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2. Molecular Biology Flashcards

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MCAT flashcards Biology 101 flashcards
1
Q

What is a dNTP?

A

deoxyribose-nucleotide-triphosphate (this is the building block of DNA, and NTPs are the building blocks of RNA).

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2
Q

What is the structural difference between purines and pyrimidines?

A

pyrimidines have one aromatic system, purines have two.

Think pyrimidine = long name, less rings
purine = short name, more rings

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3
Q

what bond connects DNA nucleotides?

A

phosphodiester bonds (the 3’ OH of the sugar attacks the next nucleotides phosphate center. this releases pyrophosphate.

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4
Q

how many hydrogen bonds in a GC pair? How many hydrogen bonds in an AT pair?

A

GC is held by 3 H bonds

AT is held by 2 H bonds

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5
Q

What is Chargoffs rule of base pairing?

A

[A] = [T] and [G] = [C]

thus, [A] + [G] = [C] + [T]

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6
Q

compare a DNA chain with mostly GC pairs compared to mostly AT pairs.

A

the more GC rich DNA will bond more tightly because GC pairs have more hydrogen bonding

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7
Q

what is the DNA melting temperature?

A

note melting = denaturation.

The Tm (melting temperature) is the T at which 50% of the DNA molecules have denatured (separated). If we increase the GC concentration, the Tm will rise.

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8
Q

t or f, DNA is a double-stranded (anti-parallel) right-handed helix.

A

True, the hydrogen bonds hold the two strands together, while Van der Waals interactions between bases stabilize the coiling helix (stacked onto each other).

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9
Q

What is DNA gyrase?

A

DNA gyrase is a prokaryotic enzyme that uses ATP to break the DNA and twist it into a super-coil (note that prokaryotic DNA is held in one large circular piece).

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10
Q

What are histones, what are nucleosomes?

A

In Eukaryotes, histones are globular proteins that DNA may wrap around. A nucleosome is DNA wrapped around an octamer of histones. Many nucleosomes created compacted DNA called chromatin.

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11
Q

Explain the chemical nature of a histone.

A

Histones are mostly basic, as they have more arginine and lysine (positive) residues. Histones need to be positively charged, as the phosphate backbone of DNA is negatively charged.

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12
Q

What is heterochromatin and euchromatin?

A

Heterochromatin –> Darker and more dense (less active DNA)
Euchromatic –> lighter, less dense (more active DNA)

Think Euchromatic = Expression (E=E)

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13
Q

Explain Metacentric, Sub-metacentric, Acrocentric, and Telocentric.

A

Every chromosome has two arms, p, and q. The lengths of these can vary

Metacentric: p = q
Sub-metacentric: p < q
acrocentric: p &laquo_space;q
telocentric: p «< q (essentially no p)

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14
Q

What are telomeres? What is the common telomere sequence?

A

Telomeres are long repeating units at the end of DNA that prevent chromosome deterioration. A common telomere sequence is 5’-TTAGGG-3’

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15
Q

What is the sense strand/coding strand?

A

The sense/coding strand is the strand of DNA that is not directly transcribed, but its sequence matches the developed mRNA molecule.

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16
Q

What is the antisense strand / non-coding strand?

A

The antisense or non-coding strand is physically being transcribed (AATG –> UUAC).

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17
Q

codons contain three base positions, which is least important?

A

The third position (1 2 3) is least important. This is because, in many cases, the first two positions determine the amino acid and therefore the third does not matter .

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18
Q

What is the start codon? What are the stop codons?

A

AUG is the start codon, which encodes Methionine.

Stop codons include: UAA, UAG, UGA and code for nothing

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19
Q

Why is the genetic code called degenerate or redundant?

A

because 64 codons exist and only 20 amino acids may be created. Therefore, multiple codons can create the same AA. However, each codon is specific for an AA (codons only ever encode their respective AA).

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20
Q

DNA replication: What are DNA helicase and ORI?

A

ORI is the origin of replication on eukaryotic genomes. Helicase comes to the ORI and unwinds the DNA to ready it for DNA replication.

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21
Q

DNA replication: what is topoisomerase? What are SSBPs?

A

helicase unwinding causes nearby regions of DNA to become strained.
topoisomerase cuts the DNA to alleviate this tension. Single-stranded DNA can be a sign of pathology, so single-strand-binding proteins bind these areas to prevent a response.

