chromatid and uses it as a template.

  1. DNA nucleases trim the 5’ sides of the broken DNA to create single stranded hangovers
  2. Helicase unwinds the homologous sister chromatid which is assembled near the DBS chromatid.
  3. the unwound regions of the normal chromatid act as a template for polymerase 2 to synthesize normal DNA on the broken chromatid.
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22
Q

Double strand break repair: explain non-homologous end joining.

A

this is the process used when a cell is not undergoing cell division / is not in the cell cycle (since using a “back up chromosome” i.e. sister chromatid, is not possible)

this is much less accurate than homologous recombination.

note: these last two mechanisms are for DSB’s. there are other pathways for single stranded breaks

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23
Q

what is monocistronic and polycistronic, which one is eurkaryotes and which is prokaryotes?

A

mono - one gene, one protein
poly - one gene, any proteins

prokaryotes are often poly while euk are mono

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24
Q

what are microRNA, siRNA, and PIWI-RNA, and lnRNA?

A

micro and siRNA are involved in post-transcription modification where they interfere with mRNA

PIWI RNA is involved in inhibiting transposon mobilization

LnRNA is involved in regulating basal transcription levels

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25
Q

what is the difference between the non-coding / antisense strand and the coding / sense strand

A

the non-coding strand is the strand of DNA that is actually being used as a template for synthesis. It is base pairing with nucleotides that RNA polymerase is brining in.

the coding strand is the strand that is identical to the transcript (i.e. it shares the transcripts code)

26
Q

explain the terms upstream and downstream in regard to transcription

A

upstream means towards the 5’ end of the CODING STRAND

downstream means toward the 3’ end of the CODING STRAND.

transcription reads the non-cdoing strand 3’ to 5’ (i.e. downstream) which synthesizes RNA in the 5’ to 3’ direction (same direction as coding strand)

27
Q

prokaryotic transcription:

explain what the core enzyme is, the sigma factor is, and the holoenzyme.

A

the core enzyme is a 5 subunit RNA polymerase which accomplishes prokaryotic transcription

the sigma factor is an additional subunit which helps the core enzyme find the appropriate promoter. It is a vital initiation factor for transcription

when sigma factor is bound to the core enzyme it is called a holoenzyme

28
Q

prokaryotic transcription:

what is the open and closed complex?

A

when sigma factor finds the appropriate promoter and allows the RNA pol to bind, it is in a closed complex.

then the DNA unwinds with sigma factor and core enzyme attached. This is the open complex

after synthesis starts, sigma factor falls off and this is now the elongation complex

29
Q

true or false, eukaryotic transcription and translation can occur simultaneously

A

false, hnRNA is first made and modified. The created mRNA is then sent to ribosomes

prokaryotes can do these simultaneously since they do not have a nucleus.

30
Q

what is the splicosome? what important RNA molecule is i it?

A

the splicosome is a huge complex that performs RNA splicing.
A lot of proteins assemble with small nuclear RNA’s (snRNA’s) to form small nuclear ribonucleic particles. These particls are responsible for the splicing rxn.

31
Q

what are exons and introns

A

exons are expressed, introns are spliced out. Alternative spilcing changes the pattern of excisions which increases genetic diversity / gene expression variability.

32
Q

true or false, all RNA in prokaryotes is made from the holoenzyme / core enzyme RNA polymerase.

A

true, eukaryotes have a bunch

33
Q 
in contrast to prokaryotes, eukaryotes have many RNA pol enzymes. 
explain the function of 
RNA pol 1
RNA pol 2 
RNA pol 3
A

RNA pol 1 –> synthesizes rRNA

RNA pol 2–> synthesizes mRNA (hnRNA)

RNA pol 3 –> synthesizes tRNA

34
Q

explain the function of prokaryotic DNA pol 1 and DNA pol 2 and DNA pol 3

A

DNA pol 1 –> replacing lagging strand primers with DNA

DNA pol 2 –> DSB repair

DNA pol 3 –> most of replication

35
Q

what is the wobble hypothesis for translation of mRNA?

A

there are 61 codons that are possible however there are less than 45 tRNA types indicating that some anti-codon sequences can base pair with non-normal codon sequences.

The Wobble hypothesis explains that the first two base pairs of the anti codon respect normal base pairing but the 3rd position of the anticodon (furthest to the right) can do more flexible base pairing.

G pairing with U
and I pairing with A, U, or C is most common

36
Q

what is aminoacyl-AMP and aminoacyl-tRNA ? (amino acid activation)

A

aminoacyl AMP is the product of an amino acid reacting with ATP. Following this reaction, the hydrolysis of pyrophosphate loads the aminoacyl group onto a tRNA molecule creating aminoacyl-tRNA (anticodon)

37
Q

what are aminoacyl-tRNA synthetase enzymes?

A

there is a specific enzyme for each amino acid. The aminoacyl-tRNA synthetase enzyme ensures the correct AA joins the correct tRNA

38
Q

80s ribosome with 60s and 40s subunits

70s ribosome with 50 and 30

euk and pro?

A 
euk = 80s 
pro = 70s
39
Q

prokaryotic translation:

what is the shine dalgarno sequence?

A

this is a sequence on the incoming mRNA molecule that binds to the small ribosome unit of the prokaryotic ribosome and to initiation factors (IF1 and IF3).

Once this sequence is recognized, the large sub unit can close along with IF3

40
Q

what is the first step in prokaryotic translation? (after shine dalgarno sequence is recognized)

A

the start codon proceeds the shine-dalgarno sequence and is placed in the P site.

this codon has formyl-methionine which is the special start amino acid for all peptides. AUG after this brings methionine

41
Q

how does the amino acid chain grow?

