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Intro To molecular biology > Mid Term 1 reveiw > Flashcards

Mid Term 1 reveiw Flashcards

1
Q

What are the 4 nucleotide bases for dna

A

A T C G

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2
Q

What are the 3 building blocks of dna

A

Phosphate, Sugar, Base

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3
Q

What section of DNA is the 3’ end

A

the oxygen on the sugar

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4
Q

WHat section of DNA is the 5’ end

A

THe phosphate group

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5
Q

WHat are the 2 categories of Nucleotides

A

Pyrimidines and Purines

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6
Q

What nucleotide bases are Purines

A

A G

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7
Q

WHat nucleotide bases are Pyrimidines

A

C T

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8
Q

What type of bonds hold together Nucleotide subunits

A

Phosphodiester Bonds

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9
Q

What way does DNA strand Run

A

5’ to 3’

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10
Q

What Type of bonds are nucleotides bonded by

A

Covalent bonds

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11
Q

What gives rise to DNA Polarity

A

3’-hydroxyl
group (-OH) of one sugar and the 5’ phosphate group

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12
Q

How many Hydrogen bonds connect A T

A

2

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13
Q

How many Hydrogen bonds hold together C G

A

3

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14
Q

What % of a typical chromosome does Heterochromatin make up

A

40

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15
Q

What % of a typical chromosome does Euchromatin make up

A

60

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16
Q

When was the first genome draft complete

A

1999

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17
Q

When was the first genome sequence complete

A

2021

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18
Q

WHat percentage of the genone is protein-coding exons

A

less than 1 %

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19
Q

How many NT are required for an average size protein

A

1300

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20
Q

WHat is the average length of a human gene

A

26000

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21
Q

How many possible reading frames are there

A

3

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22
Q

WHat is the length of a Open reading frame

A

less than 10,000 codons that lack stop codon

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23
Q

What is a SNP

A

Single-nucleotide polymorphisms

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24
Q

WHat is the chance of a SNP

A

single-base changes that are present in at
least 1% of the populations

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25
Q

Which base pairs with adenine in DNA?

A

C) Thymine

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26
Q

What is the basic unit of eukaryotic chromosome structure?

A

Nucleosome

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27
Q

In which phase of the cell cycle is chromatin least condensed?

A

Interphase

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28
Q

How many chromosomes do humans typically have?

A

46

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29
Q

Which method of DNA sequencing involves enzymatic extension with dideoxynucleotides?

A

Sanger method

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30
Q

Which region of chromatin is more condensed and contains silenced genes?

A

Heterochromatin

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31
Q

What is the flow of genetic information according to the central dogma of molecular biology?

A

DNA → RNA → Protein

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32
Q

What proteins help package DNA into chromosomes?

A

Histones

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33
Q

In what phase is chromatin most condensed

A

Metaphase

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34
Q

The human genome contains approximately how many protein-coding genes

A

20,000

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35
Q

DNA replication is said to be:

A

Semiconservative

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36
Q

What enzyme unwinds the DNA double helix during replication?

A

Helicase

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37
Q

When does DNA Replication occur

A

occur before a cell can
divide

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38
Q

What phase in dna replicated

A

synthesis phase

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39
Q

How was semiconservative dna found

A

using heavy and light Nitrogen. Heavy sank, and light floated. DNa with both sat in the middle. TRANSFERED TO LIGHT MEDIUM

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40
Q

WHat 2 methods can open DNA double helix

A

thermal energy or initiator protein

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41
Q

Where does DNA synthesis occur

A

y shaped junction called the Replication fork

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42
Q

How many replication Forks are there

A

2

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43
Q

What is it called when replication works in 2 directions

A

bidirectional replication

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44
Q

What are the rates of dna replication

A

1,000 nt/s bacteria 100 nt/s humans

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45
Q

What direction does DNA polymerase Function

A

5 to 3

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46
Q

What is the purpose of DNA polymerase

A

catalyzes the formation of phosphodiester bond. Addition of nucleotides

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47
Q

How often does DNA polymerase make errors

A

1 error in 107
nucleotide pairs it copies

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48
Q

How is the Nucleotide error from DNA Polymerase fixed

A

Fixed by proof reading

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49
Q

How many sites does DNA Polymerase contain

A

2
p: Polymeration
E: editing( Proof Reading)

