1
Q
transformation
A
A change in genotype and phenotype due to the assimilation of external DNA by a cell. When the external DNA is from a member of a different species, this results in horizontal gene transfer.
2
Q
phage T2 experiment
A
- 1952; Alfred Hershey and Martha Chase
- one of the many phages that infect E. coli
- phages grown w/ radioactive sulfur (S-35) were incorporated into phage protein
- phages grown w/ radioactive phosphorus (P-32) were incorporated into phage DNA
3
Q
Chargaff’s rules
A
1) base composition varies btwn species
2) within a species, the number of A,T bases are equal; number of G,C bases are equal
4
Q
double helix numbers
A
- Franklin’s X-ray data indicated that the helix makes 1 full turn every 3.4 nm along its length
- w/ the bases stacked just 0.34 nm apart, there are 10 layers of base pairs, in each full turn of the helix
- uniform width throughout (2 nm)
- purines (A,G) 2x as wide as pyrimidines (C,T)
5
Q
pairing
A
- A forms 2 H bonds w/ T
- G forms 3 H bonds w/ C
6
Q
3 models of DNA replication
A
- semiconservative: the replicated double helix consists of one old strand, derived from the parental molecule, and one newly made strand.
- conservative: the 2 parental strands come back together after the process.
- dispersive: all 4 strands of DNA following replication have a mixture of old and new DNA.
7
Q
replication fork
A
- Y-shaped region where the parental strands of DNA are being unwound
- HELICASES: enzymes that untwist the double helix at the replication forks, separating the 2 parental strands and making them available as template strands
- SINGLE-STRAND BINDING PROTEINS: bind to the unpaired DNA strands, keeping them from re-pairing.
- TOPOISOMERASE: the untwisting of the double helix causes tighter twisting and strain ahead of the replication fork; topoisomerase helps relieve this strain by breaking, swiveling, rejoining DNA strands
8
Q
initiation of replication
A
- the enzymes that synthesize DNA can’t initiate the synthesis of a polynucleotide; they can only add nucleotides to the end of an already existing chain that is base-paired w/ the template strand
- the initial nucleotide chain that is produced during DNA synthesis is actually a short stretch of RNA; this RNA chain is called a PRIMER, synthesized by the enzyme PRIMASE
- primer is 5 - 10 nucleotides long
9
Q
DNA synthesis rate; number
A
- 11 polymerases discovered in eukaryotes so far
- E. coli: several polymerases, but pol I and pol III play the major roles
- bacteria: 500 nucleotides per second
- humans: 50 per sec
10
Q
DNA synthesis
A
- enzymes called DNA polymerases add nucleotides to a preexisting chain
- each nucleotide added to a growing strand comes from a nucleoside triphosphate (DNA pol III)
- as each monomer joins the growing end of a strand, 2 hposphate groups are lost as a molecule of pyrophosphate
- subsequent hydrolysis of the pyrophosphate to 2 molecules of INORGANIC PHOSPHATE is a coupled exergonic rxn that helps drive the polymerization rxn
11
Q
leading strand
A
- DNA pol III remains in the replication fork on that template strand and continuously adds nucleotides to the new complementary strand as the fork progresses
- only 1 primer required
12
Q
synthesis of lagging strand
A
- primase joins RNA nucleotides into a primer
- DNA pol III adds DNA nucleotides to the primer, forming Okaz frag 1
- after reaching the next RNA primer “ahead” of it, DNA pol III detaches
- DNA pol I replaces the RNA (primer) w/ DNA
- DNA ligase forms a bond btwn the newest DNA and the DNA of the “ahead” fragment
13
Q
DNA ligase
A
joins the final nucleotide of the replacement DNA segment (that replaces the RNA of the primer) to the first DNA nucleotide of the adjacent Okaz frag
- joins the sugar-phosphate backbones of all Okaz frag into a continuous DNA strand
14
Q
DNA replication complex
A
- the various proteins that participate in DNA replication form a single large complex
- the complex may not move along the DNA; rather, the DNA may move thru the complex
- eukaryotes: multiple copies of the complex may be anchored to the nuclear matrix
15
Q
roles of primase
A
by interacting w/ other proteins at the fork, primase apparently acts as a molecular break,
- slowing progress of the replication fork
- coordinating the placement of primers and the rates of replication on the leading and lagging strands.
16
Q
proofreading
A
DNA polymerases proofread each nucleotide against its template as soon as it is added to the growing strand. Upon finding an incorrectly paired nucleotide, the polymerase removes the nucleotide and then resumes synthesis.
