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Exam 3 Flashcards

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1
Q

Building blocks / monomers to nucleic acid polymers

A

Nucleotides

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2
Q
  • Outer portion of DNA/RNA backbone
  • Gives DNA overall negative charge
A

Phosphate

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3
Q

Pentose sugars

A

DNA & RNA

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4
Q

Nitrogenous base structure

A

Nitrogen containing ring

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5
Q

Purine structure

A

Double ring

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6
Q

Purines include:

A

Adenine & Guanine

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7
Q

Pyrimidine structure

A

Single ring

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8
Q

Pyrimidines include:

A

Thymine, Uracil, Cytosine

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9
Q

Base attached to the ___ position

A

1’

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10
Q

Phosphate attaches to the ___ position

A

5’

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11
Q

Covalent linkage of nucleotides into a single strand

A

DNA strand

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12
Q

DNA strands have…

A
  • Linear linkage of individual nucleotides
  • Covalent phosphodiester bonds between oxygen and phosphorus
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13
Q

Each phosphate group in DNA is linked to the __ ‘ of one sugar and the __ ‘ of the other

A

5, 3

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14
Q

Strands of DNA always have a ___ to ___ orientation or a ___ to ___

A

5’ to 3’ or 3’ to 5’

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15
Q

5’ end of DNA strand contains ___ and the 3’ end contains a ____ group

A

A phosphate group, an -OH

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16
Q

2 DNA strands linked into an antiparallel orientation

A

Double helix

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17
Q

Double helix are formed by…

A

Two complementary strands of DNA

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18
Q

Double helix are held together by…

A

Hydrogen bonds between the bases

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19
Q

Base pairing rules

A

A - T
G - C

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20
Q

DNA strands have _____ orientation

A

antiparallel

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21
Q

One DNA strand runs from ___ to ___ and the other runs from __ to __

A

5’ to 3’
3’ to 5’

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22
Q

There are about ____ bases per turn in a DNA molecule

A

10-10.5

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23
Q

DNA and associated proteins for packaging and manipulation in nucleus

A

Chromatin

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24
Q

All of the genetic material in a cell including, nuclear/nucleoid chromosome, chloroplast, mitochondria or plasmids

A

Genome

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25
Q

Used as template for identical copies

A

DNA

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26
Q

Daughter strands generated by

A

Parent strands

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27
Q

Replication mechanism is

A

Semiconservative

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28
Q

Each new DNA strand contains

A

one parent strand and one daughter strand

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28
Q

Steps of DNA replication (general)

A
  • Separation of parent strand
  • Synthesis of complementary daughter strand
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29
Q

Separation of parent strand breaks ___

A

Hydrogen bonds

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30
Q

Synthesis of complementary daughter strands includes:

A
  • Base pairing
  • DNA polymerase and other enzymes
  • Differ between 5’ to 3’ strand and 3 to 5’ strand
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31
Q

Leading strand

A

5’ to 3’

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32
Q

Lagging strand

A

3’ to 5’

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33
Q

Designated start point for DNA replication within a chromosome

A

Origin of Replication

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34
Q

Bidirectional process

A

Proceeds in both direction from ori

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35
Q

Site of replication

A

Replication fork

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36
Q

Replication is complete after…

A

Replication forks move down molecule until they join with one another

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37
Q

Type of cell that has a single ori

A

Prokaryotes

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38
Q

Type of cell that can have hundreds of oris

A

Eukaryotes

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39
Q

Have less DNA - single circular chromosomes

A

Prokaryotes

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39
Q

More DNA - multiple linear chromosomes

A

Eukaryotes

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40
Q

Enzyme that breaks the hydrogen bonds between complementary bases - separates DNA strands

A

DNA helicase

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41
Q

Unwinding of helicase causes supercoiling and tension released by enzymes

A

DNA topoisomerase

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42
Q

Bind to exposed bases to prevent repairing between strands

A

Single - stranded binding proteins

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43
Q

Group of enzymes responsible for building complementary strand

A

DNA polymerase

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44
Q

DNA polymerase slides along parent strand and bonds to …

A

Deoxynucleoside triphosphate in daughter strands

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45
Q

Can DNA polymerase bind to a bare strand of DNA?

