Genetics Exam 2

paired DNA strands separate and become templates for replication

no only elongated, that is why primers are needed

a certain sequence of DNA where replication always begins

dna strands can not be initiated

elongation: must be added to 3' end and can only happen in one direction

error: sometimes mistakes are made in copying

has proofreading enzymes

origin of replication

any molecule or region of DNA that replicaes as an individual unit

Yes, esp in EUKs

autonomously replicating sequences

occurs in yeast

replicated DNA strand

the dna strand whose compliment is synthesized as a continuous unit

dna strand whose complement is made in short fragments that are joined together

10^-5 per template nucleotide per round of replication

each parental strand remains entact to be joined witha daughter strand

first to provide experimental evidence for conservative replication

Took E.coli and grew it in heavy N(15) and then put it in light (N14) nitrogen

Put samples in a centrifuge with cesium chloride to see how the strands separated. Showed distinct bands of intermediate densitites

to label chromosomes to observe replication in humans

shows tat eukaryotes are semiconservative

because of crossing over

cells grown in radioactive thamine and placed on photographic film. showed circulalar, theta replication

unidirectional or bidirectional

area of DNA where parent strands are separated and new strands are being made

end of replication in bidirectional synthesis

bidirectional and linear

yes

enzyme responsible for unwinding the replication fork

uses ATP hydrolysis

cleaves and swivels double strands to relieve the stress of unwinding

stabilize single strands once they are broken apart. protect so that they dont recombine

joins okazaki fragments on he lagging strand

complext that adds primers

adds new nucleotides to new strand

ribose has down OH on c2

deoxy has an H

uracil instead of thamine

dnaG gene

hybrid of RNA and DNA

12 nucleotides of RNA
20-25 DNA after

DNA polyermase alpha that is part of pimosome

e coli DNA polymerase III

ueks DNA polymerase delta

5' to 3'

intra-stand is 3' to 5' phosphodiester bonds

inter-strand is H-bonding between nucelotides

1/10,000

exonuclease in the DNA polymerase complex. it has the ability to cut nucelotides

1,000 fold

one base

fragments made on the lagging strand because it runs opposite to how dna polymerase can elongate

Polymerase III cannot join the 5' because it is a triphosphate. instead polymerase I eats the RNA primers and inserts dna instead. dna ligase does the final binding

dna polymerase delta encounters an RNA primer from prior fragment. SSB protein RPA (replicaiton protein A) flips out with a portion of DNA. Endonucleases cleave the flipped piece and dna poly continues. The primers and dna are broken down by exonucleases

aberrant ratios of gamete gene ratios

process where the products of meiotic division in an Aa genotype do not come out in a 1:1 ratio

process where an enzyme notices that there is a mismatch in bases. A small segment is removed and replaced with a nucelotide that can bind

two because it the chunk can be taken from one or the other strand

a duplex molecule of nucleic acid whose strands are derived from different sources, such as from different homologous chromosomes or different organisms

often times they do not match

strands could no be matched up properly in recombination, leading to mismatch which is changed, but it could then change the genetic composition to a different allele

dna synthesis in the presence of small amounts of nucleotides that contain dideoxyribose

lacks an OH on C3, instead H

run like PCR and run on gel electrophoresis

items needed:
template dna
polymerase
rxn buffer
dNTP (high conc)
ddNTP (low concentratin) labled with dye
oligonucleotide primers

it is a way to determine the sequence of dna. where fragments stop is where the ddNTP was incorporated. Whatever nucleotide that ddNTP is associated with is the nucelotide in that DNA parent strand.

in a capillary tube., the longer fragments are at the top in in the electrophoresis, which signify the end of the strand. The bottom is the shortest, which signifies the beginning of the strand

hitting the capillary tube with light and looking at fluorescnece. based on the wavelenght graph, the distinct peaks and colors that associate with a given nucleotide

originate in gametes in meiosis

occur in the body cells from an individual (mitosis)

when you get multiple colors (such as eye color in cats) as a result of somatic line mutation

mutations that change phenotype depending on environmental conditions

drosophilia 29C functional brown eyes
22C nonfunctional red eyes

Siamese cat: black pigment is sensitive to temp. Blocked @ normal body temperature --> white almost everywhere except on extremities

complete loss of gene function

reduces level of gene expression (mRNA level)

greater than normal gene expression (mRNA level high)

gene does something new or has new timing

expression of wildtype gene in abnormal location

nucleotide substitution

pyrimidine for pyrimidine

or

purine for purine

T and C

A and G

purine (A/G) for pyrimindine (T/C)

Pyrimindine for purine

ones where the mutation does not result in a change in the amino acid sequence

changes the amino acid encoded by the codon

leads to the coding of a stop codon

transversion of a/T to T/A on the second codon position for the 6th amino acid. changing the B globin gene because of a glutamic acid being replaced by valine.

inserts or deletions DNA and can result in the addition or loss of amino acids

when the insertion or deletion is not in a set of three, causing the frameshift to change and great differente amino acids

during the replicatino of a trinucleotide repeat the 3' end of the new strand detaches and reattaches at the beginning of the repeat upstream of original location. Replication will continue, but will expand and replicate an area twice.