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50
Q

What is the Aprox length of the RNA primer needed for DNA Polymerase

A

10 nt

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51
Q

How can DNA SYnthesis from the lagging strand be desribed as

A

discontinuous DNA synthesis

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52
Q

WHat is Nuclease

A

degrades RNA primer

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53
Q

What is repair polymerase

A

proofreading activity
replaces RNA primer
with DNA

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54
Q

What is DNA ligase

A

joins the 5’-phosphate end of one DNA fragment
to the adjacent 3’-hydroxyl end of the next
joins together Okazaki fragments on the lagging
strand during DNA synthesis

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55
Q

What is DNA helicase

A

ATP dependent
unwinding of the parent DNA double helix

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56
Q

What is Single-strand DNA binding proteins

A

latch onto ssDNA
* prevent reforming of double helix and
keeping them in elongated form

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57
Q

What is the Sliding Clamp

A

keeps
DNA pol
attached to
DNA template

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58
Q

What is the clamp loader

A

locks sliding
clamp around
newly formed
DNA double helix
* ATP dependent

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59
Q

What causes DNA ahead of thr replication fork to get wounded more tightly

A

helicase moves forward

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60
Q

What is DNA Topoisomerases

A

enzymes that relieve the tension that builds
up in front of a replication fork
produce a transient, single-stranded break
in the DNA backbone, which releases the
build-up tension
* reseals the nick before falling off the DNA

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61
Q

What is a Telomeres

A

long, repetitive nucleotide sequences
present at the ends of every chromosome
provide replication machinery with “extra”
DNA to complete the lagging strand

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62
Q

What is Telomerase

A

carries its own RNA template
* uses the RNA primer to add multiple copies
of the same repetitive DNA sequence to the
lagging-strand template

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63
Q

What is xeroderma pigmentosum

A

cannot mend the damage done to DNA by
UV radiation
* inherit defective gene for one of the proteins
involved in the DNA repair

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64
Q

What are the three types of major chemical changes in DNA

A

depurination
deamination
thymine dimer

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65
Q

What is Depurination

A
  • does not break the phosphodiester backbone
  • removes purine bases from a nucleotide
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66
Q

What is the causes of lesions in DNA

A

Depurination

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67
Q

What is Deamination

A
  • conversion of cytosine to uraci
    spontaneous loss of an amino group
    does not break the phosphodiester backbone
    NH2 converts to O
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68
Q

What is a Thymine Dimers

A

covalent linkages between two adjacent
pyrimidine bases
produce permanent mutations

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69
Q

When Deamination occurs, how do the new strands of dna differ

A

1 strand will have “A” where C is ment to be
2 strand will not be mutated

70
Q

When Depurination occurs, how do the new strands of dna differ

A

1 strand will be shorted due to the loss of A or G
2nd Strand will be normal

71
Q

What is Step 1 in the basic pathway for repairing damaged dna

A

DNA damage is recognized
and removed by a variety of
nucleases. small gap is one strand of dna

72
Q

What is Step 2 in the basic pathway for repairing damaged dna

A

a repair DNA polymerase binds
to the 3’-OH end of the cut
DNA strand
enzyme fills the gap
by making a complementary
copy

73
Q

What is Step 3 in the basic pathway for repairing damaged dna

A

DNA ligase seals the break
left in the sugar-phosphate
backbone

74
Q

What will happened if errors during
replication are not corrected?

