Lecture #15-19 Flashcards
1
Q
What is the source of genetic variation and in turn natural selection?
A
changes in DNA, mutations
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)
3
Q
What are telomeres?
A
TTAGGG
–> postpone the erosion of genes near the ends of DNA molecules (DO NOT PREVENT)
4
Q
What is Werners Syndrome?
A
premature aging disease associated with the shortening of telomeres
5
Q
What is telomerase?
A
enzyme that catalyzes the lengthening of telomeres in germ cells (e.g. fetuses)
6
Q
What is associated with the shortening of telomeres?
A
aging (e.g. premature aging diseases)
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
8
Q
An organism’s ______ is carried in its sequence of bases.
A
genotype
9
Q
The __________ is a consequence of the proteins that are expressed.
A
phenotype
10
Q
What is the central dogma (cellular chain of command)?
A
DNA –> RNA –> protein
11
Q
What is the information content of DNA used for?
A
form a specific sequence of nucleotides
12
Q
What is the link between genotype and phenotype?
A
proteins
13
Q
The ____ inherited by an organism leads to specific traits by dictating the synthesis of ____________.
A
DNA, proteins
14
Q
What is gene expression?
A
process by which DNA directs protein synthesis
includes: transcription and translation
15
Q
What is a primary transcript?
A
the initial RNA transcript from any gene
16
Q
What does transcription produce?
A
pre-mRNA
17
Q
Where does RNA processing occur at?
A
nucleus
18
Q
Where does translation occur at (in eukaryotes)?
A
in the cytoplasm, at ribosomes
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
20
Q
Where does transcription occur in eukaryotes?
A
nucleus
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
22
Q
DNA is always read in the ___ to ___ direction!
A
3’ to 5’
23
Q
What are codons? What do they correspond to?
A
triplets of bases that DNA’s read in
correspond to an amino acid
24
Q
How many codons code for “stop”? What are they?
A
total: 3
UAA, UAG, UGA
25
What is the start codon?
AUG, Methionine
26
What direction is the template strand oriented in? The coding strand?
3' --> 5' (template)
5' --> 3' (coding)
27
The genetic code is ___________ but not __________. No codon specifies more than one AA.
redundant, ambiguous
28
What is the reading frame?
groupings of the bases (in 3's because codons)
29
What type of protection does the redundancy of codons provide?
protects from mutations (especially changes in the 3rd base)
30
The genetic code is nearly _____________. This means genes can be transcribed and translated after being translated from _____________ to ___________.
universal
species to species
31
What are the three steps/stages of transcription?
initiation, elongation, termination
32
What is transcription?
DNA-directed synthesis of RNA
33
LESS THAN ___% of the human genome is translated into proteins.
5%
34
What is the promotor?
sequence in DNA that RNA polymerase attaches to
signal the initiation of RNA synthesis
35
RNA synthesis is catalyzed by _____ ____________. How?
RNA polymerase
pries the DNA strands apart and hooks together the RNA nucleotides
--> breaks H-bonds, moves along the gene
36
RNA synthesis follows the same base-pairing rules as DNA... EXCEPT...
uracil substitutes for thymine
37
What is a transcription unit?
stretch of DNA that is transcribed
38
What happens to the DNA after it is read by the RNA polymerase?
rewounds
39
What are transcription factors?
mediate the binding of RNA polymerase ad the initiation of transcription
usually proteins
40
What is the transcription initiation complex?
completed assembly of transcription factors AND RNA polymerase II bound to a promoter
41
What is a TATA box?
a promotor, indicates where transcription begins`
crucial in forming the transcription initiation complex in eukaryotes
42
During elongation, a gene can be transcribed....
simultaneously by several RNA polymerases
43
Transcription progresses at a rate of ___ nucleotides per second in eukaryotes.
40
44
As RNA polymerase moves along the DNA, it ______ the double helix, ___ to ___ bases at a time.
untwists, 10-20
45
In eukaryotes, what happens to the polymerase after the pre-MRA is cleaved?
continues transcription, eventually falls off the DNA
46
Where does RNA processing take place?
nucleus
47
What is RNA processing?
5' receives a modified nucleotide cap (guanine)
3' gets a poly-A (adenine) tail
RNA splicing
48
What does the caps on both ends of the mRNA do?
protect export or mRNA from hydrolytic enzymes
help ribosomes attach to the 5' end
49
What are introns?
noncoding regions
50
What are exons?
coding regions, eventually expressed (usually translated into AA sequences)
51
What is RNA splicing?
removes introns and joining exons
52
What are spliceosomes?
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
53
What is translation?
translates mRNA message into protein with the help of tRNA
54
What is tRNA? What's the structure?
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)
55
What end of the tRNA is the AA attachment site?
