Lecture #15-19 Flashcards
What is the source of genetic variation and in turn natural selection?
changes in DNA, mutations
What is the limitation of DNA polymerase?
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)
What are telomeres?
TTAGGG
–> postpone the erosion of genes near the ends of DNA molecules (DO NOT PREVENT)
What is Werners Syndrome?
premature aging disease associated with the shortening of telomeres
What is telomerase?
enzyme that catalyzes the lengthening of telomeres in germ cells (e.g. fetuses)
What is associated with the shortening of telomeres?
aging (e.g. premature aging diseases)
What is the relationship between telomeres and cancer cells?
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
An organism’s ______ is carried in its sequence of bases.
genotype
The __________ is a consequence of the proteins that are expressed.
phenotype
What is the central dogma (cellular chain of command)?
DNA –> RNA –> protein
What is the information content of DNA used for?
form a specific sequence of nucleotides
What is the link between genotype and phenotype?
proteins
The ____ inherited by an organism leads to specific traits by dictating the synthesis of ____________.
DNA, proteins
What is gene expression?
process by which DNA directs protein synthesis
includes: transcription and translation
What is a primary transcript?
the initial RNA transcript from any gene
What does transcription produce?
pre-mRNA
Where does RNA processing occur at?
nucleus
Where does translation occur at (in eukaryotes)?
in the cytoplasm, at ribosomes
What is the key aspect of a prokaryote (in terms of transcription and translation)?
transcription and translation are coupled (because NO NUCLEI)
–> ribosomes attach to mRNA molecule while transcription is in progress
Where does transcription occur in eukaryotes?
nucleus
(in eukaryotes) During which process and where does the primary transcript get modified before being transported where else?
modified during RNA processing (nucleus) before the finished mRNA is exported to the cytoplsm
DNA is always read in the ___ to ___ direction!
3’ to 5’
What are codons? What do they correspond to?
triplets of bases that DNA’s read in
correspond to an amino acid
How many codons code for “stop”? What are they?
total: 3
UAA, UAG, UGA
What is the start codon?
AUG, Methionine
What direction is the template strand oriented in? The coding strand?
3’ –> 5’ (template)
5’ –> 3’ (coding)
The genetic code is ___________ but not __________. No codon specifies more than one AA.
redundant, ambiguous
What is the reading frame?
groupings of the bases (in 3’s because codons)
What type of protection does the redundancy of codons provide?
protects from mutations (especially changes in the 3rd base)
The genetic code is nearly _____________. This means genes can be transcribed and translated after being translated from _____________ to ___________.
universal
species to species
What are the three steps/stages of transcription?
initiation, elongation, termination
What is transcription?
DNA-directed synthesis of RNA
LESS THAN ___% of the human genome is translated into proteins.
5%
What is the promotor?
sequence in DNA that RNA polymerase attaches to
signal the initiation of RNA synthesis
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
RNA synthesis follows the same base-pairing rules as DNA… EXCEPT…
uracil substitutes for thymine
What is a transcription unit?
stretch of DNA that is transcribed
What happens to the DNA after it is read by the RNA polymerase?
rewounds
What are transcription factors?
mediate the binding of RNA polymerase ad the initiation of transcription
usually proteins
What is the transcription initiation complex?
completed assembly of transcription factors AND RNA polymerase II bound to a promoter
What is a TATA box?
a promotor, indicates where transcription begins`
crucial in forming the transcription initiation complex in eukaryotes
During elongation, a gene can be transcribed….
simultaneously by several RNA polymerases
Transcription progresses at a rate of ___ nucleotides per second in eukaryotes.
40
As RNA polymerase moves along the DNA, it ______ the double helix, ___ to ___ bases at a time.
untwists, 10-20
In eukaryotes, what happens to the polymerase after the pre-MRA is cleaved?
continues transcription, eventually falls off the DNA
Where does RNA processing take place?
nucleus
What is RNA processing?
