1
Q
the genome must be _ before each cell division
A
must be accurately copied
-each daughter strand gets a copy
2
Q
Template strand
A
a strand of DNA that can be used for synthesis of a complementary strand of DNA
-relies on complementary base pairing (T & A, G & C)
3
Q
Replication machine
A
Cluster of proteins that work together to carry out DNA replication
4
Q
Semiconservative model
A
The daughter DNA double helix contains one strand conserved from the parental molecule and one newly synthesized strand
semi > half parent half new
5
Q
Replication origin (aka origin of replication)
A
the locations in the chromosome where DNA replication will begin
* about 100 nucletide pairs long
6
Q
how many replication origins do bacteria have?
A
one replication origin in their single circular chromosome
7
Q
how many replication origins do humans have?
A
10 000 origins (about 220 per chromosome)
-can start replication at lots of spots, allows faster replication
8
Q
what are the 3 functions of initiator proteins
A
- bind to DNA sequences at the replication origin
- pry the two DNA strands apart, breaking the hydrogen bonds
- attracts proteins that carry out replication (protein machine)
9
Q
how many hydrogen bonds between A and T?
A
2H bonds
10
Q
how many hydrogen bonds between C and G?
A
3
11
Q
Replication fork
A
Y-shaped junction where dsDNA is unwound into ssDNA
-two forks formed at each replication origin
-move away from each other in opposite directions (bidirectional DNA replication)
12
Q
what does the replication machine do at the replication fork at the beginning of replication
A
Moves along the DNA at the fork unzipping the double helix and using the DNA strand as a template to make a new daughter strand
13
Q
How fast does the replication machine move in bacteria?
A
1000 nucleotide pairs per second
14
Q
How fast does the replication machine move in humans?
A
100 nucleotides per second
-slower than bacteria bc we have a more complex chromosome structure, more bulky, so harder to get around
15
Q
how does DNA polymerase 3 add nucleotides?
A
- adds nucleotides to the 3’ end of a growing DNA strand using complementary base pairing
-catalyzes the formation of phosphodiester bonds between the 3’ end (hydroxyl group) of last nucleotide on the growing DNA strand and the 5’ end (phosphate group) of the incoming nucleotide - Nucleotides enter as a deoxyribonucleoside triphosphate
-provides the energy for its own addition to the growing strand
-hydrolysis releases pyrophosphate
16
Q
DNA polymerase 3 makes one error in every
A
10^7 nucleotide pairs
17
Q
how does DNA polymerase reduce errors?
A
- the enzyme monitors the base pairing between nucleotide triphosphates and the template strand
- the match must be correct for DNA polymerase to undergo the conformational change that allows catalysis of the phosphodiester bond (when no conformational change -bc wrong pair, there’s a stall to get it correct)
- proof reading: DNA polymerase corrects errors it has made
-before adding the next nucleotide, the enzyme double checks its work
-polymerization and proof reading are done by different domains of the enzyme
18
Q
Leading strand
A
Synthesized continuously in a 5’ -> 3’ moving towards the replication fork
19
Q
Lagging strand
A
Synthesized discontinously in a 5’ -> 3’ direction in small pieces that each move away from the replication
-forms Okazaki fragments
-more cumbersome method of replication, results in a slight delay in synthesis compared to the leading strand
20
Q
why do we need RNA primers?
A
DNA polymerase only adds nucleotides to an existing strand of nucleotides
21
Q
what does primase do?
A
Synthesizes an RNA primer
-about 10 nucleotides long
-complementary to the DNA template
-provides a 3’ end as a starting point for DNA polymerase
22
Q
Compare need for primers on the leading strand vs lagging strand
A
- leading strand: one primer at the replication origin
- lagging strand: new primer needed for each Okazaki fragment
23
Q
what does nuclease do?
A
degrades the RNA primer
24
Q
what 3 enzymes are involved in linking okazaki fragments?
A
- Nuclease
- Repair polymerase (DNA polymerase 1)
- DNA ligase
25
what does repair polymerase (DNA polymerase l) do?
Replaces the RNA primer with DNA
-uses the adjacent Okazaki fragment as a primer
26
what does DNA ligase do?
Joins the 5' phosphate end of one DNA (okazaki) fragment to the adjacent 3' hydroxyl end of the next
27
what does DNA helicase do?