A

an enzyme called peptidyl transferase catalyzes the peptide bond between amino acids in the A and P sites of the ribosome.

GTP is the energy source. About 2 GTP’s are hydrolyzed for every one amino acid joined in a peptide! (if you include the activation of amino acids to aminoacyl-tRNA’s

42
Q

t or f, eukarytic translation is similar to prokaryotic except

  1. starts with a different initiation sequence (5’UTR)
  2. methionine is start AA not Fmeth
  3. cannot be simultaneous with transcription
A

true

43
Q

What is Cap dependent translation and what is the IRES sequence of mRNA

A

Cap dependent translation is what translation is referred to since most mRNA molecules can only be made if they have been 5’ capped.

IRES = internal ribosomal entrance sequence which allows for non-cap translation. Rarer.

44
Q

in eukaryotes what two contributions does methylation of DNA have?

A
  1. inhibit transcription

2. attract chromatin remodelling complexes which alter chromatin to increase or decrease TXN

45
Q

explain what it means for an enzyme to be repressible or inducible. anabolic and catabolic enzymes are which form?

A

A repressible enzyme is an enzyme in which the activation of its gene can be repressed. This is logical for anabolic (build-up) enzymes when they begin to make too much product

An inducible enzyme is an enzyme in which its gene can be stimulated when substrate is around. This makes sense for catabolic enzymes which are only needed when the breaking down of substrates is needed.

46
Q

Lac Operon: what is it, what does it respond too?

A

it is a gene that when activated, creates proteins responsible for lactose metabolism.
It responds to glucose and lactose levels and is controlled by both inhibitory and stimulatory mechanisms.

47
Q

in low glucose environment, is the Lac operon likely to be on or off.

A

low glucose means it is likely to be on so that it can metabolize lactose for energy (high lactose levels promote this too)

48
Q 
explain the different components of the Lac operon. 
P 
O
Z
Y
A
A

P - promoter site which can be activated to transcribe genes via RNA pol
O - operator site which is subject to inhibition control via a repressor protein
Z - makes beta-galactosidase which metabolizes lactose
Y - makes permease protein to permit lactose into the cell
A - makes some acetylase enzyme

49
Q

The Lac operon: What are crp and “I” genes?

A

these are regulatory genes of the Lac operon which respond to lac operon products such Z, Y, and A

crp - makes a catabolite activation product (CAP) which stimulates the promoter region to make gene products

“I” gene makes a Lac repressor protein which binds the O site and stops Lac activity

50
Q

Lac Operon: Adenylyl Cyclase is an important membrane protein which converts ATP to cAMP (in 2nd messenger systems). How does glucose effect Adenylyl cyclase?

A

High glucose inhibits it therefore high glucose = low cAMP

Low Glucose activates it, so low glucose = high cAMP

51
Q

What is the interaction of cAMP and CAP (crp product) and what is the interaction between lactose and the Lac repressor protein?

A

CAP binds cAMP which together goes and activates the Lac operon. Therefore, in low glucose environments when adenylyl cyclase is not inhibited, cAMP levels are high and promote lactose metabolism through this binding.

Lactose allosterically binds the repressor protein which prevents its inhibitory function. Therefore the presence of lactose also stimulates Lac operon (along with absence of glucose)

52
Q

lac operon: Explain what occurs in high glucose conditions and low lactose conditions ?

A

In high glucose conditions the “I” gene expresses lac repressor protein which binds the O site and prevents gene expression. The low levels of lactose don’t prevent this proteins function.

additionally, the high levels of glucose inhibit the activity of adenylyl cyclase which means no cAMP and no CAP binding. Therefore RNA pol is not stimulated at the Lac P site.

53
Q

what would occur if there was both high levels of glucose and high levels of lactose?

A

Both crp and “I” products would be made. However the high presence of glucose would cause their to be little cAMP from adenylyl cyclase therefore CAP has little effect.

In contrast though, the high levels of lactose have allosteric inhibition effects on the repressor protein.

the result would be low levels of transcription of Z, Y, and A

54
Q

what main effect does a repressor protein have? what occurs if it cannot be synthesized?

A

repressor proteins physically block RNA pol from doing its job. Often the loss of repressor protein leads to uncontrollable transcription of RNA pol.

55
Q

What is the Trp operon?

A

bacteria have 5 energy expensive pathways to make tryptophan. So in the presence of tryptophan the enzymes should be shut off. The trpR gene makes a repressor protein which inhibits the trp gene from transcribing proteins ( in the presence of W)

W - trp - tryptophan

56
Q

true or false, chaperone proteins can assist in protein folding.

A

true, its not always simply thermodynamic (pg. 121 of bio)

57
Q

What is the difference between a Northern, Southern, Western, and Eastern blot?

A

All blotting is the transfer of a molecule from gel electrophoresis to a membrane of some kind for further study
Northern blot –> detects presence of a specific DNA target

southern blot –> detects for a RNA target (used when evaluating whether certain gene products are being produced)

Western blot - detection of a protein

eastern - uncommon, looks at post-translational modifications

58
Q

true or false, Southern blot is used for ssDNA.

A

False, northern blot = DNA

southern blot = RNA

59
Q

true or false, 5’UTR regions are not transcribed.

A

false, they are transcribed but not translated.

Promoter - TXN start site - 5’UTR - ATG——ACT –3’UTR

ACT will be transcribed into UGA (stop codon)

60
Q

true or false, DNA replication, TXN and TLN read all of their templates 3’ to 5’

A

false, replication and TXN are ready 3’ to 5’ (synthesized 5’ to 3’)

TLN is “read” 5’ to 3’ on the RNA template (3’ end makes stop codon)

protein is build N –> C terminus so C is the last terminus

MCAT BIO (BCHM/ORGO/CELL/MICRO) (8 decks)

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