The Lederbergs used replica plating where they had bacteria cells grow on a media. They took velvet stampers and moved the bacteria from the master place onto different selective and nonselective media. The selective media would only grow the mutants, while mutants and nonmutants would grow on nonselective medium. It showed that mutation must have been present in the intial population and that it was not induced by the circumstances of the plate being selective

bad aand not good for fitness

probability that a gene undergoes mutation in a single generation or in forming a single gamete

u = # mutations per bp per gene (or cell div)

U = number of mutations per genome per gene

based on the frequency of mutatino in phenotypes caused by known genes in a lab setting

mutation accumulation lines

an agent that causes an increase in the rate of mutation

originate within the bodily tissues

from sources outside of the body

electron transport chain

can oxide C=N bonds to turn into a keto group

base structures will inherently be in keto and enol forms (keto dbl and enol dbl between c and n) --> different base pairing properties

keto prefers A
enol prefers G

when a DNA sequence moves to a new position

Barbara McClintock in corn
showed that dissociation (Ds) was able to move in the genome and requires a second element Activator (Ac) to be present

cut and paste type mechanisms

transposase cuts with a given distance between target DNA strands

new element is incorporated and the gap is filled

exact sequences that are inverted on either side of the transposable element

contains binding sites for transposase

direct, the repeat is on the same strand on either side of the element

inverted, the repeat is on the opposite strand criss-cross

long terminal repeat retrotransposons

terminal direct repeats at both ends
inverted repeats in the reverse direction

use rna transcript as an intermediate

transcribe element into RNA
reverse transcriptase turns RNA to DNA with using cellular tRNA as primer
Ednonuclease cleaves RNA, leaving fragment as the primer for the 2nd DNA strand
the retrotransposon is then inserted into the genome similar to cut and paste mechanism

does not use terminal repeats at the end, but instead uses normal RNA polymerases to insert nicks into host molecule.

reverse transcription occurs at the site of the host DNA insertion

long interspersed elements

non-LTR retrotransposons 1,000 bp long and encode for a reverse transcriptase

short interspersed elements

generally less than 500 bp long and do not encode for reverse transcriptase

AluI which may be responsible for promoting translation under stress

uv radiation
environmental
chemical mutagens

molecule sufficiently similar to on of the four DNA bases that it is incorporated into a DNA duplex in replication

in keto form it will bind with adenine
enol form it will bind with guanine

AT to GC

increase SSR mutation

dna ligase

base removal by base-specific DNA glycosylast

mismatch repair (remove and resynthesize)

protein recognizes mismatch (ex: MutS)
stimulates next enzyme (MutL)
MutL activates MutH which makes a nick at the 5' end of a given sequence
Exonuclease dissolves daughter strand
DNA polymerase holoenzyme comes in and filles in the gap
DNA ligase seals the nick

10^-10

10^-5

10^-2

10^-3

supercoiling

condition where segments of dsDNA are twisted around one-another and become more compact

10^-5

10^-2

10^-3

supercoiling

condition where segments of dsDNA are twisted around one-another and become more compact

when DNA is in right hand turns

most common in bacteria

left handed twist

parrallel to left handed helix

common in archaea

no

dna topiosomerase

enzyme wraps completey around dsDNA duplex and makes a nick in single strand and swivels the broken strands around the intact strand

causes ds DNA breaks (both strand) in one molecule and grabs another molecule and passes it through the dbl strand break.

total genomic DNA and protein strucutre of a bacterial cell

proteins will help to compact

chromosome

aggregate of DNA and histoe proteins that make up euk chromosomes

repeating subunit of chromatin
comprised of two molecules of each four histone proteins
AND combined with a 55 nucleotide pair 5th histone

H1 H2A H2B H3 H4

100 to 200

20 to 30 percent lysine and arginine. these groups give a positive charge that allowed them to be attracted to the negative charge on dna