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22
Q

DNA replication: Once the open complex has formed, what is necessary before replication?

A

At the ORI, primase must come and lay down an RNA primer which is needed for DNA polymerase to initiate replication.

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23
Q

DNA replication: What direction does DNA polymerase synthesise DNA?

A

it adds dNTPs to the 3’ end of the RNA primers. Thus it creates DNA in the 5’ to 3’ direction.

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24
Q

DNA replication: What provides energy for DNA polymerization?

A

the hydrolysis of pyrophosphate from the incoming dNTP. (POP is removed while one phosphate remained attached).

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25
Q

DNA replication: Explain the leading and lagging strands.

A

The leading strand has continuous replication and moves in the direction of the replication fork.
The lagging strand has discontinuous replication with the constant addition of new primers. This problem arises because DNA Pol cannot create DNA in the 3’ to 5’ direction. the fragments of synthesized DNA are called okazaki fragments.

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26
Q

DNA replication: after the RNA primers are replaced with DNA, what connects the segments of DNA?

A

DNA Ligase

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27
Q

Prokaryotic Polymerase enzymes. Explain

  1. Pol 3
  2. Pol 1
A

in prokaryotes…
DNA polymerase 3 is responsible for the elongation of the leading strand. It is the main replicative enzyme. It also contains 3-5’ exonuclease activity to proof-read its work

DNA polymerase 1 is responsible for replacing RNA primers (5’-3’ exonuclease activity). It also has 3’-5’ exonuclease proofreading. After 400 bases DNA polymerase 3 takes over.

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28
Q

Prokaryotic polymerases, both 1 and 3 are involved in DNA repair.

A

false, only polymerase 1 (as-well-as others like Pol 2). Pol 3 is only a replicative enzyme.

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29
Q

What is theta replication?

A

prokaryotes only have one circular chromosome. The replication of this chromosome is called theta replication

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30
Q

What problem arises when replicating the ends of chromosomes?

A

DNA polymerase requires a primer and template to synthesize new DNA. Eventually, there will be no place to lay down a primer, leaving the end of chromosomal DNA unreplicated. This is where telomeres come in, as they are tandem repeats of DNA that can be lost with no consequence.

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31
Q

Where is telomerase translated?

A

Typically only in germline cells, ESC, and some whiteblood cells.

32
Q

What is UV light capable of doing to DNA?

A

If two pyrimidines (CUT) are beside each other on the DNA backbone, UV light can cause them to become covalently linked (pyrimidine dimer)

33
Q

What is the Hayflick limit?

A

The number of times a normal human cell can divide before its telomere length is too short and must become senescent or undergo apoptosis.

34
Q

Explain missense, nonsense, and silent mutations.

A

missense: the change in DNA base results in a different amino acid
nonsense: the change in DNA base results in a stop codon (UGA, UAG, UAA)
silent: the change in DNA base results in the same AA due to the codes redundancy.

35
Q

What is a genetic inversion?

A

A segment of DNA is reversed end-to-end. A chromosome undergoes a rearrangement within itself.

36
Q

What is the difference between transitions and transversions?

A

point mutations
transition –> purine for a purine or pyrimidine for a pyrimidine
transversion –> the base type switches (e.g. purine for pyrimidine)

37
Q

What is a genetic translocation?

A

A translocation is a recombination event between two non-homologous chromosomes that can result in gene fusion (two genes fuse to create one).

38
Q

What is a transposon? Explain its general structure.

A

A transposable genetic element capable of causing INDELS, inversions, and rearrangements.

A simple transposon has a transposase gene which is flanked by two IS elements (inverted repeat sequences). Transposase has cut and paste activity where it can cut out the whole system and insert itself elsewhere.

39
Q

Explain complex and composite transposons.

A

complex transposon has additional genes in between the IS elements. E.g. antibiotic resistance gene.

composite transposon contains two transposon systems with a central region in between them.

40
Q

t or f, the transposon can make a copy of itself before leaving and inserting itself elsewhere in the genome.

