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Bio 93 Midterm 2 (#10-#19) > Lecture #15-19 > Flashcards

Lecture #15-19 Flashcards

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1
Q

What is the source of genetic variation and in turn natural selection?

A

changes in DNA, mutations

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2
Q

What is the limitation of DNA polymerase?

A

no way to complete the 5’ ends

–> repeated rounds of replication produce shorter DNA molecules with uneven ends (genetic information is lost to RNA primer)

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3
Q

What are telomeres?

A

TTAGGG
–> postpone the erosion of genes near the ends of DNA molecules (DO NOT PREVENT)

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4
Q

What is Werners Syndrome?

A

premature aging disease associated with the shortening of telomeres

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5
Q

What is telomerase?

A

enzyme that catalyzes the lengthening of telomeres in germ cells (e.g. fetuses)

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6
Q

What is associated with the shortening of telomeres?

A

aging (e.g. premature aging diseases)

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7
Q

What is the relationship between telomeres and cancer cells?

A

shortening of telomeres might protect cells from cancerous growth by limiting the number of cell divisions OF CANCER CELLS

–> evidence of telomerase activity in cancer calls (may allow cancer cells to persist

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8
Q

An organism’s ______ is carried in its sequence of bases.

A

genotype

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9
Q

The __________ is a consequence of the proteins that are expressed.

A

phenotype

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10
Q

What is the central dogma (cellular chain of command)?

A

DNA –> RNA –> protein

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11
Q

What is the information content of DNA used for?

A

form a specific sequence of nucleotides

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12
Q

What is the link between genotype and phenotype?

A

proteins

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13
Q

The ____ inherited by an organism leads to specific traits by dictating the synthesis of ____________.

A

DNA, proteins

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14
Q

What is gene expression?

A

process by which DNA directs protein synthesis

includes: transcription and translation

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15
Q

What is a primary transcript?

A

the initial RNA transcript from any gene

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16
Q

What does transcription produce?

A

pre-mRNA

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17
Q

Where does RNA processing occur at?

A

nucleus

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18
Q

Where does translation occur at (in eukaryotes)?

A

in the cytoplasm, at ribosomes

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19
Q

What is the key aspect of a prokaryote (in terms of transcription and translation)?

A

transcription and translation are coupled (because NO NUCLEI)

–> ribosomes attach to mRNA molecule while transcription is in progress

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20
Q

Where does transcription occur in eukaryotes?

A

nucleus

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21
Q

(in eukaryotes) During which process and where does the primary transcript get modified before being transported where else?

A

modified during RNA processing (nucleus) before the finished mRNA is exported to the cytoplsm

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22
Q

DNA is always read in the ___ to ___ direction!

A

3’ to 5’

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23
Q

What are codons? What do they correspond to?

A

triplets of bases that DNA’s read in

correspond to an amino acid

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24
Q

How many codons code for “stop”? What are they?

A

total: 3
UAA, UAG, UGA

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25
Q

What is the start codon?

A

AUG, Methionine

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26
Q

What direction is the template strand oriented in? The coding strand?

A

3’ –> 5’ (template)
5’ –> 3’ (coding)

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27
Q

The genetic code is ___________ but not __________. No codon specifies more than one AA.

A

redundant, ambiguous

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28
Q

What is the reading frame?

A

groupings of the bases (in 3’s because codons)

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29
Q

What type of protection does the redundancy of codons provide?

A

protects from mutations (especially changes in the 3rd base)

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30
Q

The genetic code is nearly _____________. This means genes can be transcribed and translated after being translated from _____________ to ___________.

A

universal

species to species

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31
Q

What are the three steps/stages of transcription?

A

initiation, elongation, termination

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32
Q

What is transcription?

A

DNA-directed synthesis of RNA

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33
Q

LESS THAN ___% of the human genome is translated into proteins.

A

5%

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34
Q

What is the promotor?

A

sequence in DNA that RNA polymerase attaches to

signal the initiation of RNA synthesis

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35
Q

RNA synthesis is catalyzed by _____ ____________. How?

A

RNA polymerase

pries the DNA strands apart and hooks together the RNA nucleotides
–> breaks H-bonds, moves along the gene

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36
Q

RNA synthesis follows the same base-pairing rules as DNA… EXCEPT…

A

uracil substitutes for thymine

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37
Q

What is a transcription unit?