H2A H2B H4 H3 x2

145 bp to 200 bp depending on nuclease activity

enzyme that breaks phosphodiester bonds

they cleave and bind with H1 protein? leads to winding about . More nuclease activity leads to loss of H1 and less bp wrapped around

chromatin winds into 30 nm coils through binding to neighbor through linker DNA

chromatin loops (~100 kb)
chromatin domains (~1 Mb)

entire space that is occupied by a chromosome in nucleus

region of chromosome that become visible as a narrow constriction along the condense chromosome

complex of dna and proteins that the spindle fibers attach to to move chromosomes in mitosis and meiosis

centromeres are dispersed across the length of the chromosome

microtubulues attach in one region

they are small and simple in gene/protein complex

more complex with many more base pairs where numerous spindles can attach

ex: humans have 750 kb with repeating sequences

end of linear chromosome used for DNA protection

made of DNA and protein

lengthen DNA molecules at each replication

3' end

an internal RNA template

genomes will differ in size dramatically among eukaryotes with similar organismal complexity

Amphiuma salamanders is 30 times larger than the size of human genome

no

large genomes could have fewer chromosomes

repetitive DNA elements

more abundant in eukaryotes

gyrase in dna replication

chromosomes are labeled by fluorescence through incubating in mitosis in fluorescent labeled DNA

diagram that shows number and shape of chromosomes in

with staining using Geisma

transverse bands on the chromosome (g bands) that are specific to each homologue

an old method where sorting could only be done by size and centromere position

chromosomes are arranged by number from longest to shortest and then the sex chromosomes

p is the short extension of the chromosome from the centromere

q is the long extension of the chromosome from the centromere

major region-bigger number that goes from centromere to teleomere

minor region- smaller areas marked out from the centromere to ends

A-G

autosome designations

sex chromosomes

termianal portion of a chromosome

+ an addition to the chromosome wher eit is longer

- something is missing, smaller than normal

metacentric-arms equal in length
submetacentric-off center, J shape
acrocentric-off center, very close to one end, I shape

no centromere

two centromeres

overhanging 3' sicky ends of DNA on acrocentric chromosomes are bound together to create 1 chromosome

it had a dicentric fushion to creat two centromeres. one was mutated on the long arm to inactivate to leave only one centromere

a mechanism that regulates the activity of X genes so that their activities are equal in males and females

ex: in mammals, there is random inactivation of one chromosome to make it equal with males

because males only have one copy of X, but females have a duplicate copy

a protein complex in males modifies the chromatin structure of X so that transcription up-regulates the levels to be equal with XX females

a protein complex is recruited to decrease the level of transcription activity on X genes in hermaphrodites (XX) to males (X0)

In the early cleavages divisions of embryos an X chromosome is chosen at random to be be silenced. The decendents of that cell will all have the same inactive X chromosome

inactive x chromosome

because it is at random the female will receive a mosaic of X chromosomes

Cats have patches of black and orange depending on which X is inactivated

they were regular autosomes that diverged from each other at the same time that mammal and bird lineages diverges from each other

SRY

as it evolved the Y chromosome diverged in the DNA sequence from the X chromosome and less recombination occured. As this happend there was selection pressure for the genes on the Y chromosome to degenerate because of non recombination

because Y chromosome is completely linked and they remain together from generation to generation

15%

trisomy 21 another 21st chromosome

changes in the number of chromosomes for one chomosome type

the gain of one chromosome

the loss of one chromosome

there are more than the usual number of chromosomes for the entire complement of chromosomes

euploid

aneuploidy results in a loss of genetic information

monosomy - 2n - 1
trisomy - 2n + 1

recessive lethal alleles

changes the phenotype of the individual

when in a trisomy the chiasmata combines all 3 chromosomes

when the chiasmata forms between two chromosomes, as normal, but the extracopy is left out

2 with 1 chromosome copy
2 with 2 chromosome copies

when a chromosome is missing genetic information

putting in more genetic information

changing the order of genetic information

instances in the human population where there is variation in the presence or absence of certain genes often as a result of a deletion event

exchange between homologous direct repeat sequences at different sites on the same chromosome. this results in a deletion of material between repeats

repeated sequences in reverse orientation

duplicated segement is present in the same orientation imediately adjacent to the normal region in the chromosome

when tandem duplicated cross over they will mispair and when they cross over they will be unequal in length

the results of meiosis will create a 2 with duplicats, 1 single and 1 triplication

red and green pigments aros from duplication of a single ancestral pigment gene

can result in defects of red or green perception

occur from ectopic exchange between inverse repeats

occur outside the centromere region

span the centromenere

no

because in meiosis in prophase they homologue match up gene for gene. in order to do this, the homlogous must form an inversion loop

1 dicentric chromosome and an acentric chromosome

of the two chromosomes not involved in crossing over, 1 is normal and the other is inverted

yes

the switch in genes includes a centromere in between

yes

1 normal chromatid
1 inverted chromatid

2 duplicated and deleted

inversion selects against recombinant gametes and preserves the co-segregation of specifici alleles

contains multiple complete sets of chromosomes

amphibians, fungi, some higher plant species

no

because in meiosis in prophase they homologue match up gene for gene. in order to do this, the homlogous must form an inversion loop

