Ngu Genetics Final Sp-11

Front 1

size of a virus genome

Back 1

10^3 - 10^5 base pairs

Front 2

size of prokaryote genome

Back 2

10^6 base pairs or 1 Mb

Front 3

size of a eukaryotic genome

Back 3

10^8 - 10^9 base pairs

Front 4

size of human genome

Back 4

3.4 billion base pairs

Front 5

How do you tell if DNA is double-stranded or single-stranded?

Back 5

Look at the ratio of bases, does A=T and G=C?

Front 6

How do you tell if DNA is linear or circular?

Back 6

If ends are digested by exonuclease, it must be linear

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Lambda phage virus

Back 7

double-stranded single linear chromosome with single-stranded complementary ends

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T2, T4, T6

Back 8

double stranded DNA linear chromosome

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phiX174

Back 9

Single-stranded single circular chromosome

Front 10

plasmid

Back 10

smaller chromosome of 2 in prokaryotes that is dispensible

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karyotype

Back 11

complete set of metaphase chromosomes in a eukaryotic cell

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chromatin

Back 12

stainable material consisting of DNA plus proteins

Front 13

What types of histones are there?

Back 13

H1, H2A, H2B, H3, H4

small and positively charged

Front 14

nonhistones

Back 14

vary greatly, negatively charged, bind to histones

Front 15

nucleosome

Back 15

bead-like regions of DNA compacted by histone binding

Front 16

when are chromosomes most compacted?

Back 16

mitosis and meiosis

Front 17

When are chromosomes least compacted?

Back 17

During S phase when replication occurs

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centromeres

Back 18

important location on chromosome where mitotic or meiotic spindle fibers attach

Front 19

kinetochore

Back 19

centromere when proteins bind and the end of the microtubule attach

Front 20

telomeres

Back 20

important in DNA replication. At the end of the chromosome and provide stability. Extreme ends can contain a short repeating sequence

Front 21

tandem repeats

Back 21

repetitive sequences in a row

Front 22

LINEs

Back 22

long interspersed elements, long family of repeating sequence

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SINEs

Back 23

short interspersed elements, short family of repeating sequence

Front 24

Alu

Back 24

most abundant SINE in humans, about 9% of the genome

Front 25

DNA polymerases

Back 25

catalyze DNA synthesis

Front 26

DNA replication requires

Back 26

1) a primer in the presence of Mg2+
2) A DNA template
3) All 4 dNTPs

Front 27

How many DNA polymerases does E. coli have?

Back 27

I, II, III, IV, and V

Front 28

Which DNA polymerases are important for repair in E. coli?

Back 28

II, IV, V

Front 29

DNA polymerases I and III

Back 29

replicate 5' to 3' and have 3' to 5' exonuclease activity. Reduces error rate to 10^-9 bases/error

Front 30

DNA polymerase I

Back 30

5' to 3' exonuclease activity

Front 31

Initiation occurs at a gene sequence called the _______, which in E. coli is called oriC

Back 31

replicator

Front 32

initiator protein

Back 32

bind to the 9bp replicator and causes AT-rich region to denature

Front 33

DNA helicases

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unwind DNA

Front 34

primosome

Back 34

each helicase forms this complex with DNA primase that synthesizes 5-10 RNA primer that is replaced with DNA

Front 35

DNA gyrase

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a form of topoisomerase that relaxes tension in the helix ahead so helicase can continue unwinding

Front 36

DNA ligase

Back 36

seals final 5' to 3' gap left when DNA pol I replaces RNA template with DNA

Front 37

replisome

Back 37

all replication machinery moves along together at one replication fork

Front 38

DNA pol III holoenzyme

Back 38

all enzymes of DNA pol III

Front 39

rolling circle replication

Back 39

form of replication viral genomes may use; forms one long molecule that is then cut by endonuclease

Front 40

replicon

Back 40

distance between 2 replication forks in eukaryotic replication

Front 41

origin recognition complex

Back 41

protein that binds to replicator to initiate replication in eukaryotes

Front 42

cdks (cyclin dependent kinase)

Back 42

regulate the cell life cycle; become active in S phase

Front 43

eukaryotic cells have ______ polymerases

Back 43

15+

Front 44

telomerase

Back 44

adds repeating sequences to chromosome ends after replication when RNA primer is removed and there's a gap left

Front 45

When are histones translated in replication?

