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Biochem > Lecture 7- DNA/RNA/Protein > Flashcards

Lecture 7- DNA/RNA/Protein Flashcards

1
Q

What encompasses the “Central Dogma?”

A

The path from DNA being converted to a protein (Transcription and translation)

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2
Q

How are the individual deoxyribonucleotides of DNA held together? (type of bond and where bonded)

A

Covalent phosphodiester bond from 3’–>5’

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3
Q

What can cleave DNA?

A

deoxyribonuclease

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4
Q

What can cleave RNA?

A

ribonuclease

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5
Q

How are ribonucleotides linked in RNA? (type and where on structure)

A

covalent phosphodiester bonds from 3’–>5’

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6
Q

What type of backbone does DNA have?

A

sugar-phosphate backbone

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7
Q

What are the two grooves in DNA?

A

Major and minor groove

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8
Q

What binds to the major groove and minor groove?

A

Major- Regulatory proteins

Minor- Drugs

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9
Q

Number of bonds between A-T and G-C?

A

A-T 2 bonds

G-C 3 bonds

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10
Q

What type of bonds hold together the two strands of DNA?

A

hydrogen bonds

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11
Q

melting temperature Tm defines what?

A

The temperature at which half of the helical structure is lost

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12
Q

What is the loss of helical structure called?

A

denaturation

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13
Q

Which DNA structure has a higher Tm, one with many ATs or GCs?

A

The one with GCs.

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14
Q

What are the 3 forms of DNA and which one do we care about?

A

A, B and Z-DNA

We are about B-DNA (right handed helix)

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15
Q

Where is closed circular DNA found in eukaryotes?

A

mitochondria

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16
Q

In eukaryotes, what types of proteins are associated with the long linear dsDNA?

A

histone and non-histone proteins

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17
Q

In prokaryotes, (typically) is the DNA linear/circular, single/double stranded, and what type of proteins are associated with it?

A

circular
double
non-histone proteins

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18
Q

in prokaryotes, in association with the circular chromosome, what other genetic factor resides?

A

plasmids- small circular extrachromosomal DNA

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19
Q

Why are plasmids so important in bacteria?

A

They may carry genes that convey antibiotic resistance

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20
Q

What is meant when it is said that DNA replication is “semiconservative?”

A

Each daughter DNA contains one strand from the parent DNA and one newly synthesized daughter strand

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21
Q

What are the steps in Prokaryotic DNA synthesis?

A
  1. separation of 2 complimentary strands
  2. formation of the replication fork
  3. Direction of DNA replication
  4. RNA primer5. Chain elongation
  5. Excision of RNA primers and replacement by DNA
  6. DNA ligase
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22
Q

Prokaryotes: Where does separation begin of the two complimentary strands, and what characteristics does it have?

A

Origin of replication
This “consensus sequence” has almost exclusively AT base pairs that facilitate melting (AT bonds = less bonds to break than GC)

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23
Q

T/F: Eukaryotes have a single site of origin of replication.

A

False; they have many for rapid replication

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24
Q

Prokaryotes: What does DNA-A protein do?

A

binds to the origin and causes the AT rich regions to melt

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25
Q

Prokaryotes: What protein binds to the origin and causes the AT rich regions to melt?

A

DNA-A protein

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26
Q

Prokaryotes: What unwinds the double helix?

A

DNA helicases

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27
Q

Prokaryotes: What does DNA helicase do?

A

unwinds the double helix of DNA

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28
Q

Prokaryotes: What keeps the strands of DNA apart and protects the DNA from nucleases that degrade ssDNA?

A

ssDNA-binding proteins

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29
Q

Prokaryotes: What do ssDNA-binding proteins do?

A

keeps the strands of DNA apart and protects the DNA from nucleases that degrade ssDNA

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30
Q

Prokaryotes: What cuts and rejoins one strand of double helix to remove supercoils?

A

Topoisomerase I

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31
Q

Prokaryotes: What does Topoisomerase I do?