A

stretch of DNA that is transcribed

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38
Q

What happens to the DNA after it is read by the RNA polymerase?

A

rewounds

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39
Q

What are transcription factors?

A

mediate the binding of RNA polymerase ad the initiation of transcription

usually proteins

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40
Q

What is the transcription initiation complex?

A

completed assembly of transcription factors AND RNA polymerase II bound to a promoter

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41
Q

What is a TATA box?

A

a promotor, indicates where transcription begins`

crucial in forming the transcription initiation complex in eukaryotes

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42
Q

During elongation, a gene can be transcribed….

A

simultaneously by several RNA polymerases

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43
Q

Transcription progresses at a rate of ___ nucleotides per second in eukaryotes.

A

40

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44
Q

As RNA polymerase moves along the DNA, it ______ the double helix, ___ to ___ bases at a time.

A

untwists, 10-20

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45
Q

In eukaryotes, what happens to the polymerase after the pre-MRA is cleaved?

A

continues transcription, eventually falls off the DNA

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46
Q

Where does RNA processing take place?

A

nucleus

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47
Q

What is RNA processing?

A

5’ receives a modified nucleotide cap (guanine)

3’ gets a poly-A (adenine) tail

RNA splicing

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48
Q

What does the caps on both ends of the mRNA do?

A

protect export or mRNA from hydrolytic enzymes

help ribosomes attach to the 5’ end

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49
Q

What are introns?

A

noncoding regions

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50
Q

What are exons?

A

coding regions, eventually expressed (usually translated into AA sequences)

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51
Q

What is RNA splicing?

A

removes introns and joining exons

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52
Q

What are spliceosomes?

A
  1. variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize splice sites
  2. carry out RNA splicing
  3. RNAs of spliceosomes also catalyze splicing reaction
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53
Q

What is translation?

A

translates mRNA message into protein with the help of tRNA

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54
Q

What is tRNA? What’s the structure?

A

transfer RNA (each one is not identical)
- each carries a specific AA on one end
- each has an anticodon on the other end (complementary codon on mRNA)

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55
Q

What end of the tRNA is the AA attachment site?

A

3’, CCA (sequence)

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56
Q

What are the two steps that are required for accurate translation?

A
  1. correct match between tRNA and AA (done by enzyme aminoacyl-tRNA synthetase)
  2. correct match between the tRNA anticodon and an mRNA codon
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57
Q

What enzyme correctly matches a tRNA and an AA?

A

aminoacyl-tRNA synthetase

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58
Q

What is a wobble? (codons) What does this wobble allow for?

A

flexible pairing at the third base

allows for some tRNAs to bind to more than one codon`

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59
Q

Describe the steps of a tRNA and AA being bonded together.

A
  1. AA and tRNA enter active site of aminoacyl-tRNA synthetase
  2. using ATP, synthetase catalyzes covalent bonding between AA and tRNA
  3. tRNA is charged (called aminoacyl tRNA) and released
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60
Q

What are ribosomes made up of?

A

2 subunits, large & small

made of proteins and rRNA

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61
Q

What is the role of ribosomes in translation?

A

facilitate specific coupling or tRNA anticodons with mRNA in protein synthesis

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62
Q

All three stages of translation require ______ “_______” that aid in the translation process.

A

protein “factors”

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63
Q

What happens during the initiation stage of translation?

A
  1. small ribosomal unit binds to mRNA
  2. initiator tRNA (has met) binds to mRNA
  3. large ribosomal unit then binds LAST
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64
Q

What happens during the elongation stage of translation?

A

***requires elongation factors (proteins)

  1. codon recognition
  2. peptide bond formation (uses GTP)
  3. translocation (moving down by a codon, requires GTP)
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65
Q

Provide details regarding translocation during the elongation stage of translation.

A

tRNA (in P-site, no longer charged) is removed

tRNA (charged, attached to current polypeptide) moves from A-site to P-site

–> A-site is now open for new tRNA
–> mRNA goes down one codon

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66
Q

What end of the polypeptide is attached to the tRNA?