Unzips the DNA double helix
-uses energy from ATP hydrolysis
28
what are the 4 proteins in the replication machine at the replication fork?
1. DNA helicase
2. Single-strand DNA binding protein
3. DNA topoisomerase
4. Sliding clamp and clamp loader
29
what does single-strand DNA binding protein do?
* binds to the newly exposed single stranded DNA
-prevents the double helix from re-forming (on lagging strand, leading strand doesn't need bc new nucleotides are continuously being added)
30
what does DNA topoisomerase do?
Relieves tension in the double stranded DNA caused by excessive twisting as the replication fork is formed
-makes a single-stranded break in the DNA backbone
-reseals the break once tension has been released
31
what does the sliding clamp do?
keeps DNA polymerase attached to the template
32
what does the clamp loader do?
* locks a sliding clamp around a new DNA double helix
* removed and reattached each time a new Okazaki fragment is made
* clamp loader removes clamp for DNA polymerase to come off and move to next fragment
33
Leading strand can be synthesized all the way to the end till DNA polymerase falls off the end, but the lagging strand cannot, so what happens?
* when primer at the end of the strand is removed, there is nothing to add DNA nucleotides to
* so lagging strand becomes shorter with each round of DNA replication
* chromosome will become shorter and will eventually lose valuable genetic information, and can become no longer effective, bc it can no longer make functional protein
34
Telomeres
* long repetitive nucleotide sequences added to the ends of the chromosomes (to protect shortening of strands)
-allows the cell to distinguish between the natural ends of the chromosomes and the random breaks (for recognition of damage)
35
Telomerase
Enzyme that carries its own RNA template that it uses to add multiple copies of the copies of the same repetitive DNA sequence to the lagging strand template
-replicates the ends of eukaryotic chromosomes
36
Telomere Length varies by...
varies by cell type and age of a person
37
what cells keep telomerase fully active?
Rapidly dividing cells, like cells that line the digestive tract, and bone marrow cells that generate red blood cells
(bc there's so much replication telomeres would break down very quickly so you gotta keep making more)
38
what happens to cells that reduce their telomerase activity?
* telomeres in these descendent cells shrink and eventually disappear (with aging you run out of telomeres > cells deteriorate, how people die from old age)
* Cells will cease dividing (if they did replication will eventually eat into essential DNA)
39
why do some cells reduce their telomerase activity?
Provides a safeguard against uncontrolled proliferation of cells
40
How can DNA damage arise
* can happen spontaneously during DNA replication: DNA polymerase may add the wrong nucleotide, and proofreading doesn't notice
* or can happen after DNA replication: can be spontaneous due to environment
* or physical or chemical thing can cause damage (like UV radiation)
41
what's Depurination and how does the cell recognize it as damage?
Removal of a purine from a nucleotide
(sugar and phosphate still remain -just double ring -nitrogenous base of A or G removed)
* this is recognized as damage bc there's a nucleotide on the other strand that's not paired up with anything
42
what's Deamination and how does the cell recognize it as damage
* loss of amino group (NH3) from cytosine to produce uracil
* recognized in DNA bc uracil shouldn't be in DNA
43
what are Thymine dimers and how does the cell recognize it as damage?
UV radiation promotes covalent linkages between two pyrimidine bases, producing thymine dimers (pyrimidines are T & C)
* recognized as damage bc it produces buldge in double helix
44
thymine dimers common in people with what condition
* Xeroderma pigmentosum: inability to repair thymine dimers
* even if it's recognized as damage
* makes people sensitive to sun
45
what are the results of unrepaired DNA damage
* Substitution of one nucleotide pair for another
* Deletion of one or more nucleotide pairs in the daughter DNA strand after DNA replication (frame shift mutation)
* Stalling of the replication machinery at the site of damage - thymine dimers
46
what are the mechanisms of repair?
* if the sequence in one strand is accidently damage:
-information is not lost irretrievably bc of double helix: back up version of the altered strand remains in the other undamaged strand
* the cell can distinguish between good strands and damaged strands, to know when to repair
-ex: thymine dimers and uracil bases do not belong in DNA
47
what are the 3 steps of the mismatch repair system for DNA?