A

uncorrected errors will lead to permanent
mutation

75
Q

How does the mismatch pepair system work

A

rely on the genetic redundancy build into
every DNA double helix
* nucleotide damage on one strand can
be repaired using the information in the
complementary strand

76
Q

What can cause double-stranded DNA breaks

A

radiation
* mishaps at the replication fork
* various chemical assaults

77
Q

What can happen when there is a double-stranded DNA breaks

A

can lead to
* fragmentation of chromosomes
* loss of genes

78
Q

How can double-stranded DNA breaks be repaired

A

nonhomologous end joining
homologous recombination

79
Q

What is nonhomologous end joining

A

quickly stick the broken ends together
carried out by specialized group of enzymes
* nucleases
* DNA ligases
breaks are rapidly sealed, but nucleotides
are often lost at the site of repair

80
Q

What is homologous recombination

A

error-free strategy for repairing double-strand
breaks

81
Q

When does homologous recombination occur

A

shortly after DNA has been replicated
* double-strand damaged DNA
* undamaged dsDNA template

82
Q

What is the first step of Homologous recombination

A

often occurs when
duplicated helices
are still physically
close to each other
recombination specific
nuclease
* specialized enzymes
* recA bacteria
* rad52 eukaryotes

83
Q

What is the Second step of Homologous recombination

A

once an extensive,
accurate match is
made, the invading
strand is elongated
uses complementary
undamaged strand
as a template
complementary
base-pairing within
damaged duplex

84
Q

What is the Third step of Homologous recombination

A

repair is then completed
by additional DNA
synthesis at the
3’ ends of both strands
of the broken double
helix
the net result is two
intact DNA helices
genetic info from one
helix was used to
repair the other

85
Q

What is the result of Failure to repair DNA damage

A

allow mutations to arise
in protein coding genes particular position
within DNA sequence

86
Q

What is the first step of Nucleotide excision repair

A

UvrB and C endonucleases
nick the strand containing
the dimer
damaged fragment is
released from DNA

87
Q

What is the second step of Nucleotide excision repair

A

damaged fragment is
released from DNA
DNA polymerase fills
the gap with new DNA
DNA ligase seals the
repaired strand

88
Q

What is a Pyrimidine dimers

A

molecular lesions induced by UV radiation

89
Q

What are the 2 common Pyrimidine dimers

A

cyclobutene
pyrimidine dimer
(CPDs)
* 6-4 photoproduct

90
Q

what are the 4 Ribonucleic Acid

91
Q

How many Hydrogen Bonds occur between A and U

92
Q

How many strands is RNA

A

single-stranded

93
Q

What is RNA conventional base pairs

A

When RNA has folded shape, A and U or C and G line up when folded

94
Q

What is RNA nonconventional base pairs

A

When RNA has folded shape, A and C/G or U and G/C line up when folded

95
Q

What 3 roles can RNA have

A

structural,
regulatory, or catalytic roles

96
Q

What is a gene

A

a segment of DNA that directs the production
of a particular protein or functional RNA
molecule

97
Q

What strand of DNA does RNA come from

A

Coding strand of DNA

98
Q

What is RNA polymerase

A

catalyzes
formation of
phosphodiester
bond
* moves stepwise
along the DNA

99
Q

What direction does RNA polymerase work

A

5’-to-3’ direction

100
Q

What is the difference between DNA and RNA Polymerase

A

can start an RNA chain without a primer
does not accurately proofread its work
* makes about 1 mistake in every 10,000nt
minor consequences of mistakes
in RNA transcript for a cell

101
Q

What is messenger RNA (mRNA)

A

RNA molecules that ultimately direct
synthesis of proteins

102
Q

What is ribosomal RNAs (rRNAs)

A
  • form the structural and catalytic core
    of the ribosome
103
Q

What is transfer RNAs (tRNAs)

A

serve as adaptors between mRNA and
aa during protein synthesis

104
Q

What is microRNAs (miRNAs)

A

regulate gene expression

105
Q

What is small interfering RNAs (siRNAs)