3', CCA (sequence)
56
What are the two steps that are required for accurate translation?
1. correct match between tRNA and AA (done by enzyme aminoacyl-tRNA synthetase)
2. correct match between the tRNA anticodon and an mRNA codon
57
What enzyme correctly matches a tRNA and an AA?
aminoacyl-tRNA synthetase
58
What is a wobble? (codons) What does this wobble allow for?
flexible pairing at the third base
allows for some tRNAs to bind to more than one codon`
59
Describe the steps of a tRNA and AA being bonded together.
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
60
What are ribosomes made up of?
2 subunits, large & small
made of proteins and rRNA
61
What is the role of ribosomes in translation?
facilitate specific coupling or tRNA anticodons with mRNA in protein synthesis
62
All three stages of translation require ______ "_______" that aid in the translation process.
protein "factors"
63
What happens during the initiation stage of translation?
1. small ribosomal unit binds to mRNA
2. initiator tRNA (has met) binds to mRNA
3. large ribosomal unit then binds LAST
64
What happens during the elongation stage of translation?
***requires elongation factors (proteins)
1. codon recognition
2. peptide bond formation (uses GTP)
3. translocation (moving down by a codon, requires GTP)
65
Provide details regarding translocation during the elongation stage of translation.
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
66
What end of the polypeptide is attached to the tRNA?
carboxyl end
67
Provide details regarding peptide bond formation during the elongation stage of translation.
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)
68
What is aminoacyl tRNA?
charged tRNA, has an AA attached to its 3' end
69
What initiates the termination stage in translation?
occurs when a stop codon in the mRNA reaches the A site of the ribosome
--> signals for release factor
70
What happens during the termination stage of translation?
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)
71
What is a release factor?
protein that binds to the A-site, causing the addition of a water molecule instead of an AA
72
What is a polyribosome/polysome? What does this enable?
number of ribosomes that translate a single mRNA simultaneously
enables a cell to make many copies of a polypeptide very quickly
73
What happens to polypeptide chains after translation?
further modified
74
Completed proteins are ________ to specific sites in the cell.
targeted
75
Describe the process of how a ribosome becomes bound,
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
76
What are mutations?
changes in the genetic material of a cell or virus
77
What are point mutations?
chemical changes in JUST ONE base pair of a gene
78
The change of a single nucleotide in a DNA template strand can lead to the production of ___ __________ ___________.
an abnormal protein
79
What is an example of a point mutation? What was the specific change?
sickle-cell anemia
GAG --> GUG
Glu --> Val
80
What are the two categories of point mutations? Which of the two is more harmful? Define each one.
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
What are the different types of nucleotide-pair substitutions? Define each one. (HINT: 3 of them)
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
What can insertions and deletions lead to?
additions and deletions in multiples that ARE NOT 3 --> could cause a frameshift mutation
83
What are frameshift mutations? Give two examples of what could happen in a frameshift mutation.
where the reading frame of DNA is changed
1. frameshift causing immediate nonsense
2. frameshift causing extensive missense
84
When is a frameshift mutation most dangerous?
at the beginning of the DNA
85
What are the three main reasons why cell division is essential for all organisms?
reproduction, tissue renewal, growth and development
86
What is tissue renewal? What types of cells are often associated with this process?
replacement and repair of cell
stem cells
87
_________ ________ ___________ must be passed from parent cell to offspring cells.
identical genetic material
88
What are the three phases of interphase? (Try naming in order.)
G1, S, G2
89
What happens during the G1 phase?
synthesis of macromolecules and cytoplasmic organelles
90
Through what process is genetic material passed down from parent to offspring cells?
cell cycle regulation and mitosis
91
What happens during the S phase?
DNA is replicated
92
What happens during the G2 phase?
additional growth
93
What is the goal of the cell cycle?
precise replication of chromosomes and proper distribution of chromosomes to daughter cells
94
What are the phases of the mitotic phase?
mitosis and cytokinesis
95
How many subphases does mitosis have? What are they? (Try naming in order.)
total: 5
1. prophase
2. prometaphase
3. metaphase
4. anaphase
5. telophase
96
A chromosome is a _____ _____ __________.
single DNA molecule
97
What dose the metaphase chromosome look like?
X structure, 2 sister chromatids
98
What occurs during the mitotic phase?
equal distribution of genetic material to 2 daughter cells
99
What occurs during mitosis?
sister chromatids separate, one to each daughter cell
100
What occurs during cytokinesis?
process of division of the cytoplasm
101
What are the characteristics of the G2 phase?
- nuclear envelope attached
- chromosomes (duplicated, uncondensed)
- 2 centrosomes (paired)
- nuceloli present
102
What are the characteristics of prophase?