Back 45

Histone genes are transcribed in late G1 so they can be transcribed during S

Front 46

phenylketonuria

Back 46

recessive mutation on gene for phenylalanine hydroxylase. Usually converts excess phenylalanine to tyrosine but instead it accumulates at phenylpyruvic acid. Causes mental retardation.

Front 47

Tay-Sachs disease

Back 47

caused by mutation in Hex A that cleaves Gm2 in brain. It accumulates and causes reaction to sharp sounds, spot on retina, and neural degeneration. Fatal after 3-4 years

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Albinism

Back 48

1 type mutation on gene for tyrosinase to convert tyrosine to DOPA, from which melanin is made

Front 49

What are promoter sequences in prokaryotes?

Back 49

-10 5'TATAAT3'
-35 5'TTGACA3'

Front 50

rho independent termination

Back 50

has inverted repeats about 20 bp before termination followed by ATs. It is translated, forms hairpin, and dissociates

Front 51

Rho dependent termination

Back 51

rho protein binds to a C rich region and uses ATP to release the RNA transcript

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In eukaryotes, RNA polymerase I transcribes...

Back 52

transcribes some rRNA

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In eukaryotes, RNA polymerase II transcribes....

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mRNA and some snRNA

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In eukaryotes, RNA polymerase III transcribes....

Back 54

tRNA, some mRNA, some snRNA

Front 55

core promoter

Back 55

determines start of transcription; Inr sequence with +1 site, TATA box around -30

Front 56

Promoter proximal elements

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determine efficiency of transcription; -75 CAT box, -90 GC box

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Transcription factors

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must assemble on the core promoter becase RNA pol II cannot directly recognize promoter

Front 58

5' cap

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1st 2 sugars on 5' end are methylated and guanine is added in 5' to 5' linkage

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3' poly A tail

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50-250 As added with no template; protects agains exonuclease activity

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transcription termination in eukaryotes

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termination factors bind to poly A tail

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snRNA + protein =

Back 61

snRNP

Front 62

snRNPs + pre-mRNA =

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spliceosome

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the anticodon on tRNA is on loop....

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2

Front 64

the amino acid attaches to tRNA where?

Back 64

on CCA of 3' end

Front 65

wobble hypothesis

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3rd letter is not as constrained, so multiple bases can match there

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polysome

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more than 1 ribosome translating same mRNA at 1 time

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termination of translation

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release factors recognize stop codons

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mutation rate

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probability of a mutation over time, number per bp per generation

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mutation frequency

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probability of a certain mutation across individuals (percent of a population)

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depurination

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bond breaks between purines and sugar, leaving no template

Front 71

deamination

Back 71

cytosine losese amino group, forming uracil or thymine and causing transitions

Front 72

methyl-directed mismatch repair

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mechanism in E. coli to repair base pairs that remain uncorrected after replication

Front 73

insertion sequences

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contain no genes other than those needed to move the elements

Front 74

composite transposons

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contain a gene region flanked by IS modules

Front 75

noncomposite transposons

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not flanked by IS elements, so transposition enzymes are encoded by genes in central region

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cDNA libraries are not equivalent to genomic libraries because...

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cDNA libraries are made from mRNA so they do not contain introns

Front 77

composite transposons

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(in prokaryotes) contain a gene flanked by IS regions

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noncomposite transposons

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(in prokaryotes) gene flanked by repeating sequences but not IS elements, so transpositional enzymes are encoded in central gene region

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autonomous elements

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(in eukaryotes) transposable elements that can move themselves (LINEs)

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nonautonomous elements

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(in eukaryotes) lack the gene for transposition (SINEs)

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What are limitations of PCR?

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1) fragments generally can't be longer than 20 bp
2) Taq polymerase introduces errors
3) Sensitivity makes contamination a problem
4) Requires knowledge of flanking sequence

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ddNTP =

Back 82

dideoxynucleotide triphosphate

Front 83

microarray

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glass slide spotted with thousands of SNA probes. Target DNA will be flourescently labeled and mixed with probes on the microarray

Front 84

bacterial genome density

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generally 1 gene per 1-2 kb

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gene desert

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1 Mb or more without a gene

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How many gene deserts are there in humans?

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80 gene deserts, 25% of genome

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synapsis is....

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when chromosomes align in prophase I and align precisely base pair for base pair

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pseudoautosomal regions

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regions on the Y chromosome that are capable of homologous recombination with regions on the X chromosome

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penetrance

Back 89

the percentage of individuals in a population with a genotype who exhibit the phenotype associated with it

Front 90

expressivitiy

Back 90

degree to which a phenotype is expressed in an individual