A

cuts and rejoins one strand of double helix to remove supercoils

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32
Q

Prokaryotes: What cuts and rejoins both strands of DNA?

A

Topoisomerase II

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33
Q

What does DNA gyrase do?

A

cuts and rejoins both strands of DNA

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34
Q

What direction do DNA polymerases read the parental strand?

A

3’–>5’ direction

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35
Q

Which direction does DNA synthesis occur?

A

5’–>3’ direction

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36
Q

Leading/Lagging strand

A

Leading strand- in direction of replication fork (continuous)
Lagging- opposite direction of fork (discontinuous)

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37
Q

One segment of DNA on the lagging strand not yet connected is called…?

A

Okazaki fragment

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38
Q

What do DNA polymerases require, and what is needed in their chemical structure?

A

RNA primer.

need a free OH on the 3’ end

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39
Q

What enzyme makes RNA primers?

A

primase

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40
Q

T/F: RNA primers are needed for both DNA and RNA polymerases.

A

False; only needed for DNA polymerases

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41
Q

Prokaryotes: What enzyme catalyzes elongation, and how does it bind to the template?

A

DNA polymerase III

bound by its b-subunit

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42
Q

Prokaryotes: describe DNA pol III and proofreading

A

DNA pol III has 3’->5’ EXONUCLEASE activity to correct mismatch bases (can come back)

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43
Q

What happens when DNA pol III gets to the end of the segment? (blocked by an RNA primer)

A

RNA (from the RNA primer) is then excised and the gap is filled by DNA pol I

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44
Q

What does DNA ligase do, specifically?

A

makes the phosphodiester linkage between the 5’-phosphate on the DNA chain synthesized by DNA pol III and the 3’-OH on the chain made by DNA pol I

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45
Q

In eukaryotic DNA replication, what removes RNA primers?

A

RNase (rather than DNA polymerase)

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46
Q

What are the steps of the cell cycle?

A 
M (Mitosis)
G0 (enters into G1)
G1 (can go to G0)
S (DNA synthesis)
G2
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47
Q

What happens in G1 phase?

A

Cell prepares to initiate DNA synthesis

Biosynthesis occurs

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48
Q

What happens in S phase?

A

DNA is replicated (DNA content doubled)

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49
Q

What happens in G2 phase?

A

Biosynthesis for mitosis occurs

preparation

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50
Q

What happens in G0 phase?

A

Cells stop dividing

  • but can enter back into G1 phase later on
    ex: Brian and heart cells
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51
Q

Polymerase a (alpha) function

A

Contains primase

Initiates DNA synthesis

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52
Q

Polymerase b (beta) function

A

Repair

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53
Q

Polymerase y (gamma)

A

Replicates mitochondrial DNA

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54
Q

Polymerase δ (delta)

A

Elongates Okazaki fragments of the lagging strand

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55
Q

Polymerase ε (epsilon)

A

Elongates the leading strand

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56
Q

What are telomeres and what is their function?

A

Complexes of noncoding DnA plus proteins located at the ends of linear chromosomes

  • Maintain structural integrity of the chromosome, preventing attack by nucleases
  • Allow repair enzymes to distinguish between a true end from a break in dsDNA
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57
Q

Describe the physical structure of telomeres

A

Consist of several thousand tandem repeats of noncoding AGGGTT base paired with a complementary region of Cs and As
-The GT strand is longer than its complement, leaving a few hundred nucleotides in length at the 3’ end
(If it is not there, it means the DNA is broken)

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58
Q

In somatic cells, what happens to telomeres upon each successive division?

A

They are shortened

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59
Q

What happens once telomeres are shortened beyond a critical length?

A

The cell is no longer able to divide and is said to be SENESCENT

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60
Q

What is unique about stem cells and cancer cells in respect to telomeres?

A

They have the enzyme TELOMERASE which maintains telomeric length (can divide forever)

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61
Q

What is reverse transcriptase?