A

No

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46
Q

Enzyme that primes DNA at the ori with RNA sequence

A

DNA primase

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47
Q

DNA primase readies DNA template for…

A

Replication

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48
Q

DNA polymerase can only move in the ____ direction

A

5’ to 3’

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49
Q

DNA double helix is

A

antiparallel

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50
Q

In leading strand synthesis is …

A

continuous

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51
Q

In lagging strand synthesis is …

A

discontinuous

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52
Q

Lagging strand synthesized in

A

Okazaki fragments

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53
Q

Three types of DNA polymerase required in

A

I, II, III

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54
Q

DNA polymerase I function

A

lagging strand synthesis

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55
Q

DNA polymerase II function

A

proof-reading activity

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56
Q

DNA polymerase III function

A

leading and lagging strand synthesis

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57
Q

Fragments in lagging strand synthesis begin with …

A

short RNA primers

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58
Q

In lagging strand synthesis ____ are removed by DNA polymerase __

A

Primers, I

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59
Q

Resulting gaps filled in at ___ of next fragment in lagging strand synthesis

A

end

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60
Q

Fragments in lagging strand synthesis are linked ___ via ___

A

Covalently, DNA ligase

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61
Q

Function of DNA helicase

A

Separates double-stranded DNA into single strands

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62
Q

Function of single-strand binding protein

A

Binds to single-stranded DNA and prevents it from re-forming a double helix

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63
Q

Topoisomerase function

A

Removes tightened coil ahead of the replication fork

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64
Q

DNA primase function

A

Synthesizes short RNA primers

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65
Q

DNA polymerase function

A

Synthesizes DNA in leading and lagging strands, removes RNA primers, and fills in gaps

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66
Q

DNA ligase function

A

Covalently attaches adjacent Okazaki fragments in the lagging strand

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67
Q

T/F: Errors in DNA replication are common

A

F

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68
Q

How many mistakes are made per nucleotide ___ million nucleotides?

A

1/100

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69
Q

DNA replication enzyme that has proof-reading ability

A

DNA polymerase

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70
Q

Have circular chromosomes with no chromosome ends

A

Prokaryotes

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71
Q

Have multiple linear chromosomes

A

Eukaryotes

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72
Q

Short repeated sequences at the end of chromosomes are called

A

Telomeres

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73
Q

Telomeres found in

A

Non-coding regions of DNA: 5’ - GGGTTA - 3’

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74
Q

DNA polymerase cannot copy…

A

3’ tip of DNA molecule

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75
Q

Eukaryotic nuclear DNA is composed of

A

Multiple linear chromosomes

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76
Q

Each chromosome is composed of

A

one DNA double helix molecule

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77
Q

Humans are

A

Diploid with 23 pairs of chromosomes

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78
Q

How many total DNA molecules are there in the nucleus

A

46

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79
Q

DNA and associated packaging

A

Chromatin

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80
Q

Step I of Nuclear packaging

A

DNA wraps around histone, Histones aggregate into repeating structures called nucleosomes, linker regions between nucleosomes, H1 bound to linker region

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81
Q

Step II of nuclear packaging

A

Nucleosomes further condensed into a fiber, folds nucleosomes, 50x compaction

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82
Q

Step III

A

Radial loop domains contain 25,000-200,000 bp, anchored to the nuclear matrix, includes nuclear lamina - thin fibrous protein matrix connected to nuclear membrane

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83
Q

Regions of heterochromatin are

A

highly condensed

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84
Q

Areas of euchromatin are

A

in 30 nm fiber form

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85
Q

Euchromatin DNA is

A

expressed

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86
Q

Chromosomes undergo max compaction during

A

Cell division

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87
Q

Segments of DNA that code RNA or protein product

A

Genes

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88
Q

Gene function at trait level

A

Physical manifestation of gene

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89
Q

Gene function at the molecular level

A

DNA > RNA > Protein, Transcription and translation, Protein - encoding and protein non-coding RNAS (ncRNA)

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90
Q

Composed of multiple polypeptides encoded for by multiple genes

A

Protiens

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91
Q

Carries the code to an amino acid sequence

A

Messenger RNA (mRNA)

