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Molecular Biology > Final Review > Flashcards

Final Review Flashcards

1
Q

What type of cell has a Kozak sequence?

A

Eukaryotes

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2
Q

What site does the mRNA enter first?

A

The A site (except for MET and fMET). Just remember the acronym A.P.E. where the tRNA moves from A->P->E, but A is on the right and E is on the left of the ribosome

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3
Q

What protein is bound to tRNA when it is in the cytoplasm?

A

EFTU hydrolyzes GTP to GDP when the tRNA enters the ribosome, which causes a conformational change to EFTU. This allows EFTU to dissociate and allows the tRNA to fit in the A-site and move through the ribosome

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4
Q

Where does the MET tRNA go first when entering the ribosome?

A

The P-site.

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5
Q

What is the function of EF-G-GTP in translation?

A

It powers the ribosome and allows it to ratchet, or translocate, allowing the next mRNA to be read

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6
Q

In eukaryotes what happens first in translation?

A

The 40S and the MET tRNA move along the mRNA until they find the Kozak sequence

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7
Q

What is mismatch repair?

A

One base doesn’t match up with the other, the mismatch repair system will cut out the mismatch and replace it with the correct base

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8
Q

How does a Prokaryotic cell recognize a mismatch? How about a Eukaryotic cell?

A
  • -The newly formed prokaryotic DNA strand will be methylated.
  • -Newly synthesized eukaryotic DNA strands will have Okazaki fragments (prokaryotes also have these fragments)
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9
Q

What is direct repair and how does it work?

A

Any type of repair that directly reverses the mutation (Ex. reversal of dimer formation)

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10
Q

What is base excision repair?

A

The incorrect base/damaged base is cut out, and then a cut is made in the backbone

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11
Q

What is nucleotide excision repair?

A

When two phosphodiester bonds (on either side of the nucleotide) are cut in the DNA backbone and an entire nucleotide is removed

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12
Q

When does non-homologous chromosome recombination occur?

A

When the chromosomes are massively damaged the cell will simply put together chromosomes that are nearest each other. This is a last ditch effort to save the genetic information.

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13
Q

Which amino acids are acidic/positively charged and how can you recognize them?

A

Aspartate and Glutamate

–Look for the carboxylic acid side chain

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14
Q

Which amino acids are basic/negatively charged and how can you recognize them?

A

Histidine, Lysine, Arginine

–Look for multiple nitrogens or nitrogens at the end of a chain of carbons

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15
Q

Which amino acids are subject to phosphorylation by kinase and why?

A
  • -Serine, Threonine, Tyrosine (Remember PSTT)

- -B/c they contain terminal OH groups

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16
Q

Which amino acid can disrupt an alpha helix?

A

Proline

–“I am a pro at disrupting the alpha helix”

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17
Q

What amino acid can form di-sulfide bonds?

A

Cysteine

–Just look for the terminal Sulfur, or think “The Cysteine chapel is a stable structure”

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18
Q

What type of bond stabilizes secondary structures and where does it occur?

A

Hydrogen bonding between the protein backbone atoms

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19
Q

What does Urea do to proteins?

A

Breaks non-covalent bonds

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20
Q

What does beta-mercaptoethanol do to proteins?

A

Breaks disulfide bonds

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21
Q

What is the single molecular difference between a dNTP and an NTP, and where is it located?

A

There is only a hydrogen attached to the 2’ carbon in dTNP’s (hence deoxyribose)

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22
Q

What is a nucleoside composed of?

A

Sugar and a base

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23
Q

What is the diameter of the double helix?

A

2nm

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24
Q

What is the height of one turn of the double helix?

A

3.4nm

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25
Q

What is the average weight of a nucleotide?

A

310 daltons

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26
Q

What is an example of a palindrome sequence?

A

5’-AACGTT-3’

Its compliment 3’-5’ readsTTGCAA, but 5’-3’ it reads AACGTT

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27
Q

What does methylation do to genes?

A

It silences them

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28
Q

How many types of histones are there?

A

5 types: H1, H2A, H2B, H3, H4

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29
Q

What is an octomer made of?

A

2 copies each of: H2A, H2B, H3, and H4

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30
Q

Why is GAPDH used in experiments?

A

It is the housekeeping gene. It is a loading control to ensure that all samples were not contaminated and that the actual experimental procedure didn’t vary from sample to sample. The GAPDH signal should be comparable across your blot.

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31
Q

Is the sense/coding strand what is read when RNA is made?

A

No, the template strand is read. This is why the RNA has the same sequence as the coding strand, but with U replacing T.

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32
Q

In which direction do restriction enzymes recognize and cut a recognition sequence?

A

5’ to 3’

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33
Q

Do bacteria have nucleosomes?

A

No, but they do have small proteins which aid in condensing their DNA

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34
Q

What is a nucleosome?