A

carboxyl end

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67
Q

Provide details regarding peptide bond formation during the elongation stage of translation.

A

polypeptide is attached to tRNA in P-site

bond forms between polypeptide to AA in A-site (moving polypeptide from tRNA in P-site to tRNA in A-site)

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68
Q

What is aminoacyl tRNA?

A

charged tRNA, has an AA attached to its 3’ end

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69
Q

What initiates the termination stage in translation?

A

occurs when a stop codon in the mRNA reaches the A site of the ribosome

–> signals for release factor

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70
Q

What happens during the termination stage of translation?

A
  1. stop codon signals for termination
  2. A site accepts a protein called a release factor (causes the addition of water molecule instead of AA)
  3. RNA is released (as well as ribosomal subunits and other components)
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71
Q

What is a release factor?

A

protein that binds to the A-site, causing the addition of a water molecule instead of an AA

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72
Q

What is a polyribosome/polysome? What does this enable?

A

number of ribosomes that translate a single mRNA simultaneously

enables a cell to make many copies of a polypeptide very quickly

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73
Q

What happens to polypeptide chains after translation?

A

further modified

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74
Q

Completed proteins are ________ to specific sites in the cell.

A

targeted

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75
Q

Describe the process of how a ribosome becomes bound,

A
  1. polypeptide synthesis begins (has signal peptide)
  2. SRP binds to signal peptide, pausing synthesis
  3. SPR binds to receptor protein at a pore of the ER
  4. SRP detaches, synthesis resumes
  5. signal-cleaving enzyme cuts off signal peptide (ribosome disassembles)
  6. polypeptide enters ER lumen, folds
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76
Q

What are mutations?

A

changes in the genetic material of a cell or virus

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77
Q

What are point mutations?

A

chemical changes in JUST ONE base pair of a gene

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78
Q

The change of a single nucleotide in a DNA template strand can lead to the production of ___ __________ ___________.

A

an abnormal protein

79
Q

What is an example of a point mutation? What was the specific change?

A

sickle-cell anemia
GAG –> GUG
Glu –> Val

80
Q

What are the two categories of point mutations? Which of the two is more harmful? Define each one.

A

nucleotide-pair substitutions: replaces one nucleotide and its partner with another pair of nucleotides

one or more nucleotide-pair insertions or deletions: additions or losses of nucleotide pairs in a gene (more harmful)

81
Q

What are the different types of nucleotide-pair substitutions? Define each one. (HINT: 3 of them)

A

silent mutation: no effect on AA

missense: codes for different AA (because of redundancy of genetic code)

nonsense: codes for stop codon (usually leads to nonfunctional protein)

82
Q

What can insertions and deletions lead to?

A

additions and deletions in multiples that ARE NOT 3 –> could cause a frameshift mutation

83
Q

What are frameshift mutations? Give two examples of what could happen in a frameshift mutation.

A

where the reading frame of DNA is changed

  1. frameshift causing immediate nonsense
  2. frameshift causing extensive missense
84
Q

When is a frameshift mutation most dangerous?

A

at the beginning of the DNA

85
Q

What are the three main reasons why cell division is essential for all organisms?

A

reproduction, tissue renewal, growth and development

86
Q

What is tissue renewal? What types of cells are often associated with this process?

A

replacement and repair of cell

stem cells

87
Q

_________ ________ ___________ must be passed from parent cell to offspring cells.

A

identical genetic material

88
Q

What are the three phases of interphase? (Try naming in order.)

A

G1, S, G2

89
Q

What happens during the G1 phase?

A

synthesis of macromolecules and cytoplasmic organelles

90
Q

Through what process is genetic material passed down from parent to offspring cells?

A

cell cycle regulation and mitosis

91
Q

What happens during the S phase?

A

DNA is replicated

92
Q

What happens during the G2 phase?

A

additional growth

93
Q

What is the goal of the cell cycle?

A

precise replication of chromosomes and proper distribution of chromosomes to daughter cells

94
Q

What are the phases of the mitotic phase?

A

mitosis and cytokinesis

95
Q

How many subphases does mitosis have? What are they? (Try naming in order.)

A

total: 5

  1. prophase
  2. prometaphase
  3. metaphase
  4. anaphase
  5. telophase
96
Q

A chromosome is a _____ _____ __________.