1. Damaged DNA is recognized and removed using nucleases
-cuts the sugar phosphate backbone (excision)
-leaves a gap on one strand of the double-helix
2. Repair DNA polymerase binds the 3' end of the cut DNA strand and fills the gap with complementary nucleotides
-works in the same way as DNA polymerase does in DNA replication
-in many cells this is DNA polymerase l
3. DNA ligase seals the break between the new nucleotides and the full DNA strand
48
what percent of replication errors does the mismatch repair system repair?
99% of replication errors
49
the mismatch repair system allows only one mistake in how many nucleotides to remain permanent?
* one mistake in 10^9 nucleotides synthesised remains permanent
50
If a mistake remains permanent in the DNA we're ok because why?
* Because there's 2 copies of each gene in every person due to homologous chromosomes (for an issue to occur both homologous chromosomes have to be mutated)
-if you inherit a damaged gene in one homologous chromosome, it will not result in cancer
-only need to spontaneously develop one mutation in the same gene to cause disease
-mutation in mismatch repair genes in very common in colon cancer (bc colon cells are constantly repairing, they're more likely to have mutation)
51
how do Double-Strand DNA breaks occur? what's the result of them
**Can occur from: **
* mishaps at the replication fork (if strands are pulled apart too hard, can break), radiation, chemicals
**Results in:**
* fragmentation of the chromosome and loss of genes
* no copies that can be used as a template to reconstruct lost information (no undamaged strand)
* Nonhomogous end joining
52
what's nonhomologous end joining?
* Stick the broken ends of a double stranded break back together before the DNA fragments drift apart and get lost
* Specialized group of enzymes clean-up and ligate the broken ends (if ends are jagged, nucleotides are cut to make them straight, lose nucleotides and get deletions though)
* Nucleotides are often lost at the site of repair
53
what's homologous recombination?
* if damage occurs after the stretch of DNA has been replicated, the undamaged double-helix can serve as a template for repair
* the two DNA molecules (sister chromatids) have identical or nearly identical nucleotide sequences across the broken region
* this mechanism has been conserved in virtually all cells on Earth
54
what's the best method of DNA repair, why?
Homologous recombination because no nucleotides are lost
55
describe the steps of homologous recombination?
1. Nuclease degrades 5' ends of broken strands
2. 3' end invades the unbroken homologous DNA and finds a complementary sequence
-bacteria: recA
-Eukaryotes: rad52
3. Invading strand is elongated by repair DNA polymerase (l) using the complementary undamaged strand as a template
4. Newly elongated strand rejoins its original partner forming base pairs that hold the two strands of the double helix together
5. DNA ligation completes the repair
56
what are the recombinase enzymes that push the 3' end into the unbroken homologous DNA to find the complementary sequence in homologous recombination in bacteria vs eukaryotes?
* Bacteria: recA
* Eukaryotes: rad52
57
Mutation
* Permanent change in the DNA sequence (not repaired)
* May or may not alter the amino acid sequence of a protein making it non-functional (if it's silent doesn't change AA, just codon changes)
* some are detrimental, some are neutral some are beneficial
58
what results from mutation in germ-line cells? (cells that go through meiosis)
Mutation in germ-line cells will be passed on to all the cells in a multicellular organism, including the gametes that produce the next generation
59
what results from mutation in somatic cells? (anything that's not sperm and egg)
Somatic cell mutation can give rise to variant cells that grow and divide in an uncontrolled fashion at the expense of other cells in the organism
-causing cancer
60
what happens to mutations that have harmful consequences?
Natural selection eliminates the ones that result in harmful consequences -bc that organism doesn't live long enough to pass on genes
61
what are two harmful consequences that result from mutations which natural selection eliminates?
Death or decreased fertility
62
when no selection against a mutation occurs (bc mutation was in a site that did not affect the organism) what happens?
The genetic message can remain preserved over tens of millions of years
* 100 million years of evolution have barely changed the essential content of the DNA (DNA that codes for things needed for replication, ribosomes, transcription, translation, making lipids, nucleic acids etc)
Cell bio
flashcards
Decks in class (9)
# Cards
-
Topic 1. Introduction to Cell biology54
-
Topic 2: Chemical Components of Cells94
-
Topic 3: Bioenergetics, Enzymes, and Metabolism51
-
Topic 4: Protein Structure and Function106
-
Topic 5: DNA and Chromosomes41
-
Topic 6: DNA replication62
-
Topic 7: From DNA to Protein89
-
Topic 8: Control of Gene Expression67
-
Topic 9: Genetic Evolution and the Study of Genes66