A

true

41
Q

Composite transposons. Explain…

  1. If the two transposons point in the same direction
  2. If the two transposons point in opposite directions
A
  1. If they line up in the same direction, the one transposon can loop over to be parallel with the other transposon. In a recombination event, the DNA in the middle gets excised along with one transposon (therefore this DNA can insert elsewhere)
  2. If they are in opposite directions, they still align with each other, but this simply causes the DNA to become inverted.
42
Q

Explain loss of heterozygosity.

A

Humans have 2 copies of most genes (diploid organisms). If a mutation occurs in one gene that inactivates or loses it, then the person no longer has two genes to form that gene product. This is loss of heterozygosity. This may be caused by a transposon deletion event.

43
Q

What is hemizygosity? What is a haploid organism?

A

Hemizygous: this explains a diploid organism that has only one gene copy of a particular gene (due to a loss of heterozygosity event)

Haploid: explains an organism with only one gene copy for every gene (i.e. one chromosome set)

44
Q

In what way are humans hemizygous, other than when mutations cause loss of heterozygosity?

A

Human sex chromosomes are hemizygous. males have one X and one Y. females have one X chromosome silenced so they really only have one X chromosome.

45
Q

What is haploinsufficiency?

A

Haploinsufficiency occurs when hemizygous gene cannot produce enough gene product needed.

46
Q

DNA repair: Explain direct reversal.

A

In some cases, DNA damage can be directly repaired. This occurs when UV light causes pyrimidine dimerization.

47
Q

DNA repair: Explain homology-dependent excision repair.

A

Before DNA replication, the non-mutated DNA strand acts as a template for the single-stranded break.

48
Q

DNA repair: Explain homology-dependent post-replication repair. What is another name for this?

A

After DNA replication, the mismatch repair pathway fixes the SSB.

in prokaryotes, MMR uses DNA methylation to flag the wrong base and replace it. This ensures that the body knows which strand has the correct base, and which does not.

49
Q

DNA repair (DSBR): Explain Homologous Recombination

A

After DNA replication, the healthy sister chromatid is used as a template to repair the DSB of the mutated sister chromatid.

  1. The DSB chromosome is trimmed by a nuclease (break phosphodiester bonds). helicase opens it up.
  2. SSBP’s bind
  3. Proteins search for the sister chromatid region
  4. the chromatids join and polymerase and ligase repair the DNA
50
Q

DNA repair (DSBR): Explain non-homologous end joining.

A

If the cell is not actively in the cell cycle, then homologous recombination is not an option. Here broken ends are stabilized, then DNA ligase connects the fragments. non-homologous end-joining is not ideal, it simply reattaches the chromosome pieces.

51
Q

t or f, prokaryotes contain heterogenous-RNA.

A

FALSE, prokaryotes do not have post-transcription modifications. They directly produce mRNA.
In contrast, eukaryotes do (5’cap, poly-A tail, splicing). First HnRNA –> mRNA

52
Q 
Explain 
Small-nuclear RNA
MicroRNA and siRNA 
PIWI RNA
long ncRNA
A

Small-nuclear RNA –> forms a part of the splicosome
MicroRNA and siRNA –> inhibit mRNA via degradation or silencing
PIWI RNA –> prevent transposon mobilization
long ncRNA –> Modulate basal transcription levels

53
Q

t or f, RNA polymerase does not contain 3-5 exonuclease activity like DNA pol.

A

True, thus RNA pol is more prone to error.

54
Q

t or f, the DNA strand that is actually transcribed is called the template, non-coding, anti-sense strand. The other DNA strand is called the coding or sense strand.

A

true - the DNA strand that is not being transcribed we be identical to the new RNA template (U instead of T). Thus it is the coding / sense strand.

55
Q

prokaryotic transcription: Explain the core enzyme and the sigma factor.

A

The core enzyme is the RNA pol that creates the mRNA. However, a subunit called the sigma factor binds the core enzyme which is necessary for the RNA to find the right DNA promoter which lies 30 bases upstream of the start site.

sigma factor + RNA pol = holoenzyme

56
Q

Can prokaryotes perform splicing?

A

No

57
Q

Prokaryotes have many DNA pols (in previous question). Prokaryotes only use one RNA pol (core enzyme). In contrast, eukaryotes have many RNA pols too. T or f?

A

True
eukaryotes have many DNA (don’t need to know) and RNA pols.
prokaryotes only have one RNA pol - core enzyme

58
Q

In eukaryotes, explain

RNA pol 1, 2, and 3.