A

single DNA molecule

97
Q

What dose the metaphase chromosome look like?

A

X structure, 2 sister chromatids

98
Q

What occurs during the mitotic phase?

A

equal distribution of genetic material to 2 daughter cells

99
Q

What occurs during mitosis?

A

sister chromatids separate, one to each daughter cell

100
Q

What occurs during cytokinesis?

A

process of division of the cytoplasm

101
Q

What are the characteristics of the G2 phase?

A
  • nuclear envelope attached
  • chromosomes (duplicated, uncondensed)
  • 2 centrosomes (paired)
  • nuceloli present
102
Q

What are the characteristics of prophase?

A
  • early mitotic spindles (MTs)
  • nuceloli disappear
  • 1 chromosome seen as 2 sister chromatids attached at centromeres
  • 2 centrosomes (asters) further away from each other
103
Q

What are the characteristics of prometaphase?

A
  • fragments of nuclear envelope
  • chromosomes are more condensed
  • kinetochore formed at centromeres of each sister chromatid
  • MTs attaching to kinetochore (kinetochore MTs)
  • non kine. MTs interact with each other at opposite poles, lengthening cell
104
Q

What are the characteristics of metaphase?

A
  • centrosomes are opposite poles
  • chromosomes at metaphase plate (middle of cell)
  • each kinetochore of sister chromatid is attached kinetochore MTs (from oppo. poles)
105
Q

What are the characteristics of anaphase?

A
  • cohesin proteins are cleaved
  • daughter chromosomes move towards oppo. ends
  • cell elongates
106
Q

During anaphase, are chromosomes “reeled in” or do they “walk in” by using what motor protein?

A

walk in by using dynein

107
Q

What are the characteristics of telophase?

A
  • two daughter nuclei
  • nuclear envelope forms
  • nucleoli reappear
  • MTs are depolymerized
  • (animal cells) cleavage furrow forms for cytokinesis
108
Q

What was the experiment conducted to determine whether chromosomes were “reeled in” or whether they “walked” in? (Describe it.)

A
  1. spindle MTs were dyed
  2. some MTs were “marked” (bleached) between the left pole and the chromosome
  3. length of MTs on pole side did not change
  4. length of MTs on chromosome side shortened

–> chromosomes walk in

109
Q

What end of kinetochore MTs is positive? Which is negative?

A

chromosome side: +
pole side: -

110
Q

Mutations in genes of the mitotic spindle and centrosome cause many types of __________ __________.

A

human disorders

111
Q

Spindle defects are associated with _________ ________ and ________.

A

brain disorders, cancer

112
Q

What is microcephaly? What gene(s) is affected?

A

small brain, structurally normal but exhibit reduced number of cortical neurons

(9 genes, protein products all localize to centrosomes)

113
Q

What is lissencephaly? What gene(s) is affected?

A

small brain, smooth surface

Lis1 gene, protein product stablizes MTs/dynein complex

114
Q

What are the characteristics of cytokinesis? What’s motor protein is involved?

A

animal cells: cleavage furrow
plant cells: cell plate

myosin (MFs)

115
Q

What phase has the least amount of DNA?

A

G1

116
Q

What is data analysis?

A

organizing and presenting the data

117
Q

A drug that blocks cohesin degradation would have what effect on mitosis?

A

sister chromatids would fail to separate during anaphase

118
Q

What type of protein binds sister chromatids together?

A

cohesin proteins

119
Q

What are checkpoints?

A

critical control points where stop and go signals regulate the cycle

120
Q

What molecule regulates the G1 phase/checkpoint?

A

cyclin D and E, Cdk4/6 and Cdk2 respectively

121
Q

Protein kinases must be attached to _______ to be active.

A

cyclin

122
Q

What is MPF?

A

when cyclin combines with Cdk

123
Q

What regulates the G2 checkpoint? What does this molecule promote?

A

MPF, promotes mitosis

124
Q

MPF causes ________ of various proteins of the nuclear lamina.

A

phosphorylation

125
Q

What checkpoint does 93stop trigger?

A

G1 checkpoint

126
Q

After the M phase, what happens to the cyclin?