- 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
What are the characteristics of prometaphase?
- 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
What are the characteristics of metaphase?
- centrosomes are opposite poles
- chromosomes at metaphase plate (middle of cell)
- each kinetochore of sister chromatid is attached kinetochore MTs (from oppo. poles)
105
What are the characteristics of anaphase?
- cohesin proteins are cleaved
- daughter chromosomes move towards oppo. ends
- cell elongates
106
During anaphase, are chromosomes "reeled in" or do they "walk in" by using what motor protein?
walk in by using dynein
107
What are the characteristics of telophase?
- two daughter nuclei
- nuclear envelope forms
- nucleoli reappear
- MTs are depolymerized
- (animal cells) cleavage furrow forms for cytokinesis
108
What was the experiment conducted to determine whether chromosomes were "reeled in" or whether they "walked" in? (Describe it.)
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
What end of kinetochore MTs is positive? Which is negative?
chromosome side: +
pole side: -
110
Mutations in genes of the mitotic spindle and centrosome cause many types of __________ __________.
human disorders
111
Spindle defects are associated with _________ ________ and ________.
brain disorders, cancer
112
What is microcephaly? What gene(s) is affected?
small brain, structurally normal but exhibit reduced number of cortical neurons
(9 genes, protein products all localize to centrosomes)
113
What is lissencephaly? What gene(s) is affected?
small brain, smooth surface
Lis1 gene, protein product stablizes MTs/dynein complex
114
What are the characteristics of cytokinesis? What's motor protein is involved?
animal cells: cleavage furrow
plant cells: cell plate
myosin (MFs)
115
What phase has the least amount of DNA?
G1
116
What is data analysis?
organizing and presenting the data
117
A drug that blocks cohesin degradation would have what effect on mitosis?
sister chromatids would fail to separate during anaphase
118
What type of protein binds sister chromatids together?
cohesin proteins
119
What are checkpoints?
critical control points where stop and go signals regulate the cycle
120
What molecule regulates the G1 phase/checkpoint?
cyclin D and E, Cdk4/6 and Cdk2 respectively
121
Protein kinases must be attached to _______ to be active.
cyclin
122
What is MPF?
when cyclin combines with Cdk
123
What regulates the G2 checkpoint? What does this molecule promote?
MPF, promotes mitosis
124
MPF causes ________ of various proteins of the nuclear lamina.
phosphorylation
125
What checkpoint does 93stop trigger?
G1 checkpoint
126
After the M phase, what happens to the cyclin?
degraded, later attaches to inactive kinases once the cycle begins again
127
What is the process of cyclin during the cell cycle?
G1: inactive kinases
S: cyclin begins to be synthesized
G2: sufficient MPF to pass G2 checkpoint
M: MPF promotes mitosis & cyclin's degraded
128
When is the stop signal issued during prometaphase?
when chromosomes aren't attached
129
When is the go-ahead signal issued during metaphase to enter anaphase?
when all chromosomes are attached
130
During the G1/S checkpoint, what Cdk and cyclin protein complex signaling is key?
CDK4/6 and Cyclin D
131
What happens to cyclin levels between the S & G2 phases and M phase?
drop abruptly
132
Where are the three checkpoints? Which of these three is the most important?
G1, G2, M
most important: G1
133
What does the CDK4/6 and Cyclin D signaling do?
remove inhibition of gene expression
--> expression of genes necessary for DNA replication
134
What activates the signals requires for the G1 checkpoint?
growth factor receptor activation
135
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.
PDGF
w/o PDGF: cells fail to divide
w/ PDGF: cells proliferate
136
What happens when cell cycle regulation fails?
cancer
137
What are the 2 characteristics of a normal cell? Define each one.
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
What two aspects of normal cells do cancer cell lose?
anchorage dependence, density inhibition (form a single layer)
139
When does metastasis of a malignant tumor start?
when the cell loses anchorage dependence
--> can spread to other parts of the body
140
What is a proto-oncogene?
normal cellular gene corresponding to an oncogene
has the potential to cause cancer
141
What do proto-oncogenes code for?
codes for proteins that stimulate normal cell growth and division
142
What is an oncogene?
gene found in viruses or as part of the normal genome that is involved in triggering cancerous characteristics
143
How do viruses cause cancer?
carry oncogenes, insert that DNA into cell
144
What are the 4 different ways a proto-oncogene can turn into an oncogene?
epigenetic modifications, translocation, amplification, point mutations
145
(Regarding cancer) What are epigenetic modifications?
behaviors and environment affecting the way genes work
146
(Regarding cancer) What is translocation?
contain broken chromosomes that have been rejoined incorrectly (translocation of fragments)
gene moved to new locus
147
(Regarding cancer) What is amplification?
increases the number of copies of the proto-oncogene through repeated gene duplication
148
(Regarding cancer) What is a point mutation?