A

The enzyme that synthesizes DNA from RNA

62
Q

Where do we typically see reverse transcriptase (association)?

A

With RNA viruses

63
Q

Describe the organization of eukaryotic DNA

A

Eukaryotic DNA is associated with tightly bound basic proteins called histones
The histones order the DNA structural units called nucleosomes
Nucleosomes are further arranged into chromosomes

64
Q

What are histones primarily made from?

A

Basic amino acids

Lysine and Arginine mostly

65
Q

What are nucleosomes? (and structure)

A

A structural component of DNA composed of (H2A, H2B, H3, H4)2

66
Q

What are the different types of histones?

A

H2A, H2B, H3, H4, H1

67
Q

Which histone protein is the linker, and not associated with the nucleosome core?

A

H1

68
Q

What are the 4 steps in eukaryotic DNA structural organization

A
  1. Naked DNA
  2. Nucleosome “bead” (histones + DNA)
  3. Nucleofilament (30 nm fiber)
  4. Nucleofilament is coiled and anchored to scaffold protein
69
Q

What are the 5 types of DNA damage?

A
  1. hydrolysis
  2. oxidation
  3. methylation
  4. UV light
  5. Ionizing radiation
70
Q

What does Hydrolysis of DNA lead to (examples)?

A

Leads to deamination of:

  • Cytosine to Uracil
  • Adenine to Hypoxanthine
  • Guanine to Xanthine
71
Q

What happens when DNA is oxidized?

A

Leads to the formation of

  • 8-hydroxyguanine from Guanine
  • 5-hydroxymethyluracil from Thymine
72
Q

What happens when DNA is methylated?

A

Leads to the formation of

  • N7-methyl dG (guanine)
  • N3-methyl dA (adenine)
73
Q

What happens to DNA in the presence of UV light?

A

Pyrimidine dimers form

thymidine in particular

74
Q

What happens to DNA in the presence of ionizing radiation?

A
  • damages DNA directly

- strand breaks

75
Q

What are the 3 types of DNA repair?

A
  1. Base Excision Repair (BER)
  2. Nucleotide Excision Repair (NER)
  3. Mismatch Repair
76
Q

Describe base excision repair

A

removes and replaces individual damaged bases

77
Q

Describe nucleotide excision repair

A
  • removes and replaces damaged BULKY lesions (2-30 nucleotides)
  • recognize physical distortion rather than specific base sequences
78
Q

Describe mismatch repair

A

removes nucleotides that do not form correct base pairs

79
Q

DNA repair diseases, and describe them

A
  1. Xeroderma Pigmentosum
    - pyrimidine dimers formed in skin cells exposed to UV light
    - defects in excision repair due to a mutant UV-specific endonuclease
  2. Ataxia Telangiectasia
    - defects in excision repair
    - neurodegenerative disease
    - poor coordination
80
Q

What are the species of ribosomal RNA in eukaryotes?

A 
5S
5.8S
18S
28S
(comprise about 80% of RNA in cell)
81
Q

What are the units for ribosomal RNA?

A

Svedberg

82
Q

What are the species of ribosomal RNA in prokaryotes?

A

5S
16S
23S

83
Q

What is the smallest type of RNA?

A

Transfer RNA (4S)

84
Q

How many different types of tRNA are there?

A

At least one for each of the 20 amino acids

85
Q

What is the function of tRNA?

A

carries its amino acid on the 3’ end to the site of protein synthesis
(comprises about 15% of RNA in the cell)

86
Q

What is the function of mRNA?

A

To carry genetic information from the nucleus to the cytosol, where it is used as a template for DNA synthesis

87
Q

Notes on the structure of mRNA

A
  • has a poly A tail on the 3’ end

- has a 5’ cap consisting of a 7-methylguanosine attached via triphosphate linkage

88
Q

How many species of RNA polymerase does it take to synthesize RNA in prokaryotes?

A

One species

-One synthesizes all of the RNA (except for the short RNA primers needed for DNA replication)

89
Q

What is, and what does RNA polymerase do?