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92
Q

mRNA is translated into a

A

polypeptide via ribosome

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93
Q

One gene / one enzyme hypothesis

A

Protein encoding genes code for single polypeptide

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94
Q

Transcription results in

A

pre-mRNA that must be modified to become mature mRNA

95
Q

Out comes of transcription

A

Protein or ncRNA, DNA sequences copied into RNA sequences

96
Q

Transcription allows DNA to

A

be used multiple times

97
Q

At transcription level gene is defined as

A

Segment of DNA to be transcribed into RNA sequence

98
Q

Protein encoding genes transcribe

A

mRNA

99
Q

Provides a binding site for proteins that influence transcription

A

Regulatory sequence

100
Q

Upstream of transcribed regions that controls start of transcription

A

Promoter

101
Q

Carries the code for a sequence of amino acids in a polypeptide

A

Transcribed region

102
Q

Downstream of transcribed region and ends transcription

A

Terminator region

103
Q

Transcription process

A

Initiation, Elongation, Termination

104
Q

Promoters and terminators are transcribed by

A

RNA polymerase

105
Q

RNA polymerase 1 and 3 job

A

Synthesis of ncRNAs

106
Q

RNA 2 job

A

Synthesis of mRNAs, requires 5 transcription factors

107
Q

2 events of mRNA modification

A

Capping and tailing, Splicing

108
Q

Capping and tailing

A

Addition of 5’ cap and poly - A tail

109
Q

Removal of introns and linkage of exons

A

Splicing

110
Q

Introns, and exons

A

Non - coding sequences, coding sequences

111
Q
  • Transcript is covalently linked to modified form a guanine
  • Facilitates binding with cap binding proteins on ribosome
A

5’ cap

112
Q

100-200 bp repeats of adenine

A

Poly-A Tail

113
Q

Introns are

A

intervening regions, spliced out

114
Q

Exons are

A

Expressed and retained

115
Q

Small nuclear RNAs recognize intron-exon junctions

A

Spliceosomes

116
Q

Alternative splicing

A
  • Allow single gene to code for more than two polypeptides
    • Spliceosome can be regulated to produce different mRNA transcripts from same pre-mRNA via inclusion or exclusion of particular exons
117
Q

How many codons code for 20 amino acids

A

64

118
Q

Start codons for DNA sequences and RNA sequences

A

TAC, AUG

119
Q

Stop codons for DNA sequences

A

ATT, ATC, ACT

120
Q

Stop codons for RNA sequences

A

UAA, UAG, UGA

121
Q

make up components of ribosomes

A

Ribosomal RNA (rRNA)

122
Q

Translate RNA into polypeptide

A

Transfer RNA (tRNA)

123
Q

Results in a linear polypeptide chain where amino acids are held together by peptide bonds

A

Translation

124
Q

N - terminus

A

First amino acid to be synthesized, Nitrogen end

125
Q

C - terminus

A

Last amino acid to be synthesized, Carboxyl end

126
Q

Clover leaf structure

A

Three step loops in 3’ overhang

127
Q

Anticodon loop is located on

A

middle stem

128
Q

Base pairs complementarily with codons in

A

mRNA

129
Q

Where does translation occur

A

Ribosomes

130
Q

How many types of ribosomes do bacteria have

A

1

131
Q

Where are ribosomes found in Eukaryotes

A

Found in cytosol but also have ribosomes in mitochondria and chloroplasts

132
Q

Small subunit

A

Initially binds to mRNA transcript and initiates translation

133
Q

3 functional sites of large subunit

A

Aminoacyl, Peptidyl, Exit

134
Q

Steps of elongation

A
  • Ribosome moves along mRNA in the 5’ and 3’ orientation
  • tRNAs recognize codons and bring in complementary amino acid
  • Amino acids joined into polypeptide chain
135
Q

Polysomes occur if

A

Multiple ribosomes are translating same mRNA

136
Q

Disassembly of ribosome and release of polypeptide

A

Termination

137
Q

Stop codon is

A

Recognized by protein called release factor, mimics tRNA structure and fits into the A site of the ribosome

138
Q

Sequence of events in Translation

A

1) After initiation, first tRNA is in the P site

2) Next tRNA will bind to the next codon in the A site

3) Peptidyl transfer reaction forms a bond beteen amino acids associated with tRNA in the P and A site

4) tRNA with growing polypeptide chain is transferred from the A to P site

5) Uncharged tRNA moves from the P to the E site

6) Leaves the A site open for the next tRNA to bind

139
Q

produce protein

A

mRNA

140
Q

Do not proceed proteins but produce function RNA products

A

ncRNA

141
Q

Are abundant in prokaryotic and eukaryotic cells, outnumber mRNA

A

ncRNA

142
Q

Transfer RNA and Ribosomal RNAs are both

A

ncRNAS

143
Q

ssRNA

A

Single - stranded RNA

144
Q

dsRNA

A

Double - stranded RNA

145
Q

Functions of ncRNA

A

Scaffolds, guides, alter protein function/stability

146
Q

Alters chromatin structure and represses transcription

A

Hox transcript antisense intergenic RNA (HOTAIR)

