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88 Cards in this Set

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How many chromosomes in somatic, diploid cells?
46 chromosomes (2 each of numbers 1-22 + 2 sex chromosomes)
Females vs. males chromosomes
Females have 2X's
Males have X and Y
- One from dad and one from mom
Compare cells in the body/ makeup of DNA and expression of genes
- Every single cell in the body has same cell material/ DNA
- Expression of genes changes
Size of DNA
48-280 million basepairs
What phase is DNA replicated
S phase
When do daughter sister chromatides become attached to each other?
G2, M phase
Centromere
joining site, site of microtubule attachement during movement of sister chromatids to opposite m=poles o=in mitoses and meioses
What is centromeric DNA composed of?
AT-rich, short (171 bp) satellite repeats
What is a telomere
- ends that protect DNAs from shortening during replication
Number of genes in humans vs. mouse
27,000-mouse
29,000-human
Transposon
piece of DNA that can jump from one position to another
- create antibiotic resistance in bacteria
What percentage is the protein coding region?
1.5%
Breakdown- genes, transposons, misc
Genes- 30%
Transposons- 45%
Misc- 25%
What is included in breakdown of transposons?
- 21% LINEs
- 13% SINEs
- 8% retrovirus like
What is a gene?
- entire DNA sequence required for synthesis of useful RNA (rRNA, tRNA, mRNA or other RNA)
- includes promoters, enhancers, UTR's
What amount is expressable sequences?
29%
The protein-encoding, reading frames (without introns) are what percent of genome?
1.4%-
What is the rest of DNA that is not expressable sequence or protein encoding?
Spacer DNA between genes, and half of the spacer DNA is derived from ancient mobile genetic elements, some of which is still jumping form place to place in the genome
Introns + Exons in Ovalbumin gene and hemoglobin B subunit
Ovalbumin- 7 introns, 7 exons
Hemoglobin- 3 exons, 2 introns
90, 131, 222, 851, 126
Ex, In, Ex, In, Ex
4 steps of cell cycle, what is interphase and mitosis?
S, G2, M, G1
Interphase- G1, G2, S
Mitosis= PMAT
Cell cycle: what process occurs between S and G2?
- What are cohesins
replication and cohesion
- Replication occurs from multiple origins of replication; daughter chromatids are linked by cohesins
What occurs between G2 and Prophase of mitosis?
Condensins add for condensation
What leaves after prophase? What happens during this time?
Cohesins leave
- Alignment of chromatids
What happens in metaphase?
DNA condensed
What occurs between metaphase and anaphase?
separation of sister chromatids
What occurs between anaphase and G1?
- Condensins leave
Trace chromatid --> DNA
Two chromatids: 10 coils each
One coil: 30 rosettes
One rosette: 6 loops
One loop: 75,000 bp
30 nm fiber
"Beads on a string" form of chromatin
DNA
Mutation definition
permanent change in nucleotide sequence
Point mutation
permanent change of single nucleotide
Long term DNA mutation rate
Stable DNA mutation rate (mutations in gene pool) is 1% / million years
These mutations are basis of evolutionary process
Short term evolution rate
- What happens when somatic cell mutates?
- Mutations in somatic cells are more frequent and cause 20% of premature deaths in western hemisphere
- Most cancers are clones of cells with mutated DNA
Protecting somatic cell protects who? Protecting germline cell DNA protects...
- Somatic protects individual
- Germline protects species
(sperm and oocytes)
Types of Mutations (6 types)
mis- replication
depurinations
deaminations
alkylations
pyrimidine dimers
other
Mis-replication (frequency and cause)
- 10^-8 frequency
- DNA damage from environmental factors
- 1 error every 10 billion letters
Depurinations- what is it, how, how many
- Spontaneous hydrolysis of the beta N-glycosidic bonds
- Heat fluctuations in nucleus
- 5000 / cell/ DAY
How do deaminations occur? How many?
What are the products?
C, A, G deaminate to what products?
- Spontaneously
- 100 / cell/ DAY
- Unnatural base is product
C --> Uracile
A--> HX hypoxanthine
G --> X (xanthine)
Alkylations include what type of mutations? What is the effect?
- Methylations (metal group attaches)
- Large adducts such as benzo(a)pyrene from smoke
- Distort DNA
Pyrimidine dimers- what happens? How?
- UV induced covalent bonds between adjacent pyrimidines on same strand
Other types of mutations
- Ring opening
- Oxidation
- Cross-linkage
- Single and double strand breaks
Point Mutations (3)
Transitions
Transversions
Single base insertions/ deletions
A. Transitions, give example
Purine converted to different purine
A--> G
Pyrimidine converted to different pyrimidine C--> T
With transition mutations, what happens after a round of replication to the base pairs?
- A-T becomes G-C
- C-G becomes T-A
B. Transversions, give example
Purine converted to pyrimidine
Pyrimidine converted to purine
A-C, A-T, G-C, G-T
When transitions or transversions occur in gene-encoding a protein, what are 3 possible consequences?
