polymorphic?

polymorphism?

DNA MArker?

anonymous locus?

• Two or more alleles at a locus
• the particular variation( 2 different phenotypes)
• polymorphic useful for mapping studies, disease diagnosis
• position on genome with no known function

• SNP( single nucleotide polymorph)
• microsatellite
• minisatellite
• deletion or duplication

• single bp substitutions
• biallelic- only affect 2 allleles
• most occur at anonymous loci
• useful as DNA markers

• repeats of 2-5 bp
• highly useful as DNA markers
• mutate by replication error

• repeates 20-100 bp long
• cam be generated by unequal crossover because sequence is so alike for so long

unequal crossover or transposable elements insertion

- much less common

1. once section is amplified, single nucleotide changes can change amount of restriction sites, then gel electrophoresis
2. can detect changes in fragment sizes due to missing restriction sites

What are ASO's

• allele specific oligonucleotides
• short frags <21, which hybridize to one allele or the other
• therefore they are allele specific

ASO with microarrays can be how accurate?

what do they find?

can functionally give you gene sequence

-heterozygotes

Histones are?

5 types, which ones make up nucleosome (core histones)?

• small proteins with basic, positively charged amino acids lysine and arginine
• bind to and neutralize negative DNA
• 5 types: H1, H2A, H2B, H3, H4
• core = all but H1

Nucleosome properties:

diameter?

How many bp's?

histones?

bp's between nucleosomes?

• 100 A
• about 160bp
• 8 histones (2 x (H2A,H2B,H3,H4))
• 40 bp's

Non-Histone proteins are? Function?

• half of all chromatin proteins
• scaffold - backbone of chromosome
• DNA replication - DNA polymerases
• chromosome segreagation - motor proteins of kinetochores
• Transcriptional regulation - regulates transcription during gene expression

Which is the function of chromatin?

 A - scaffolding DNA

 B - replication complexes

 C - Chromosome segregation

 D - All of the Above

• gene expression
•  more space = and increase in gene expression by RNA polymerase
• less space = less room for protein interaction and RNA polymerase = less gene expression

solenoid is?

how is it possible?

superwrapping of nucleosomes

• radial loop scaffold - each loop contains 60-100 kb of DNA tethered by non-histone scaffold proteins

Karyotypes are useful because?

what phase is the chrom. in?

- they produce unique reproducible banding patterns, help locate genes, disease, and differences in species

- Chromosome in highly compacted metaphase stage

replicon?

how many origins in mammals?

each bidirectional replication

- 10,000

• binds to TTAGGG of DNA and extends the ends with addition RNA.
• creates a 3' end for DNA polymerase I to fill

structure and function of centromeres?

satellite DNA?

• constriction sites on chromosomes that are contained with blocks of repeated, non-coding DNA 5 -300 bp in length called satellite DNA.
• hold sister chromosomes together
• kinetochores - structure composed of DNA and protein that power chromosome movement

heterochromatin?

Euchromatin?

• darkly stained, highly compacted, near centromere = Y chromosome
• lightly stained regions, contains most genes

Heterozygosity for deletion is good/bad?

homozygosity?

bad, detrimental

lethal

Tandem

non-tamdem duplications?

- duplications next to each other(reverse, same)

- duplications apart from each other

(reverse, same)

chromosomal breakage (X-ray)

• location of gene on chromsome which modifies expression
• either 1 or 3 copies of a gene
• generates families of tandemly repeated genes

pericentric

paracentric inversions?

both create .....?

across centromere

aside centromere

imblalanced gametes

can an inversion affect phenotype? If so, how?

Inversion also ... recombinance?

Yes, if it disrupts a gene (cuts it in half)

suppresses

translocation?

reciprocal translocation?

• part of one chromosme combines with another non-homologous chromosome
• Two different parts of chromosomes switch places with each other

• dicentric( 2 centromeres) chromosome that will break

• Acentric Chromosome (no centromere) that will be lost

one large metacentric chromosome and one tiny chromosome that may be lost

- drives evolution( elimination of chromosomes in body)

Retroposons do what?