147
Q

ncRNA that interferes or silences mRNA activities

A

RNA interference (RNAi)

148
Q

Two types of RNA interference

A

MicroRNAs (miRNA) - endogenous
Small-interfereing RNAs (siRNA) - usually exogenous

149
Q

Origin of miRNA

A

Distinct genomic loci, encoded by own genes

150
Q

Origin of siRNA

A

Encoded by transposons, viruses, heterochromatin

151
Q

Biogenesis in miRNA

A

Single RNA molecules that include an imperfect stem-loop secondary structure

152
Q

Biogenesis in siRNA

A

Long bimolecular RNA duplexes or extended hairpins

153
Q

Evolutionary conservation in miRNA

A

Nearly always conserved in related organisms

154
Q

Evolutionary conservation in siRNA

A

Rarely conserved in related organisms

155
Q

Nature of regulatory target in miRNA

A

Regulate different genes

156
Q

Nature of regulatory target in siRNA

A

Mediate the silencing of the same or similar genes from which they originate

157
Q
  • Transcribed by genes in eukaryotic genome
  • Partial match for target mRNA
  • 60% of human protein-encoding genes regulated
A

miRNA

158
Q
  • Introduced from outside sources such as viruses
  • Exact match for target mRNA
  • Tool in biotechnology
A

siRNAs

159
Q

Guide proteins to specific locations in cells

A

ncRNAs

160
Q

Targets proteins to ER membrane

A

Signal recognition particle (SRP)

161
Q

Abnormal expression of miRNAs associated with

A

cancer

162
Q

Over expression of HOTAIR stimulates

A

Cell division and tumor formation

163
Q

Process by which a gene is made into a functional product

A

Gene regulation

164
Q

Regulation is key to:

A

Environmental response and development in multicellular organisms, cell differentiation

165
Q

Expression can be

A

up - regulated or down - regulated

166
Q

Regulatory transcription factors in bacteria

A
  • Binding to regulatory sequences near promoter and affect transcription
  • Negative and positive control via repressors and activators
  • Small effector molecules
167
Q

Bind to transcription factors and influence binding of transcription factors to DNA

A

Small effector molecules

168
Q

Two sites where small effector molecules can bind

A
  • Where protein binds to the DNA
  • Site specifically for the molecule
169
Q

What are operons in prokaryotes

A

Sets of two or more genes under transcriptional control of single promoter

170
Q

Polycistronic mRNAs encode for

A

More than 1 protein

171
Q

Contains genes for lactose breakdown in E. Coli

A

Iac operon

172
Q

Components of lac operon

A
  • CAP site
  • IacP
    -IacO
  • lacZ
  • lacA
173
Q

Cap site function

A

Binding for Cap-cAMP activator complex

174
Q

IacP function

A

Promoter of lac operon, site for RNA polymerase binding

175
Q

Iac O function

A

Operator is where lac repressor binds

176
Q

IacZ function

A

Encodes lactose permease, a membrane protein that transports lactose into the cell

177
Q

lacA function

A

Encodes galactosidase transacetylase, add an acetyl group to beta-galactosidase

178
Q

CAP

A

Catabolite activator protein

179
Q

cAMP

A

small effector molecule

180
Q

Glucose levels influence

A

CAP - cAMP complex and transcription

181
Q

Heritable changes in genetic material, change in sequence of bases or DNA damage

A

Mutation

182
Q

What system can detect and correct mutations

A

DNA repair

183
Q

Mutations can be

A

Harmful, deleterious, beneficial, or neutral

184
Q

Results from a missense mutation in beta-globin gene

A

Sickle cell

185
Q

Promoter effect on mutation

A

Increase or decrease rate of transcription

186
Q

Transcriptional regulatory / operator site effect on mutation

A

May alter the regulation of transcription

187
Q

Splice sites effect on mutation

A

May alter the ability of pre-mRNA to be properly spliced

188
Q

Translational regulatory element effect on mutation

A

May alter the ability of mRNA to be translationally regulated

189
Q

Intergenic region effect on mutation

A

Not as likely to have an effect on gene expression

190
Q

Timing and location of mutation determines

A

Severity and heritability

191
Q

Germ - line cells

A

Progenitor cells give rise to gametes, mutations in cells passed on

192
Q

Somatic cells

A

Body cells are non-germ-line cells, mutations can occur early or late in development - genetic mosaic