A

provide protection from viruses and
proliferating transposable elements

106
Q

What is long noncoding RNAs (lncRNAs)

A

act as scaffolds and serve other diverse
functions, many of which are still being
discovered

107
Q

How does Transcription initiation in bacteria occur

A

RNA polymerase recognizes specific nucleotide
sequence which lies immediately upstream
of the transcription start site, a gene region
called a promoter

108
Q

What is a sigma factor

A

RNA polymerase contains a subunit
called sigma factor – recognizes the promoter

109
Q

How is the double helix opened in transcription

A

RNA polymerase opens up the DNA double helix
immediately in front of the promoter

110
Q

What happens to the Sigma factor when Rna synthesis starts

A

Sigma factor is reduced

111
Q

What type of dna contains promotor and terminator

A

bacteria dna

112
Q

How many DNA Polymerases are used for eukaryotic cells

113
Q

What is RNA polymerase I

A

Most rRNA genes

114
Q

What is RNA polymerase II

A

All proteins-coding genes, miRNA genes, plus genes for other noncoding RNAs
mRNA

115
Q

What is RNA Polymerase III

A

tRNA, 5S rRNA,

116
Q

What RNA polymerase is used to make mRNA

A

RNA polymerase 2

117
Q

What does eukaryotic RNA polymerases require the
assistance of

A

general transcription factors

118
Q

What is a Elongation factors

A

allow the RNA pol II to move through DNA
that is packed into nucleosomes

119
Q

What is located at the -35 of a Eukaryotic promoters contain
sequences

120
Q

What is located at the -30 of a Eukaryotic promoters contain
sequences

121
Q

What is located at the transcription start site of a Eukaryotic promoters contain
sequences

122
Q

What is located at the +30 of a Eukaryotic promoters contain
sequences

123
Q

Where in the cell is a Eukaryotic mRNAs are processed

A

in the nucleus
* capping, splicing, and polyadenylation
* carried out by enzymes bound to
phosphorylated tail of RNA pol II

124
Q

What is RNA capping

A
  • modifies the 5’ end
    of the RNA transcript
    introduces atypical nt
    methyl-guanine
125
Q

What is polyadenylation

A

special structure
at the 3’ end
* series of repeated
adenines

126
Q

What is the purpose of Capping and polyadenylation of
eukaryotic mRNA

A

increase the stability of the mRNA molecule
facilitate export from the nucleus to the
cytosol
* mark the RNA molecule as mRNA

127
Q

What is an intron

A

non coding sequence of nucleotides

128
Q

How are Introns removed from Pre RNA

A

RNA splicing

129
Q

When does RNA Splicing occur

A

after capping and as the RNA pol II continues
to transcribe the gene, RNA splicing begins

130
Q

In what form are Introns cut out by the splicing machine

A

lariat” structure
this structure is
produced when an
adenine nucleotide
within the intron reacts
with the beginning of
the intron

131
Q

What is required at each RNA splicing reaction

A

5 snRNPs and about 200 additional
proteins

132
Q

What is the function of the U1 protein in RNA splicing

A

U1 recognized 5’
splice site

133
Q

What is the function of the U2 protein in RNA splicing

A

U2 recognizes the
lariat branch-point site

134
Q

What is the function of the U1 protein in RNA splicing

A

U6 rereads the 5’ splice
site by displacing U1

135
Q

What is a spliceosome

A

arge assembly of RNA and protein
molecules that carry out splicing in
the nucleus

136
Q

What protein partners do export ready mRNA molecule require

A

cap-binding protein
* poly-A binding protein
* exon junction complex

137
Q

Where does mRNA molecules become degraded

A

becomes degraded in the cytosol by the ribonucleus

138
Q

how many different types of amino acids are there

139
Q

how many different triplets possibilities are there

140
Q

What is the start codon

141
Q

how many stop codons are there

A

3
UAA
UAG
UGA

142
Q

What acts as intermediaries
between the codons of mRNA and aa

143
Q

What is the shape of tRNA

A

a cloverleaf

144
Q

What is tRNA

A
  • ~ 80nt long
  • 4 short segments form
    double helical structures
  • each region plays
    important function
  • anticodon region
  • aa binding region (3’-end)
145
Q