A

degraded, later attaches to inactive kinases once the cycle begins again

127
Q

What is the process of cyclin during the cell cycle?

A

G1: inactive kinases
S: cyclin begins to be synthesized
G2: sufficient MPF to pass G2 checkpoint
M: MPF promotes mitosis & cyclin’s degraded

128
Q

When is the stop signal issued during prometaphase?

A

when chromosomes aren’t attached

129
Q

When is the go-ahead signal issued during metaphase to enter anaphase?

A

when all chromosomes are attached

130
Q

During the G1/S checkpoint, what Cdk and cyclin protein complex signaling is key?

A

CDK4/6 and Cyclin D

131
Q

What happens to cyclin levels between the S & G2 phases and M phase?

A

drop abruptly

132
Q

Where are the three checkpoints? Which of these three is the most important?

A

G1, G2, M

most important: G1

133
Q

What does the CDK4/6 and Cyclin D signaling do?

A

remove inhibition of gene expression

–> expression of genes necessary for DNA replication

134
Q

What activates the signals requires for the G1 checkpoint?

A

growth factor receptor activation

135
Q

What’s an example of a growth factor that actives that G1 checkpoint? Explain what happens when the growth factor is and isn’t present.

A

PDGF

w/o PDGF: cells fail to divide
w/ PDGF: cells proliferate

136
Q

What happens when cell cycle regulation fails?

A

cancer

137
Q

What are the 2 characteristics of a normal cell? Define each one.

A
  1. anchorage dependence: cells require a surface for division
  2. density-dependent inhibition: cells form a single layer, cells divide to fill a gap and then stop
138
Q

What two aspects of normal cells do cancer cell lose?

A

anchorage dependence, density inhibition (form a single layer)

139
Q

When does metastasis of a malignant tumor start?

A

when the cell loses anchorage dependence

–> can spread to other parts of the body

140
Q

What is a proto-oncogene?

A

normal cellular gene corresponding to an oncogene

has the potential to cause cancer

141
Q

What do proto-oncogenes code for?

A

codes for proteins that stimulate normal cell growth and division

142
Q

What is an oncogene?

A

gene found in viruses or as part of the normal genome that is involved in triggering cancerous characteristics

143
Q

How do viruses cause cancer?

A

carry oncogenes, insert that DNA into cell

144
Q

What are the 4 different ways a proto-oncogene can turn into an oncogene?

A

epigenetic modifications, translocation, amplification, point mutations

145
Q

(Regarding cancer) What are epigenetic modifications?

A

behaviors and environment affecting the way genes work

146
Q

(Regarding cancer) What is translocation?

A

contain broken chromosomes that have been rejoined incorrectly (translocation of fragments)

gene moved to new locus

147
Q

(Regarding cancer) What is amplification?

A

increases the number of copies of the proto-oncogene through repeated gene duplication

148
Q

(Regarding cancer) What is a point mutation?

A

promoter of enhancer that controls a proto-oncogene

could change the gene’s product to a protein that is more active and more resistant to degradation

149
Q

What is a tumor-suppressor gene?

A

inhibit cell division, prevent uncontrolled cell growth

150
Q

What is a key tumor-suppressor gene? What is it’s nickname? What does it do?

A

p53 (guardian of the genome)

inhibits the cell cycle with damaged DNA

specific: activates p21 (stops cell cycle, binds to Cdks), activate mircoRNA (stops cell cycle), turn on “DNA repair” genes or “suicide” genes

151
Q

What is a Ras protein?

A

protein that has ras gene, usually hyperactive (triggers kinase without GF)

G-protein that relays a signal from a growth factor

152
Q

What happens if there is a defective p53?

A

cell cycle is not inhibited, increased cell division

153
Q

What do you think is the best way to uncontrollably increase cell division?

A

express an oncogene

OR

lose a tumor-suppressor gene to remove the inhibitory signaling of cell cycles

154
Q

What is the key steps of the multistep model for development of colorectal cancer?

A

activation of ras oncogene

loss of tumor-suppressor gene DCC and p53

155
Q

The incidence of cancer ______ greatly with age.

A

increases

156
Q

What is the relationship between body size and cancer across species? What is this relationship called? Why is this the case?