193
Q

Mutations during development result in

A

Genetic mosaics

194
Q

Mutations found in cells originating from

A

Parent cells

195
Q

Fusion of two embryos results in

A

Genetic chimeras

196
Q

How do mutations occur

A

Spontaneous and induced

197
Q

Spontaneous mutations

A

Errors in normal biological processes

198
Q

Induced mutations

A
  • Environmental Causes
  • Occur at higher rate than spontaneous
  • Induced by mutagens - chemical or physical
199
Q

A mistake by DNA polymerase may cause a point mutation

A

Errors in DNA replication

200
Q

The products of normal metabolic processes may be reactive chemicals such as free radicals that can alter the structure of DNA

A

Toxic metabolic products

201
Q

Linkage between a purine and deoxyribose can spontaneously break. Changes in base structure (isomerization) may cause misfiring during DNA replication

A

Changes in nucleotide structure

202
Q

Small segments of DNA that insert at various sites in the genome. If they insert into a gene, they may inactivate the gene

A

Transposons

203
Q

Chemical substance may cause changes in structure of DNA

A

Chemical agents

204
Q

Physical agents such as UV light and X rays can damage DNA

A

Physical agents

205
Q

Mutation rates - high to low

A

Viriods
RNA viruses
DNA viruses
Prokaryotes
Eukaryotes

206
Q

Chemical mutagens

A

Disrupt base-pairing, modify nucleotide structure, Base deamination - nitrous oxide, Base analogues, Insert between bases and distort helix

207
Q

Mispairing causes

A

Point mutation

208
Q

Ionizing radiation can cause

A

Deletions or breaks in DNA strands

209
Q

Non-ionizing radiation such as UV rays causes

A

Thymine dimers - gaps or mispaired bases

210
Q

Fixes physical damage: thymine dimers, base analogs, missing bases

A

NER

211
Q

NER in E. coli, four proteins

A

UvrA, UvrB, UvrC, UvrD

212
Q

Cancer originates from

A

Single cell, mutation results in uncontrolled cell growth - tumor

213
Q

Tumors…

A

Press on blood vessels, constricting flow of oxygen, nutrients and waste

214
Q

Cancer cell characteristics

A
  • Abnormal morphology
  • Loss of differentiated structure and function
  • Angiogenesis
  • Metastasis
  • Loss of contact inhibition
  • Degrade neighboring tissues
  • Immortal
215
Q

Hayflick limit

A

Replicative capacity of cells

216
Q

Only ___% of cancer is heritable

A

10

217
Q

Errors in normal biological processes

A

Spontaneous mutation

218
Q

Carcinogens - mutagens that are known or suspected to cause cancer

A

Induced mutations

219
Q

Group 1 IARC Classification

A

There are sufficient evidence the agent causes cancer in humans

220
Q

Group 2A IARC Classification

A

There is sufficient evidence that the agent causes cancer in humans

221
Q

Group 2B IARC Classification

A

Limited evidence in humans and less than sufficient evidence in animals

222
Q

Group 3 IARC classification

A

Evidence is inadequate in humans and inadequate or limited in animals

223
Q

Gas pedal

A

Proto-oncogenes stimulate cell division

224
Q

Proto-oncogenes mutate to become

A

Oncogenes

225
Q

Mutations impact

A

Growth factors or up-regulate gene expression

226
Q

Cell division is regulated by

A

Hormones called growth factors

227
Q

Growth factors function

A
  • Bind to cell surface and initiate cascade that leads to cell division
  • Mutations increasing their activity can lead to cancer
228
Q

Change in a single amino acid into a protein

A

Missense mutation

229
Q

Copy number of gene increases, results in too much gene product

A

Gene amplification

230
Q

Piece of one chromosome becomes attached to another chromosome, can result in fused genes

A

Chromosomal translocation

231
Q

Viral DNA insertion steps

A
  • Virus inserts DNA into a chromosome
  • Promoter of viral gene placed next to an oncogene
  • Some viruses carry oncogenes in their genomes
232
Q

When cells are mutated they

A

Lose their function

233
Q

Typical tumor function

A

Maintaining genome integrity or inhibitors of cell division

234
Q

Dependent kinases advance the cell through the cell cycle

A

Cyclins or cyclin

235
Q

G1 checkpoint protein, regulatory transcription factor, DNA damage induces expression to prevent cell from advancing to the synthesis (S-phrase), allows for DNA to be repaired

A

p53

236
Q

Loss of mutation functions can be attributed to

A
  • Mutations in coding regions, faulty protein products
  • Mutations in non-coding regions, gene expression turned off or down-regulated

Bio II (2 decks)

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