A

A multisubunit enzyme that recognizes a nucleotide sequence (promoter) at the beginning of the length of DNA to be transcribed

90
Q

What is the sense strand?

A

The DNA strand with the same sequence as the mRNA

91
Q

What is the antisense strand?

A

The DNA strand that is being transcribed into mRNA (the copy)

92
Q

What direction does transcription occur?

A

5’ –> 3’

93
Q

What is the first step in transcription (prokaryotes)

A

begins with the binding of RNA polymerase to the promoter region (which is not transcribed)
(promoter contains characteristic consensus sequences)

94
Q

Are promoter sequences upstream or downstream from the start of transcription? and what is an example? (prokaryotes)

A

Upstream

-Pribnow box

95
Q

Does RNA polymerase require a primer?

A

NO

96
Q

Which DNA strand does RNA polymerase transcribe?

A

anti-sense strand

97
Q

Where does transcription terminate in prokaryotes?

A

at the site of a hairpin loop, followed by a string of Us

98
Q

T/F: Transcription in Eukaryotes requires a single polymerase.

A

False:

separate polymerases are used in the synthesis of rRNA, tRNA and mRNA

99
Q

Where do Transcription Factors (TFs) bind to?

A

Bind to either:

  • within the core promoter region
  • proximally (close to it)
  • distally (some distance away)
100
Q

T/F: Each eukaryotic RNA polymerase has its own promoters and TFs.

A

True

101
Q

What is the active form of transcribed genes?

A

relaxed chromatin called EUCHROMATIN

102
Q

What is the inactive form of gene segments?

A

condensed chromatin called HETEROCHROMATIN

103
Q

What is the term used for interconversion between euchromatin and heterochromatin?

A

chromatin remodeling

104
Q

What is a major mechanism of chromatin remodeling?

A

acetylation of lysine residues

105
Q

What enzyme catalyzes the acetylation of lysine residues?

A

Histone acetyltransferases

106
Q

What enzyme catalyzes the deacetylation of lysine residues?

A

Histone deacetylases

107
Q

What types of groups does histone acetylation block? +/-

A

histone acetylation blocks positive (+) groups

108
Q

What does RNA polymerase I do?

A

Synthesizes the precursor of the 5.8S, 18S and 28S rRNA in the nucleolus

109
Q

What does RNA polymerase II do?

A

Synthesizes mRNA

110
Q

What does RNA polymerase III do?

A

Synthesizes tRNA and 5S rRNA

111
Q

What transcribes RNA from all mitochondrial genes?

A

Mitochondrial RNA polymerase

112
Q

Describe RNA processing in prokaryotes vs eukaryotes

A 
Prokaryotes
-RNA is used as unaltered primary transcript as soon as it is made (no processing)
Eukaryotes
-capping at 5' end
-addition of poly A tail at 3' end
-removal of introns
113
Q

What is the 5’ cap, and what is its function?

A

7-methylguanosine at the 5’ end to the 5’ribose via a triphosphate linkage
-it protects the 5’end from exonucleases and promotes mRNA translation by ribosomes

114
Q

What is the poly A tail comprised of?

A

40 to 200 adenine nucleotides attached to the 3’ end

115
Q

When is the poly A tail added?

A

after transcription

116
Q

What enzyme catalyzes the reaction of the addition of the poly A tail?

A

Polyadenylate polymerase

117
Q

What are the functions of the poly A tail?

A

-Helps stabilize the mRNA
-Facilitates mRNA exit from the nucleus and aid in translation
(gradually shortened after entering the cytosol; no longer needed)

118
Q

In RNA processing, which segments are removed? How is this done?

A

introns

-via RNA splicing (introns cut out of the primary transcript and exons are linked together to form functional product)

119
Q

Where does transcription happen?

A

nucleus

120
Q

Where does translation happen?

A

cytosol

121
Q

Where is the anti-codon located?

A

on the tRNA

122
Q

What is the start codon and what does it code for?