1 dicentric chromosome and an acentric chromosome

of the two chromosomes not involved in crossing over, 1 is normal and the other is inverted

yes

the switch in genes includes a centromere in between

yes

1 normal chromatid
1 inverted chromatid

2 duplicated and deleted

inversion selects against recombinant gametes and preserves the co-segregation of specifici alleles

contains multiple complete sets of chromosomes

amphibians, fungi, some higher plant species

increase in chromosome number from meiosis from unreduced gametes forming a zygote

chromosome number doubling during mitosis right after zygote is formed

polypoids species derive from one diploid ancestral species

colchicine which inhibits microtubulue polymerization and inhibits the separation of chromosomes in meiosis

derive from two diploid ancestral species

the probability of genomic errors

a chromosomal change resulting from interchange of parts between nonhomologous chromosomes

chunks of DNA switched

when equla amount of DNA are swapped

a fraction of gametes are sterile because of translocation

when a chunk of dna is added to a different chromosome

when the synapsis forms, it is of a T shape rather than side by side because of like genes needing to meet up.

sequences that can be transferred between dna molecules from one cell to another

nonessentail dna molecules that exist inside bacteria cells

independently of the bacteria genome

circular or linear
large or small
high copy (50/cell) or low copy(1-2)
often contain resistence genes

a plasmid that is containing both conjunctive and nonconjunctive sequences

joining of bacterial cells

a plasmid encoding protiens and other factors that make possible its transmission between cells

a nonconjunctive and conjugative plasmid both contain a transposable element

they undergow homologous recomination

the smaller nonconjuative is incorporated into the large conjugative

1-3 kb that encode for the transposase protein required fro transposition

genetic elements that can move to/from conjugative elements to/from nonconjugatie elements

inhabits intestinal tracts
non pathogenic
grows in liquid culture or solid media

has enzymes from amino acid synthsesis so it can grow on minimal media

divides every hour (24 gen/a day)

unable to breakdown complex molecules
unable to synthesize ertain materials from minimal media

small, big, shiny, dull, round, irregular

a cell that can grow on minimal media

usually considered the wildtype strain

a cell tha requires something for growth that can be produced in the wildtype cell

cell cannot grow w/o histidine

considered to be wildtype (+)

a media in which only the mutant 9or desired) strain will grow

a wildtype strain

through conjugation

the temporary fusion of two cells for the transfer of genetic material

one direction

F+ give genetic material
F- receive it

through a tube like structure called a pilius created from the F+

it can replicate it own DNA
carries genes for synthesis of pilli

sometimes integrates into bacterial chromosomes

high frequency recombination

when the f plasmid integrates into the host cell chromosome through recombination

a genetic element that can exist free in the ell or as a segment of dna integrated into the chromosome

"mates" with F- cell

a single strand of the plasmid is cut and transferred to F-

When the informatin is received the pilli cuts off and homologous recombination occurs

The cell will still be F- because it does not incorporate the plasmid but it does incorporate some of the Hfr chromosome

break in the pilus will stop conjugation

can be used to obtain a genetic map because transfer occurs at a constant rate

1/10,000 so most stay f-

F factor excises out of the Hfr chromosome back into plasmid form

usually near lac
and will carry that genetic information with it

it will act like an f+

partially diploid for genes copied on the f plasmid

process where bacterophages can carry a piece of any part of the host bacterial genome

bacteriophage inserts phage dna --> destruction of cell and the creation of more phages with phage dna that when the cell lysis --> distribution

some phages will have fragments of the cell's original chromosomeand it can lead to a tranductant (not bad?) bacterial cell

process where recipeint cells acquire genes from free dna molecules in the surrounding medium

the incorporation of two genes into a host dna

that it is highly likely that the two genes are close together

spontaneous mutation

1 to 10^6 or 10^7 cells

every 10^9 bases

let bactieral cells grow on medium to create a lawn

introduce phage, its lysis of cells end up creating little clearing regios known as plaque

because it has duplicated termian redundancy that can be cut into head ful packages

when a piece of bacterial dna is transferred from one bacterial cell to another by a phage

lytic - viral life that results in death and lysis of the cell to release new phages

lysogenic- virus dna become infocorporated into the host cell's chromosome

phage inserts virus DNA
host cell processes are shut down
host cell physiology used to do work of phage
phage DNA is replicated and capsules are made
phages reassembled

the dna is recombined into the host DNA forming a prophage

a virus that can integrate into the genome

a bacteriophage only capable of lytic growth

generalized - bacteriophage can carry any part of the host bacterial genome

when a phage is cutting from the prophage and a portion of the host dna is taken with it

yes

inhibits further infection by prophage under normal conditions, but when the cell is under stress, the repressor protein is blocked and the prophage exits into the lytic cycle