17
Q
mismatch repair
A
- when mismatched nucleotides evade proofreading by a DNA polymerase, other enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors.
- a hereditary defect in one of these repair enzymes is associated w/ a form of colon cancer.
18
Q
UV light
A
- one resulting type of damage is the covalent linking of THYMINE bases that are adjacent on a DNA strand
- such THYMINE DIMERS cause the DNA to buckle and interfere w/ DNA replication.
19
Q
one DNA repair system
A
- a segment of the strand containing the damage is excised (cut out) by a DNA-cutting enzyme – a NUCLEASE – and the resulting gap is then filled in w/ nucleotides, using the undamaged strand as a template
- the enzymes involved in filling the gap are a DNA polymerase and DNA ligase
- one such DNA repair system is called NUCLEOTIDE EXCISION REPAIR
20
Q
UV light: disorder
A
- xeroderma pigmentosum
- in most causes, caused by an inherited defect in a nucleotide excision repair enzyme
- individuals are hypersensitive to sunlight; mutations in their skin cells caused by UV light are left uncorrected, resulting in skin cancer
21
Q
shortening of the ends of DNA molecules
A
- linear molecules
- lagging strand: after the end primer is removed, it can’t be replaced w/ DNA b/c there’s no 3’ end available for DNA polymerase to add nucleotides
22
Q
telomeres
A
- eukaryotic chromosomal DNA molecules have these special nucleotide sequences at their ends
- no genes; just multiple repetitions of one short nucleotide sequence
- in each human telomere: the 6-nucleotide sequence TTAGGG is repeated btwn 100 and 1,000 times
- specific proteins associated w/ telomeric DNA prevent the staggered ends of the daughter molecule from activating the cell’s systems for monitoring DNA damage. (staggered ends, which often result from double-strand breaks, can trigger signal transduction pathways leading to cell cycle arrest / cell death)
23
Q
telomerase
A
- enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication
- NOT active in most human somatic cells, but its activity in germ cells results in telomeres of max length in the zygote
24
Q
telomere shortening
A
- normal shortening may protect organisms from cancer by limiting the number of divisions that somatic cells can undergo
- cells from large tumors often have unusually short telomeres `
- further shortening would presumably lead to self-destruction of the tumor cells; however, researchers have found telomerase activity in cancerous somatic cells, suggesting that telomerase’s activity to stabilize telomere length may allow these cancer cells to persist
25
levels of chromatin packing
(eukaryotic)
1. DNA, the double helix
2. histones
3. nucleosomes "beads on a string" (10-nm fiber)
4. 30-nm fiber
5. looped domains (300-nm fiber)
6. metaphase chromosomes
26
histones
- each histone is small; contains only ~100 amino acids
- total mass of histone in chromatin approximately equals the mass of DNA
- >0.2 of a histone's amino acids are positively charged (LYSINE/ARGININE) and therefore bind tightly to the negatively charged DNA
- 4 types are most common: H2A, H2B, H3, H4
27
nucleosome
- beads on a string (nucleosomes are the beads); 10 nm in diameter
- basic unit of DNA packing; the 'string' btwn 'beads' is called linker DNA
- a nucleosome consists of DNA wound twice around a protein core composed of 2 molecules each of the 4 main histone types
- the amino end (N-terminus) of each histone (HISTONE TAIL) extends outward from the nucleosome
28
30-nm fiber
- results from interactions btwn the histone tails of one nucleosome and the linker DNA and nucleosomes on the other side. these interactions cause the extended 10-nm fiber to coil/fold, forming a chromatin fiber roughly 30 nm in thickness
- a 5th histone, H1, is involved
- quite prevalent in the interphase nucleus
29
looped domains
- the 30-nm fiber forms loops called LOOPED DOMAINS attached to a chromosome scaffold made of proteins, thus making up a 300-nm fiber
- the scaffold is rich in one type of TOPOISOMERASE; H1 also present
30
interphase chromatin
although it lacks an obvious scaffold, its LOOPED DOMAINS appear to be attached to the nuclear lamina, on the inside of the nuclear envelope, and perhaps also to fibers of the nuclear matrix
31
heterochromatin
- even during interphase, the centromeres and telomeres of chromosomes, as well as other chromosomal regions, exist in a highly condensed state similar to that seen in a metaphase chromosome
- visible as irregular clumps w/ a LM
- largely inaccessible for transcription b/c of its compaction
32
euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription.