What is a anticodon

A

form by a set of three consecutive nt
that bind, through base-pairing, to the
complementary codon in an mRNA
molecule

146
Q

What is aminoacyl-tRNA synthetase

A

enzyme that recognizes and attaches the correct Amino acid to tRNA
Needs ATP

147
Q

What are the 2 sub units of a ribosome

A

one large subunit
* one small subunit

148
Q

What makes up the weight of a ribosome

A

2/3 RNA
* 1/3 protein

149
Q

What is the function of a small ribosomal subunit

A

matches the tRNA to the codon of the mRNA

150
Q

What is the function of a large ribosomal subunit

A

atalyzes the formation of the peptide bonds
that covalently link the aa together into
a polypeptide chain

151
Q

What are the 3 binding sites of a ribosome

A

A site - aminoacyl-tRNA
* P site - peptidyl-tRNA
* E site - exit

152
Q

What are the 4 steps of translation

A

1 a charged tRNA enters
at the A site by base-
pairing with the
complementary codon
on the mRNA molecule
2 C-term of the polypeptide
chain is uncoupled from
the tRNA at the P site and
joined to the free aa
linked to tRNA in A site
3 large ribosomal subunit
shifts relative to small subunit
* moves the two bound tRNAs
* P site → E site
* A site → P site
4 small ribosomal subunit moves
exactly three nt along the mRNA
* ejects the spent tRNA
* resets the A site for new
incoming charged tRNA

153
Q

At what rate do eukaryotic ribosome add amino acids

A

adds about 6 amino acids to
a polypeptide chain each second

154
Q

At what rate do bacterial ribosome add amino acids

A

adds about 20 amino acids to
a polypeptide chain each second

155
Q

What is the first step in Initiation of protein synthesis

A

initiator tRNA binds tightly
to the P site on the small
ribosomal subunit
the small ribosomal subunit
scans the mRNA until it
encounters the first AUG

156
Q

What is the second step in Initiation of protein synthesis

A

binding of large ribosomal
subunit and completion of
ribosomal assembly

157
Q

What is the Third step in Initiation of protein synthesis

A

tRNA binds to the A site, the first peptide bond is formed.

158
Q

What binds to the stop codon in the ribosome

A

release factors

159
Q

What happens when a release factor binds to a stop codon

A

alters
the activity of peptidyl
transferase in the ribosome

160
Q

How far away can ribosomes be on a mrn strand

A

ribosomes may be as
close as 80nt apart

161
Q

What is the function of an antibiotic

A

inhibitors of prokaryotic protein synthesis

162
Q

WHat is Tetracycline

A

Blocks binding of aminoacly-tRNA site of Ribosomes

163
Q

What is Streptomycin

A

prevents the transition from initiation complex to chain elongation

164
Q

What is Chloramphenicol

A

Blocks the peptidyl transferase reaction on ribosomes

165
Q

What is Erythromycin

A

Binds in the exit channel of the ribosome and inhibits elongation of the peptide chain

166
Q

What is Rifamycin

A

Block initiation of Transcription by binding to and inhibiting RNA Polymerase

167
Q

What is proteases

A

enzymes responsible for degrading proteins
hydrolyze the peptide bond between aa

168
Q

What is proteosomes

A

large protein machines responsible for
breaking down proteins
in eukaryotes, proteins marked for destruction
are modified by small protein – ubiquitin

169
Q

What is post-translational modification

A

covalent modification
* more than 100 types
* most common:
* phosphorylation
and glycosylation

Intro To molecular biology (2 decks)

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