A

An octomer, H1 histone, and associated DNA

–Just remember it is like a spool and thread

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35
Q

What does acetylation do to the histone tails?

A

It converts them from a positive state to a neutral state (this loosens the DNA. Just remember that DNA is negative and de-acetylated histones are positive)

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36
Q

What is aneuploidy?

A

Is any abnormal number of chromosomes

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37
Q

What is the polylinker?

A

A segment of several unique recognition sites for restriction enzymes in a plasmid

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38
Q

What is the difference between stable and transient transfection?

A

Transfection is the process by which foreign DNA is incorporated into and expressed by native DNA. In transient transfection, the DNA does not integrate with its hosts DNA. In stable transfection it does.

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39
Q

What is significant about cDNA?

A

It is made from mRNA, and therefore the introns have been removed.

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40
Q

What first binds to OriC to prepare for DNA replication?

A

DnaA

41
Q

Helicase and Primase are the first enzymes on the scene after DnaA binds to OriC. What does Primase do?

A

Primase is RNA polymerase that lays down an RNA primer to initiate replication

42
Q

What direction does DNA Pol 1 proofread and what direction does it remove RNA primers and add DNA nucleotides?

A

It performs exonuclease function in both directions. It proofreads 3’-5’, and replaces primers 5’-3’

43
Q

When/why are ddNTP’s used?

A

They are used in Sangar sequencing because they will stall replication. This allows scientists to determine the sequence of DNA.

44
Q

The forward primer base pairs with the _______ strand?

A

The beginning of the Template strand (written 5’ to 3’)

45
Q

The reverse primer base pairs with the ______ strand?

A

The end of the Coding or sense (written 5’ to 3’)

46
Q

What is an expression vector used for?

A

When we want bacteria to make copies of the DNA, but to also use its machinery to make the appropriate proteins from that sequence.
–Think INSULIN

47
Q

What is different between the conservative, dispersive, and semi-conservative replication models considered by Meselson & Stahl?

A

Conservative-Parent strand comes back together and daughter strands stay together (no mixing)
Dispersive-Random patchwork of parent and daughter strands
Semi-conservative-The parent strands split, each becoming the template for the new daughter strand to be replicated onto. The resulting two strands have one strand one parent and one daughter.

48
Q

What do alkylating agents do?

A

Damages DNA by adding methyl groups

49
Q

What does TFIIH do?

A

[1] Opens DNA with its helicase activity

[2] Phosphorylates the CTD with its kinase activity

50
Q

What does phosphatase do?

A

It removes 5’ phosphate groups to prepare a vector for cloning

51
Q

What are the three components that an mRNA must have to be spliced?

A

A 5’ splice site, a 3’ splice site, and a branchpoint

52
Q

What binds to the splice sites?

The branchpoint site?

A
  • -U1

- -U2

53
Q

If a process results in a single nucleotide being changed, what is this called?

A

RNA editing

54
Q

Which type of RNA sequence is shown in the amino acid coding table?

A

mRNA

55
Q

What is the primary source of energy for protein synthesis?

A

GTP (remember that GTP is converted to GDP via EFTU. This is what powers the ratcheting motion of the ribosome)

56
Q

What do N and C terminals mean for proteins?

A

N=terminal amino group

C=terminal carboxyl group

57
Q

What is the difference between a slow stop and a fast stop?

A

Slow stop constitutes a stop in initiation (all proteins already initiated will be completed, and the protein synthesis rate will eventually taper off), whereas fast stop deals with elongation (an immediate halt of protein synthesis)

58
Q

Is bacterial mRNA capped?

A

NO

59
Q

Do prokaryotes incorporate a 5’ cap or 3’ poly A tail?

A

NO, only eukaryotes have these

60
Q

What happens to the Trp repressor when Trp is bound to it?

A

It binds to the Trp operon and suppresses transcription (negative regulation)

61
Q

What happens to the Lac repressor when Lac binds to it?

A

It exposes the Lac operon and allows transcription (it is bound when Lac levels are low)

62
Q

When does the Lac regulator CAP bind to cAMP?

A

When there are low levels of glucose. The CAP/CRP with cAMP complex binds to the Lac operon and allows/increases transcription of the Lactose digestion/facilitation proteins (positive regulation)

63
Q

What does the acetylation of histones do and what complex does this?

A 
Loosens DNA (and consequently the chromatin structure)
--HAT
64
Q

Which of the following key consensus sequences is commonly present in eukaryotic promoters; TATA box or Kozak sequence?

A

TATA Box, because Kozak sequences are only found in mRNA (which don’t have promoters)

65
Q

What does the helix-turn-helix do?

A

Interacts with the major groove in DNA

66
Q

What does the homeodomain motif do?

A

Interacts with the minor groove

67
Q

What does the Zinc-finger motif do?