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
What is a tumor-suppressor gene?
inhibit cell division, prevent uncontrolled cell growth
150
What is a key tumor-suppressor gene? What is it's nickname? What does it do?
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
What is a Ras protein?
protein that has ras gene, usually hyperactive (triggers kinase without GF)
G-protein that relays a signal from a growth factor
152
What happens if there is a defective p53?
cell cycle is not inhibited, increased cell division
153
What do you think is the best way to uncontrollably increase cell division?
express an oncogene
OR
lose a tumor-suppressor gene to remove the inhibitory signaling of cell cycles
154
What is the key steps of the multistep model for development of colorectal cancer?
activation of ras oncogene
loss of tumor-suppressor gene DCC and p53
155
The incidence of cancer ______ greatly with age.
increases
156
What is the relationship between body size and cancer across species? What is this relationship called? Why is this the case?
no correlation, larger animals have more p53 genes
called Peto's paradox
157
Elephants have ___ copies of the p53 gene.
20
158
null hypothesis
will not have an effect
no difference
159
alternate hypothesis
opposite of null
has effect/ there is a difference
160
What is mitosis?
way in which somatic (non-sex) cells divide, asexual reproduction (clone)
161
What is meiosis?
a special type of cell division used in sexual reproduction for the formation of gametes
162
What's the notation for a haploid? How many chromosomes does a haploid have in a human?
n, n=23
163
What's the notation for a diploid? How many chromosomes does a diploid have in a human?
2n, 2n=46
164
In humans, what are the haploid cells?
egg and sperm
165
What is a karyotype?
a display of condensed chromosomes arranged in pairs
ordered from largest to smallest
166
How do you get cells in the right phase of the cll cycle to be able to observe condensed chromosome pairs?
use a growth factor to stimulate cell cycle
167
Where do you want the cells to stop in the cell cycle to create a karyotype? Why?
in metaphase
why: chromosomes are in sister chromatid pairs and condensed
168
(In regards to creating a karyotype) What does the hypotonic solution do to the cells?
makes the cells swell and makes them easier to rupture to get the condensed chromosomes
169
What are homologous chromosomes?
chromosome pairs that are approx. the same length, centromere position, and staining pattern
***genes have the same corresponding loci
170
Somatic cells of each species contain a specific ___________ ______ ______________.
number of chromosomes
171
How many chromosomes does humans have? How many pairs of homologous chromosomes?
46, 23
172
Which human chromosome was the first to be entirely sequenced?
22
173
What separates during meiosis I?
homologous chromosomes
174
What separates during meiosis II?
sister chromatids
175
What is the result of meiosis I?
two haploid cells form, each having two sister chromatids
176
A sister chromatid is a ___________.
chromosome
177
What happens when a pair of homologous chromosomes does NOT separate and it happens to chromosome 21?
down syndrome (also called Trisomy 21)
178
How is genetic variability generated in meiosis?
crossing over, independent assortment of chromosomes, random fertilization
179
What is the approximate amount chromosome combinations due to independent assortment? (in one HAPLOID)
2^23 = 8 million
180
What is the approximate amount chromosome combinations due to independent assortment? (in one DIPLOID)
2^23 X 2^23 = 70 TRILLION combinations
181
What happens when chromosomes fail to separate in meiosis I?
homologous chromosomes fail to separate
of chromosomes in each haploid cell:
3, 3, 1, 1
182
What is the term called when chromosomes fail to separate?
nondisjuction
--> pair of homologous chromosomes or sister chromatids (depends on meiosis I or II) FAIL to separate during anaphase
183
What happens when chromosomes fail to separate in meiosis II?
sister chromatids fail to separate
of chromosomes:
3, 1, 2, 2
**two normal haploid cells
184
Where are telomeres found?
at the end of chromosomes
185
What are the two bases that are most commonly found at the origins of replication?
T and A (because of TATA box)
186
Why is there usually a bigger peak/more cells in G1?
G1 phase takes the most amount of time
187
What are recombinant chromosomes?
result of crossing over, different from parent chromosomes
188
What's the result of meiosis II?
4 haploid cells containing unduplicated chromosomes
189
What is crossing over?
occurs in prophase of meiosis I
homologous chromosomes line up and cross over some genes (random)
190
What is independent assortment?
random way each pair of alleles that may be found within any given chromosome
191
What is random fertilization?
random egg and random sperm fuse together
192
What bonds are formed within to keep tRNA intact?
H-bonds
193
(In cellular respiration in animals), ATP synthase pumps H+ from where to where?
intermembrane space to mitochondrial matrix