Neutral- no change in AA
Missense- substitution change of one amino acid
Nonsense- creation of a stop codon leading to truncation of the AA sequence
Single Base Insertions/ Deletions: causes, consequences
- Caused by DNA polymerase stuttering
- If in protein reading frame, results in codon frameshift- all downstream codons incorrect
- Accidental stop codon crops up in new aberrant reading frame
DNA Replication- what is it?
- Make or reproduce an exact copy
Eukaryote- length of DNA
- Drosophila
- Human
Drosophila kB = 165, 000
length = 56,000

Human kB = 2,900,000
Length = 990,000
How many origins of replication do stem cells have?
20,000 origins of replication
Complexity of DNA- packaging
All eukaryotic DNAs are folded and packaged into dense, compact structures
- Associated with chromatin
What is chromatin?
tightly packed DNA-binding proteins which help to organize the package
What is relationship between complexity and replication?
- Complex structures are impediments to the replication mechanism that requires that two parental strands be totally separated by the end of the process
What is the meaning of DNA replicated semi-conservatively?
- Each daughter molecule ends up with a parental strand and a nascent strand
How is replication semi-discontinuous?
One strand is replicated continuously from 5'--> 3'
One strand replicates on 3'--> 5' strand, but discountinuously in segments
So 2 characteristics of DNA synthesis
- Semidiscontinuous
- Semiconservative
Where does replication start?
- Origin of replication, or multiple origins in nuclei
How is timing of replication of both strands related?
Growth of each "replicon" is bidirectional with both strands being replicated simultaneously
What enzyme works in replication?
Synthesis is carried out by DNA polymerases
What direction do DNA polymerases synthesize?
5' to 3' direction
- READ TEMPLATE IN 3' to 5' direction
What is proofreading by DNA polymerase?
- What 2 types of polymerases lack proofreading?
3' to 5' exonuclease activity is called proofreading
- Polymerases alpha and beta are exceptions that lack proofreading
What types of polymerase have 5 to 3' exonuclease activity that functions in repair? What other activity are they involved in?
- Prokaryotic DNA Pol I
- Eukaryotic Pol E (epsilon)
- Both involved in PRIMER REMOVAL
Why is DNA replication thermodynamically favorable? (4 conditions)...Drive polymerase reaction
1. dNTPs --> dNMPs + PPi
2. PPi --> 2 Pi (loss of product)
3. Base stacking
4. Hydrogen bond formation (adds energy)
What is the first step of the replication mechanism?
1- Initiation at ori (origin of replication)
What sequences originate the DNA strand?
- Tandem array of three 13 bp sequences
What is the significance of the 4 9bp sequences in the DNA
Binding sites for DnaA protein
What proteins promote unwinding at ori?
dsDNA-binding proteins
Function of ssDNA-binding proteins
Keep separated ssDNAs in an extended form
- binds to DNA and prevents strands from meeting
Function of helicase
- Uses ATPs to mechanically invade and separate strands at replication fork
Function of primase
- Synthesizes short RNA primers of 3-20 nucleotides in length
Direction of synthesis, free hydroxide
Synthesis is in the 5' to 3' direction, giving free 3'-OH for subsequent nucleotide extension
What is the name of primases in eukaryotes?
Prokaryotes- primase
Eukaryotes- DNA Pol alpha is RNA-synthesizing primase
Why is Pol alpha primase different from other DNA polymerases?
- With exception of Pol alpha, DNA polymerases cannot initiate a new strand (de novo)
- Only elongate a pre-existing primer
Function and kinds of DNA polymerases
- Elongates primer with deoxynucleotides
- DNA Pol alpha, beta, gamma, delta, epsilon
DNA Pol alpha function
Primes both strands
DNA Pol beta
functions in repair fo nuclear DNA
- incorporates one nuc and leaves
DNA Pol gamma
carries out all mitochondrial DNA synthesis
DNA Pol delta
replication elongation of both strands (very processive)
- DOES MOST OF WORK!
What is processivity?
Avg number of nucleotides added before the enzyme dissociates from the DNA
DNA Pol epsilon
involved in repair of nuclear DNA and probably primer removal, using 5' to 3' exonuclease activity
Prokaryotic DNA polymerases
DNA Pol I
DNA Pol II
DNA Pol III
DNA Pol I
- repair synthesis and primer removal with 5' to 3' exonuclease activity
- First polymerase to be characterized
DNA Pol II
- participates in repair
DNA Pol III
- replication elongation (highly processive)
- Does most of replicative work in bacteria
Topoisomerase I
1- Cleaves one strand of parental DNA beyond forks
2- permits further unwinding of parental DNA
3- reseals (rejoins) the nicked ends
Topoisomerase II
- cleaves both strands
- allows unwinding of overwound Watson-Crick strands
- rejoins ends
What is the cofactor for Topo II?
- ATP
What is a version of Topo II in bacteria?
Gyrase
- makes a double strand scission
- forcibly underwinds DNA
- reseals scision
What is result of undwerwining strain in gyrase?
- Relieved by supercoiling
Is topo I or II more important for bacteria?
- Topo II is more crucial to the viability of the cell