A

no correlation, larger animals have more p53 genes

called Peto’s paradox

157
Q

Elephants have ___ copies of the p53 gene.

A

20

158
Q

null hypothesis

A

will not have an effect
no difference

159
Q

alternate hypothesis

A

opposite of null
has effect/ there is a difference

160
Q

What is mitosis?

A

way in which somatic (non-sex) cells divide, asexual reproduction (clone)

161
Q

What is meiosis?

A

a special type of cell division used in sexual reproduction for the formation of gametes

162
Q

What’s the notation for a haploid? How many chromosomes does a haploid have in a human?

A

n, n=23

163
Q

What’s the notation for a diploid? How many chromosomes does a diploid have in a human?

A

2n, 2n=46

164
Q

In humans, what are the haploid cells?

A

egg and sperm

165
Q

What is a karyotype?

A

a display of condensed chromosomes arranged in pairs

ordered from largest to smallest

166
Q

How do you get cells in the right phase of the cll cycle to be able to observe condensed chromosome pairs?

A

use a growth factor to stimulate cell cycle

167
Q

Where do you want the cells to stop in the cell cycle to create a karyotype? Why?

A

in metaphase

why: chromosomes are in sister chromatid pairs and condensed

168
Q

(In regards to creating a karyotype) What does the hypotonic solution do to the cells?

A

makes the cells swell and makes them easier to rupture to get the condensed chromosomes

169
Q

What are homologous chromosomes?

A

chromosome pairs that are approx. the same length, centromere position, and staining pattern

***genes have the same corresponding loci

170
Q

Somatic cells of each species contain a specific ___________ ______ ______________.

A

number of chromosomes

171
Q

How many chromosomes does humans have? How many pairs of homologous chromosomes?

A

46, 23

172
Q

Which human chromosome was the first to be entirely sequenced?

A

22

173
Q

What separates during meiosis I?

A

homologous chromosomes

174
Q

What separates during meiosis II?

A

sister chromatids

175
Q

What is the result of meiosis I?

A

two haploid cells form, each having two sister chromatids

176
Q

A sister chromatid is a ___________.

A

chromosome

177
Q

What happens when a pair of homologous chromosomes does NOT separate and it happens to chromosome 21?

A

down syndrome (also called Trisomy 21)

178
Q

How is genetic variability generated in meiosis?

A

crossing over, independent assortment of chromosomes, random fertilization

179
Q

What is the approximate amount chromosome combinations due to independent assortment? (in one HAPLOID)

A

2^23 = 8 million

180
Q

What is the approximate amount chromosome combinations due to independent assortment? (in one DIPLOID)

A

2^23 X 2^23 = 70 TRILLION combinations

181
Q

What happens when chromosomes fail to separate in meiosis I?

A

homologous chromosomes fail to separate

of chromosomes in each haploid cell:
3, 3, 1, 1

182
Q

What is the term called when chromosomes fail to separate?

A

nondisjuction

–> pair of homologous chromosomes or sister chromatids (depends on meiosis I or II) FAIL to separate during anaphase

183
Q

What happens when chromosomes fail to separate in meiosis II?

A

sister chromatids fail to separate

of chromosomes:
3, 1, 2, 2
**two normal haploid cells

184
Q

Where are telomeres found?

A

at the end of chromosomes

185
Q

What are the two bases that are most commonly found at the origins of replication?

A

T and A (because of TATA box)

186
Q

Why is there usually a bigger peak/more cells in G1?

A

G1 phase takes the most amount of time

187
Q

What are recombinant chromosomes?

A

result of crossing over, different from parent chromosomes

188
Q

What’s the result of meiosis II?

A

4 haploid cells containing unduplicated chromosomes

189
Q

What is crossing over?

A

occurs in prophase of meiosis I

homologous chromosomes line up and cross over some genes (random)

190
Q

What is independent assortment?

A

random way each pair of alleles that may be found within any given chromosome

191
Q

What is random fertilization?

A

random egg and random sperm fuse together

192
Q

What bonds are formed within to keep tRNA intact?

A

H-bonds

193
Q

(In cellular respiration in animals), ATP synthase pumps H+ from where to where?

A

intermembrane space to mitochondrial matrix

Bio 93 Midterm 2 (#10-#19) (1 decks)

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