2 types?

generate an RNA that encodes a reverse transcriptase enzyme.

• one that has two LTR's( long terminal repeats) at either ends
• one that has a poly A tail at the end

• transposon is moved to a new location
• broken chromosome of transposon is then either fixed to give it an identical transposon as beore or sealed up without it
• it depends on the homologous chromosome

non-autonomous elements?

autonomous elements?

• need activity of non-deleted copies of the same TE for movement
• can move freely

Aneuploidy?

monosomy

trisomy?

• the loss or gain of one or more chromosomes(creates odd number of total chromosomes)
• monosomy - 1 copies of one chromosome #
• trisomy - 3 copies of one chrom. #

mitotic nondisjunction?

chromosome loss?

• the failure of sister chromatids to separate in first meiotic division of anaphase
• produces one monosomic and one diploid daughter cell

• region between two break points on the chromosome
• region of overlap where one strand is from original chrom. and one chrom. is from the new chrom.

gene conversion?

mismatch repair?

•  a mismatch repair that results in something other than a 2:2 segregation of alleles.
• the repair of a heteroduplex

• strand is broken by enzymes
• resection - strands are degraded to two 3' ends
• invasion - rads bind 3' tails and double helix allowing invasion and migration
• formation of X or holliday function
• branch migration- both invading strands zip up and heteroduplexes rewind behind

• holliday intermediate of non homologous chromosomes is formed as they disengage to form an X
• endonuclease cuts holliday intermediate

two vert cuts =?

tow hor. cuts = ?

hor. and vert cuts =?

• no crossover
• no crossover
• crossover

1. transformation - cell lysis
2. conjugation - donor plasmid sends one strand over via connection bridge
3. transduction - through bacteriophage

Hfr cells?

episomes?

exconjugates?

• cells have integrated part of chromosome
• plasmids that can integrate into chromosome
• recipient cell with integrated DNA

• natural - foreign dNA enters cell via import machinery
• artificial - DNA enters through damage in the cell wall

merizygotes?

heterogenotes?

partial diploids in which two gene copies are identical

partial diploids carrying different alleles of the same gene

• initiation - sigma factor pulls in RNA pol
• elongation - movement away from promoter, sigma unit released
• termination - release signal reached by RNA pol

• Rho dependent - Rho factor recognizes DNA sequence, binds to it and pulls it away from RNA pol
• RHo independent - stem loop structure and repetitive U's tells RNA pol to release

Operon theory of gene regulation?

OPERONS?

• a single signal can simultaneously affect the expression of multiple genes that are clustered on the same chromosome involved with the same function
• clusters of genes

Repressor?

inducer?

induction?

Operator?

trans-acting elements?

cis?

corepressor?

Activater

• protein that blocks translation
• molecule that stimulates gene expression
• turning on of genes
• negative regulatory switch
• elements that can affect any DNA strand
• elements that can affect only their own DNA strand
• stimulates repression of genes
• stimulates increased expression of genes

CRP and cAMP when binded together are?

High levels of glucose .... availability of cAMP

activators

decrease

araC acts as?

with no arabinose present it forms a .... that.... RNA pol from binding

both a repressor and an activator

loop that inhibits

leader sequence can fold into two different stable conformations

            -tryptophan present

            -no tryptophan

• present - allows ribosome that pass quickly by trp codon and 3-4 termination loop forms to stop transcription. no more tryptophan formed
• not - ribosome gets stalled at trp codon and allows 2-3 loop to form instead allowing transcription to continue to allow translation of tryptophan molecules.

control after transcription starts

-reduce signal

• under normal conditions
• heat shock

mRNA of sigma 32 stabilizes at higher temps increasing gene expression

sigma 70 becomes ineffective and therefore decreases competition

under normal conditions DNA J and K inhibit binding of sigma 32.

at high temps this binding/blocking doesnt occur

most repressors

fits into major groove of DNA

fuses to DNA

reports of how much product that it is making along with other genes that are cis to it

- expression is quantifiable by protein detection