A

RNA Pol 1 - transcribes most of rRNA
RNA Pol 2 - transcribes hnRNA (mRNA)
RNA Pol 3 - transcribes tRNA

59
Q

What is the wobble hypothesis?

A

The first two bases in the codon - anticodon pair follow normal base pairing rules. However, the third position is less strict and allows for non-traditional base pairing. this is why there are only 45 t-RNA molecules that can match the 61 possible codons (i.e. some tRNAs match more than one codon due to the wobble hypothesis).

60
Q

t or f, loading an amino acid to a t-RNA is an unfavorable reaction. What is the consequence?

A

True, it requires reaction coupling. Breaking the tRNA-AA bond to will drive the unfavorable peptide bond formation.

61
Q

how much ATP is needed to load an AA to tRNA?

A

2 ATP equivalents. Amino-Acyl tRNA synthetase loads the AA to the tRNA

62
Q

Explain the difference between the prokaryotic and eukaryotic ribosomes.

A 
P = 70s (30s and 50s)
E = 80s (40s and 60s)
63
Q

Which part of the ribosome for P and E, contains the ribozymic activity?

A

the large sub-unit - for both P and E

64
Q

prokaryotic translation: What is the Shine-Dalgarno seqeunce?

A

The ribosome binding site on a mRNA molecule.

65
Q

prokaryotic translation: At initiation, What is the first AA of the polypeptide?

A

Formylmehtionine, whose anticodon sequence binds the start codon: AUG

66
Q

prokaryotic translation: What is the peptidyl transferase enzyme?

A

An AA sits at the P-site. A new AA comes into the A-site. Peptidyl transferase forms a peptide bond with the AA in the P-site and A-site. Peptides are made in the N to C direction.

67
Q

prokaryotic translation: t or f, it costs 4n high energy bonds to make a polypeptide of n amino acids.

A

true

68
Q

Eukaryotic translation: What is the first amino acid?

A

simply methionine (unlike in P’s which is f-met)

69
Q

Eukaryotic translation: What is the Kozak seqeunce?

A

the start sequence on the mRNA molecule. Eukaryotes do not have a shine-dalgarno sequence.

70
Q

Eukaryotic translation: What does the 5’cap do on mRNA?

A

it is used by the ribosome to recognise the end the 5’ end of the RNA for translation

71
Q

Eukaryotic translation: What is cap-independent translation? What is an IRES?

A

translation does not have to start at the 5’ end. Thus, cap-independent translation does not require the 5’cap for translation initiation.
IRES = interal ribosome entry site.

72
Q

What is genomic imprinting?

A

imprinting is the epigentic process of silencing certain genes. (e.g. x chromosome inactivation). Genomic imprinting will silence one of your two alleles, essentially making you haploid for that gene (hemizygous)

73
Q

The lac operon: Explain the
P and O regions
Y, Z, and A genes

A

P region = promoter region where RNA pol binds to initiate transcription of the Y, Z, and A genes
O region = location where the lac repressor binds to prevent transcription

Z gene = codes for the enzyme that cleaves lactose
Y gene = codes for permease, an enzyme that transports lactose into the cell for catabolism
A gene = does not matter

74
Q

The lac operon: Explain the
crp gene
I gene

A

crp gene = distant gene that encodes the catabolic activator protein (CAP)
I gene = distant gene that encodes the lac repressor protein.

75
Q

What influences the expression of the lac operon?

A
  1. lactose levels : this determines the level of lac repressor protein (lactose binds this protein and inhibits it)
  2. glucose levels: this determines the level of CAP (CAP binds cAMP which together binds the P region of the lac operon).
76
Q

The lac operon: Explain

  1. high glucose, low lactose
  2. high glucose, high lactose
  3. low glucose, high lactose
A
  1. high glucose, low lactose
    - little cAMP, no CAP
    - no lactose, repressor protein high
    - no transcription
  2. high glucose, high lactose
    - little cAMP, no CAP
    - lactose present, repressor protein low
    - weak transcription
  3. low glucose, high lactose
    - high cAMP, high CAP
    - lactose present, repressor protein low
    - high transcription
77
Q

What is a chaperone protein?

A

A protein that helps with the 3D folding of other newly made proteins.

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