5’ receives a modified nucleotide cap (guanine)
3’ gets a poly-A (adenine) tail
RNA splicing
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
What are introns?
noncoding regions
What are exons?
coding regions, eventually expressed (usually translated into AA sequences)
What is RNA splicing?
removes introns and joining exons
What are spliceosomes?
- variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize splice sites
- carry out RNA splicing
- RNAs of spliceosomes also catalyze splicing reaction
What is translation?
translates mRNA message into protein with the help of tRNA
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)
What end of the tRNA is the AA attachment site?
3’, CCA (sequence)
What are the two steps that are required for accurate translation?
- correct match between tRNA and AA (done by enzyme aminoacyl-tRNA synthetase)
- correct match between the tRNA anticodon and an mRNA codon
What enzyme correctly matches a tRNA and an AA?
aminoacyl-tRNA synthetase
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`
Describe the steps of a tRNA and AA being bonded together.
- AA and tRNA enter active site of aminoacyl-tRNA synthetase
- using ATP, synthetase catalyzes covalent bonding between AA and tRNA
- tRNA is charged (called aminoacyl tRNA) and released
What are ribosomes made up of?
2 subunits, large & small
made of proteins and rRNA
What is the role of ribosomes in translation?
facilitate specific coupling or tRNA anticodons with mRNA in protein synthesis
All three stages of translation require ______ “_______” that aid in the translation process.
protein “factors”
What happens during the initiation stage of translation?
- small ribosomal unit binds to mRNA
- initiator tRNA (has met) binds to mRNA
- large ribosomal unit then binds LAST
What happens during the elongation stage of translation?
***requires elongation factors (proteins)
- codon recognition
- peptide bond formation (uses GTP)
- translocation (moving down by a codon, requires GTP)
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
What end of the polypeptide is attached to the tRNA?
carboxyl end
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)
What is aminoacyl tRNA?
charged tRNA, has an AA attached to its 3’ end
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
What happens during the termination stage of translation?
- stop codon signals for termination
- A site accepts a protein called a release factor (causes the addition of water molecule instead of AA)
- RNA is released (as well as ribosomal subunits and other components)
What is a release factor?
protein that binds to the A-site, causing the addition of a water molecule instead of an AA
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
What happens to polypeptide chains after translation?
further modified
Completed proteins are ________ to specific sites in the cell.
targeted
Describe the process of how a ribosome becomes bound,
- polypeptide synthesis begins (has signal peptide)
- SRP binds to signal peptide, pausing synthesis
- SPR binds to receptor protein at a pore of the ER
- SRP detaches, synthesis resumes
- signal-cleaving enzyme cuts off signal peptide (ribosome disassembles)
- polypeptide enters ER lumen, folds
What are mutations?
changes in the genetic material of a cell or virus
What are point mutations?
chemical changes in JUST ONE base pair of a gene
The change of a single nucleotide in a DNA template strand can lead to the production of ___ __________ ___________.
an abnormal protein
What is an example of a point mutation? What was the specific change?
sickle-cell anemia
GAG –> GUG
Glu –> Val
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)
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)
What can insertions and deletions lead to?
additions and deletions in multiples that ARE NOT 3 –> could cause a frameshift mutation
What are frameshift mutations? Give two examples of what could happen in a frameshift mutation.
where the reading frame of DNA is changed
- frameshift causing immediate nonsense
- frameshift causing extensive missense
When is a frameshift mutation most dangerous?
at the beginning of the DNA
What are the three main reasons why cell division is essential for all organisms?
reproduction, tissue renewal, growth and development
What is tissue renewal? What types of cells are often associated with this process?
replacement and repair of cell
stem cells
_________ ________ ___________ must be passed from parent cell to offspring cells.
identical genetic material
What are the three phases of interphase? (Try naming in order.)
G1, S, G2
What happens during the G1 phase?
synthesis of macromolecules and cytoplasmic organelles
Through what process is genetic material passed down from parent to offspring cells?
cell cycle regulation and mitosis
What happens during the S phase?