A

Interacts with the major groove with zinc fingers

68
Q

What does the Leucine-zipper motif do?

A

Makes a dimer with another identical subunit.

69
Q

What does the JAK-STAT pathway do, and how does it work?

A

Cytokine causes an increase in translation
–Cytokine binds to receptors allowing STAT to come in cell, which proteins bind to forming a dimer. This dimer then binds to DNA promoting translation

70
Q

What does the PSTT acronym stand for?

A

It tells you which amino acids can be phosphorylated by kinase
–Serine, Threonine, Tyrosine

71
Q

What post-translational modification occurs when insulin binds to its receptor?

A

Phosphorylation

72
Q

What are the five post-translational modifications that can occur to proteins?

A

Ubiquitination, Glycosylation, Phosphorylation, Acetylation, Methylation

73
Q

Where do translational activators or repressor proteins bind to?

A

3’ UTR of mRNA

74
Q

When binding proteins interact with _________ the assembly of the small and large ribosomal subunits is disrupted?

A

eIF4E binds to itself and eIF4G

75
Q

What happens to eIF when they are phosphorylated?

A

They are innactivated

76
Q

What does methylation of histone H3 do?

A

It activates genes

77
Q

What type of cells can totipotent stem cells differentiate into?

A

Embryonic and extraembryonic (pluripotent stem cells cannot become extraembryonic cells)

78
Q

What is chromatin?

A

DNA will ALL associated proteins bound to it (ex. histones, etc)

79
Q

What is Chromatin Immunopreciptiation (ChIP) used for?

A

To find out where on the DNA particular proteins bind

80
Q

True/False: A mutation must change the amino acid sequence of a protein in order to have a phenotypic effect.

A

False. The sequence could stay the same, and more/less of the protein could be made, thus altering the phenotype.

81
Q

What is a Mediator Complex?

A

30+ subunit structure which allows enhancer-bound proteins to interact with promoter-bound proteins

82
Q

When does Chargoff’s rule apply?

A

With double stranded DNA only!!

83
Q

What is the difference between Uracil and Thymine?

A

Both have two oxygens, but Thymine has a methyl group

84
Q

How can you recognize Cytosine?

A

It has one oxygen (the other two pyrimidines have two)

85
Q

What is the difference between Adenine and Guanine?

A

Guanine has an oxygen, Adenine does not

86
Q

How do you change Cytosine to Uracil?

A

Through hydrolysis

87
Q

When are RNA primers used?

A

During prokaryotic (and eukaryotic) DNA replication. These RNA primers are then removed by DNA Pol 1 and RNase H (RNase H doesn’t proofread though)

88
Q

What is an Okazaki fragment?

A

In both prokaryotes and eukaryotes it is created by the lagging strand(s) that form during DNA replication. These are sealed together by ligase

89
Q

What is Telomerase?

A

A eukaryotic enzyme that contains its own RNA template, which adds nucleotides at the ends of chromosomes to postpone genetic information degradation

90
Q

What two bonds in a nucleotide are subject to spontaneous hydrolytic cleavage?

A

The covalent bond between the amino group and the nucleotide base, and the N-beta-glycosyl bonds (This can change a Cytosine to a Uracil)

91
Q

What do intercalating agents do?

A

They open up space to allow an insertion mutation by getting in between the DNA ladder rungs

92
Q

What is spontaneous depurination?

A

The hydrolytic cleavage of the glycosidic bond between base and sugar in a nucleotide

93
Q

What is the result of a tautomeric shift?

A

Mismatched base pairing due to structural rearrangement

94
Q

What do riboswitches do and where are they located?

A

When ligands bind to it, it undergoes a conformational change
[1] Hide Shine-delgarno sequence
[2] Form an attenuation sequence (premature termination of transcription)
[3] mRNA self-cleavage
–Located in the 5’ UTR

95
Q

Why are eIF4E and eIF4G important?

A

The repressors interact with initiation factors eIF3, eIF4E, and eIF4G or with the ribosome to prevent or slow translation. The factor eIF4G mediates an interaction between eIF4E at the 5′ cap and poly(A) binding protein at the 3′ poly(A) site. This interaction is needed for efficient translation, and factors that disrupt it repress translation.

96
Q

What subunits make up the large/small subunits of the ribosome in eukaryotes?

A 
•	Pol 1 → 45s
•	Pol 3→ 5s
o	45s is cut into three subunits to make the    28s, 18s, and 5.8s
o	40s and 60s (even numbers)
•	Small→40s
•	Large→5s, 5.8s, 28s
97
Q

What size are the large/small subunits of the ribosome in prokaryotes?

A

o 30s and 50s (remember odd numbers)

98
Q

Which transcription factor brings RNA Pol 2 with it?

A

TFIIF

99
Q

When are forward and reverse primers used?

A

In PCR (Polymerase Chain Reaction)

Molecular Biology (4 decks)

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