A

AUG

Methionine

123
Q

What are the stop codons?

A

UAG
UGA
UAA

124
Q

What are the two forms of substitution? describe them

A

Transition- replace purine with purine or pyrimidine with pyrimidine
Transversion- replace purine with pyrimidine or vice versa

125
Q

What do insertions or deletions lead to (regarding genetic code)?

A

frameshift mutations

126
Q

What are the 3 different types of point mutations, and what do they do?

A

Silent mutation- base change still codes for same AA
Missense- now codes for different AA
Nonsense- now codes for a stop codon (terminal codon)

127
Q

What is the organelle where protein synthesis occurs?

A

Ribosomes

128
Q

What transfers amino acids?

A

tRNA

129
Q

What catalyzes the attachment of AA to tRNA?

A

Aminoacyl-tRNA synthetases

130
Q

What is the template for protein synthesis?

A

mRNA

131
Q

If no ends are labeled when looking at a genetic code, what is assumed?

A

that it is being read left to right 5’ –> 3’

132
Q

Where is the attachment site on the tRNA and which part of the AA binds to which part of the tRNA?

A

The attachment site is at the tRNA 3’ end

The carboxylic group of AA binds to the OH of ribose at 3’ end of tRNA

133
Q

When a tRNA has a covalently attached AA; the tRNA is ___? and the AA is ___?

A

the tRNA is CHARGED

the AA is ACTIVATED

134
Q

What would you read on the tRNA when the start codon is present?

A

the tRNA would read 3’->5’ UAC (anticodon), because the start codon AUG would be read on the mRNA from 5’ -> 3’

135
Q

What is the prokaryotic ribosome and its subunits?

A

70S
Large subunit- 50S
Small subunit- 30S

136
Q

What is the eukaryotic ribosome and its subunits?

A

80S
Large subunit- 60S
Small subunit- 40S

137
Q

What does the small ribosomal subunit do?

A

binds mRNA and is responsible for the accuracy of translation by ensuring correct base pairing between teh codon and anticodon

138
Q

What does the large ribosomal subunit do?

A

catalyzes peptide bond formation

139
Q

Wobble hypothesis

A

States that tRNAs can recognize more than one codon for a specific AA.
-First base of the anticodon (5’ end) or (3rd of codon; auG) can code for the same AA with different bases

140
Q

First initial steps of protein synthesis

A

Recognition of AUG start codon
-A special initiator tRNA recognizes AUG (eukaryotes)
-Initiator tRNA enters P site on small subunit of ribosome carrying methionine
-A site is empty
Large ribosomal subunit then joins the complex

141
Q

What are the sites in the ribosomal complex?

A

E P A, mRNA is moving from right to left so “E” is the exit site

142
Q

During elongation of protein synthesis, which end do new AAs bind to, and what enzyme catalyzes the rxn?

A

New AAs bind to the carboxyl end of the growing chain

Catalyzed by Peptidyltransferase

143
Q

Process of protein degradation?

A

Defective proteins are attached by a chain of small proteins, UBIQUITIN
Then degraded by the PROTEASOME in the cytosol
(degraded by proteasome after being ubiquitinated)

144
Q

What does gel electrophoresis measure?

A

separates macromolecules based on size and charge

145
Q

What does Western blotting measure?

A

Detects PROTEINS

146
Q

What does Southern blotting measure?

A

detects DNA

147
Q

What does Northern blotting measure?

A

detects RNA

148
Q

What does PCR stand for and do?

A

Polymerase Chain Reaction

-amplifies small samples of DNA

149
Q

What does High Performance Liquid Chromatography (HPLC) do?

A

separates the components of a mixture via a column

150
Q

What does X-ray Crystallography and Nuclear Magnetic Resonance do?

A

determines 3D structure

151
Q

What are two methods used to determine an AA sequence?

A

Edman Degradation- method (label each AA and cleave off one at a time
Mass Spectrometry

Biochem (8 decks)

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