DNA is replicated
What happens during the G2 phase?
additional growth
What is the goal of the cell cycle?
precise replication of chromosomes and proper distribution of chromosomes to daughter cells
What are the phases of the mitotic phase?
mitosis and cytokinesis
How many subphases does mitosis have? What are they? (Try naming in order.)
total: 5
- prophase
- prometaphase
- metaphase
- anaphase
- telophase
A chromosome is a _____ _____ __________.
single DNA molecule
What dose the metaphase chromosome look like?
X structure, 2 sister chromatids
What occurs during the mitotic phase?
equal distribution of genetic material to 2 daughter cells
What occurs during mitosis?
sister chromatids separate, one to each daughter cell
What occurs during cytokinesis?
process of division of the cytoplasm
What are the characteristics of the G2 phase?
- nuclear envelope attached
- chromosomes (duplicated, uncondensed)
- 2 centrosomes (paired)
- nuceloli present
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
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
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)
What are the characteristics of anaphase?
- cohesin proteins are cleaved
- daughter chromosomes move towards oppo. ends
- cell elongates
During anaphase, are chromosomes “reeled in” or do they “walk in” by using what motor protein?
walk in by using dynein
What are the characteristics of telophase?
- two daughter nuclei
- nuclear envelope forms
- nucleoli reappear
- MTs are depolymerized
- (animal cells) cleavage furrow forms for cytokinesis
What was the experiment conducted to determine whether chromosomes were “reeled in” or whether they “walked” in? (Describe it.)
- spindle MTs were dyed
- some MTs were “marked” (bleached) between the left pole and the chromosome
- length of MTs on pole side did not change
- length of MTs on chromosome side shortened
–> chromosomes walk in
What end of kinetochore MTs is positive? Which is negative?
chromosome side: +
pole side: -
Mutations in genes of the mitotic spindle and centrosome cause many types of __________ __________.
human disorders
Spindle defects are associated with _________ ________ and ________.
brain disorders, cancer
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)
What is lissencephaly? What gene(s) is affected?
small brain, smooth surface
Lis1 gene, protein product stablizes MTs/dynein complex
What are the characteristics of cytokinesis? What’s motor protein is involved?
animal cells: cleavage furrow
plant cells: cell plate
myosin (MFs)
What phase has the least amount of DNA?
G1
What is data analysis?
organizing and presenting the data
A drug that blocks cohesin degradation would have what effect on mitosis?
sister chromatids would fail to separate during anaphase
What type of protein binds sister chromatids together?
cohesin proteins
What are checkpoints?
critical control points where stop and go signals regulate the cycle
What molecule regulates the G1 phase/checkpoint?
cyclin D and E, Cdk4/6 and Cdk2 respectively
Protein kinases must be attached to _______ to be active.
cyclin
What is MPF?
when cyclin combines with Cdk
What regulates the G2 checkpoint? What does this molecule promote?
MPF, promotes mitosis
MPF causes ________ of various proteins of the nuclear lamina.
phosphorylation
What checkpoint does 93stop trigger?
G1 checkpoint
After the M phase, what happens to the cyclin?
degraded, later attaches to inactive kinases once the cycle begins again
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
When is the stop signal issued during prometaphase?
when chromosomes aren’t attached
When is the go-ahead signal issued during metaphase to enter anaphase?
when all chromosomes are attached
During the G1/S checkpoint, what Cdk and cyclin protein complex signaling is key?
CDK4/6 and Cyclin D
What happens to cyclin levels between the S & G2 phases and M phase?
drop abruptly
Where are the three checkpoints? Which of these three is the most important?
G1, G2, M
most important: G1
What does the CDK4/6 and Cyclin D signaling do?
remove inhibition of gene expression
–> expression of genes necessary for DNA replication
What activates the signals requires for the G1 checkpoint?
growth factor receptor activation
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
What happens when cell cycle regulation fails?
cancer
What are the 2 characteristics of a normal cell? Define each one.
- anchorage dependence: cells require a surface for division
- density-dependent inhibition: cells form a single layer, cells divide to fill a gap and then stop
What two aspects of normal cells do cancer cell lose?
anchorage dependence, density inhibition (form a single layer)
When does metastasis of a malignant tumor start?
when the cell loses anchorage dependence
–> can spread to other parts of the body
What is a proto-oncogene?
normal cellular gene corresponding to an oncogene
has the potential to cause cancer
What do proto-oncogenes code for?
codes for proteins that stimulate normal cell growth and division
What is an oncogene?
gene found in viruses or as part of the normal genome that is involved in triggering cancerous characteristics
How do viruses cause cancer?
carry oncogenes, insert that DNA into cell
What are the 4 different ways a proto-oncogene can turn into an oncogene?
epigenetic modifications, translocation, amplification, point mutations
(Regarding cancer) What are epigenetic modifications?
behaviors and environment affecting the way genes work
(Regarding cancer) What is translocation?
contain broken chromosomes that have been rejoined incorrectly (translocation of fragments)
gene moved to new locus
(Regarding cancer) What is amplification?
increases the number of copies of the proto-oncogene through repeated gene duplication
(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
What is a tumor-suppressor gene?
inhibit cell division, prevent uncontrolled cell growth
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
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
What happens if there is a defective p53?
cell cycle is not inhibited, increased cell division
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
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
The incidence of cancer ______ greatly with age.
increases
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
Elephants have ___ copies of the p53 gene.
20
null hypothesis
will not have an effect
no difference
alternate hypothesis
opposite of null
has effect/ there is a difference
What is mitosis?
way in which somatic (non-sex) cells divide, asexual reproduction (clone)
What is meiosis?
a special type of cell division used in sexual reproduction for the formation of gametes
What’s the notation for a haploid? How many chromosomes does a haploid have in a human?
n, n=23
What’s the notation for a diploid? How many chromosomes does a diploid have in a human?
2n, 2n=46
In humans, what are the haploid cells?
egg and sperm
What is a karyotype?
a display of condensed chromosomes arranged in pairs
ordered from largest to smallest
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
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
(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
What are homologous chromosomes?
chromosome pairs that are approx. the same length, centromere position, and staining pattern
***genes have the same corresponding loci
Somatic cells of each species contain a specific ___________ ______ ______________.
number of chromosomes
How many chromosomes does humans have? How many pairs of homologous chromosomes?
46, 23
Which human chromosome was the first to be entirely sequenced?
22
What separates during meiosis I?
homologous chromosomes
What separates during meiosis II?
sister chromatids
What is the result of meiosis I?
two haploid cells form, each having two sister chromatids
A sister chromatid is a ___________.
chromosome
What happens when a pair of homologous chromosomes does NOT separate and it happens to chromosome 21?
down syndrome (also called Trisomy 21)
How is genetic variability generated in meiosis?
crossing over, independent assortment of chromosomes, random fertilization
What is the approximate amount chromosome combinations due to independent assortment? (in one HAPLOID)
2^23 = 8 million
What is the approximate amount chromosome combinations due to independent assortment? (in one DIPLOID)
2^23 X 2^23 = 70 TRILLION combinations
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
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
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
Where are telomeres found?
at the end of chromosomes
What are the two bases that are most commonly found at the origins of replication?
T and A (because of TATA box)
Why is there usually a bigger peak/more cells in G1?
G1 phase takes the most amount of time
What are recombinant chromosomes?
result of crossing over, different from parent chromosomes
What’s the result of meiosis II?
4 haploid cells containing unduplicated chromosomes
What is crossing over?
occurs in prophase of meiosis I
homologous chromosomes line up and cross over some genes (random)
What is independent assortment?
random way each pair of alleles that may be found within any given chromosome
What is random fertilization?
random egg and random sperm fuse together
What bonds are formed within to keep tRNA intact?
H-bonds
(In cellular respiration in animals), ATP synthase pumps H+ from where to where?
intermembrane space to mitochondrial matrix
