Genetics test 2

what are nucleotides composed of

deoxyribose sugar, phostphate group, and nitrogenous base

Where is the phoshodiester bond in nucleotides

between the 5’ phophate and the 3’ hydroxyl on the sugar

What was griffith’s experiment

griffith worked with strpococcus pneumonia, a smooth virulent form and a rough non-virulent form. When injecteing the S cells into rats they died. When injecting R cells into rats they lived. When injecteding heat killled S cells they lived. When he injected heat killed S cells milxed with living R cells the rats died

What was Avery, MacLeod, and McCarty’s experiment

Avery, Macleod, and McCarty’s looked at what substance was being transformed. They added protease (protein destroyed) and the R cells transformed into S cells. They added Rnase(RNA destroyed) and the R cells transformed in to S cells. They added DNase (DNA destroyed) and the R cells was not transformed. They added ultracentrifugation (fats eliminated) and the R cells transformed into S cells.

What did both the Griffith and Avery, MacLeod, and McCarty experimetns look at

Transformation of bacteria

What was the Hershey Chase experiment

Used to figure out the genetic material. Used radioacive P-32 (for DNA) and radioactive S-35 (proteins) to see if protein or DNA was inserted into bacteria by phages. With p-35 (DNA) radioacivity was recovered in host and passed onto phage progeny. With S-35 (protein) radioactivity was recovered in phage ghosts

What did the and Hershey and Chases experiment prove

DNA enetrs cells and carries genetic information

How do bacteria tranfer DNA

Transformation: takes DNA from environment

Transduction: genes transfered directly from bacteria

Conjugation: two cells in contact

What helped find the shape of DNA

Rosalind Franklin’s lap used X-ray to take a photo DNA and showed Helical pattern

Watson and Crick built the double helix model of DNA in 1953

Which experiment confirmed DNA’s replication pattern

The Mesleson-Stahl experiment confirmed the semi - consevatitve replication pattern of DNA

What was done in the Meleson-Stahl experiment

E.Coli was grown for many generations with Nitrogen 15. The colony was moved to a medium with Nitrogen 14 and started to replicate. Daugher DNA had one strand of nitrogen 14 DNA and one strand of nitrogen 15 DNA

What catalyzes phosphodiester bonds

DNA polymerase

What are the two stages of DNA replication

Initation and Elongation

What does DNA polymerases need to begin

Four dNTPs , a single-stranded template, and primer with exposed 3’ hydroxyl

which side of the strand does DNA polymerase add nucleotides to

the 3’ OH of the new strand

What is initation in DNA replication and what is involved

Iniation: proteins open up the double helix and prepare it for complentary bass paring

involved: iniator protein, DNA helicase, Single stranded binding proteins (ssbs), and primase

What does the initiator protein do?

bind to the origin of replication

what does DNA helicase do

unwinds helix

what does SSBPs do

keep the helix open

What does primase do

synthesizes RNA primers

What does topoisomerase do

relieves spercoil casued by helicase unwinding

What is elongation in DNA replication and what is involved

Elongation: proteins connect the correct sequence of nucleotides on newly formed DNA strands

involved: DNA pol III, DNA pol I, DNA ligase, leading and laggind strand

What does DNA pol III do

catalyzes phosphodiester bonds- works off the primase

What is the leading strand

continously synthesised strand (5’→ 3’)

What is the lagging strand

discontinoususly synthesiszed strand (3’ → 5’)

What does DNA pol I do

replaces RNA primer with DNA

What does ligase do in DNA replication

join okazaki fragments togeher to make lagging strand continuous

What are the steps of recombination at the moleclular level

double strand break fromation, resection, strand invasion, formation of double holliday junction , branch migration, and resolution of the holiday junction

In DNA recombination what happens at double strand break formation

Spo11 breaks phosphodiester bonds of both strands of one chromatid

In DNA recombination what happens at resectioning

5’ end of each broken strand is degrated by exonuclease to create 3’ single stranded tails

In DNA recombination what happens at strand invasion

• Dmc1 helps one single strand tail invade a non-sister chomatid and forms stable hertoduplex

• Displacement loop (D-loop) from invaded chromatid is stabliized by single strand binding protein

in DNA recombination what happens at the formation of double holliday junction

• d-loop and othe 3’ tail form a second heterduplex

• DNA synthesis replaces the DNA degerated during formation of the 3’ tails

• DNA ligase reseals the DNA backbone

In DNA recombination what happens at Brach migration

heteroduplex region of both DNA molecuels is lengthened

in DNA recombination what happens at the resolution of the Holliday junction

holliday junctions are resolved by resolvase and ligase

How does recombination happen without crossing over

anticrosser heicase disentangles the invading strand from the nonsister chromatid preventing holliday junction formation

what is site specific recombination and what catalyzes it

Site specific recombination promotes breakage and rejoing of DNA molecules at particular sequence. A single protien call recombinase sufficeintly catalyzes all breakage and joining steps

What are the main types of point mutations

substitution, deletion, and insertion

What is the differnt between a transition and trasverstion mutations

transition: changes a purine for a purine or a pyrimidine for another pyrimidine

transversion: chages a purine for a purimidine or pyrimidine for a purine

What is a forward mutation

changes the wild-type allele to a differnt allele

what is a reverse mutation

changes mutant allele back to wild-type

what type of mutations are transfered to progeny

germ line mutations

what are protogrophs

wild type bacteria that can grow on minimum media

what experiment proved mutations are spontaneous and random

the Luria-Delbruck Fluctuation experient

what are auxotrophs

mutant- cannot grow on minimal media without a supplement

why is relica plating used and what is the technique

verifies the bacterial resistance is the result of preexisting mutations and can be used to test the origin of bacterial resistance. Stamps the bacteria from master plate onto new plate

What mutations happens with depurination

hydrolysis of purine bases, bond breaks betwen the purine and the sugar

what mutation happens with deamination

the amino (NH2) group is removed, can chagne C → U or A → G

What mutation is the result of X-rays and Cosmic rays

a break in the sugar-phosphate backbone of DNA, causes deleation of bases

What mutation is the result of ultraviolet light

adjacent thymines form abnormal covalent bonds, thymine dimers

what mutations happens with oxidation

damage of individual bases, G mis-pairs with A

What happens with slipped misparing

trinucleotide repeats happen up to 50 times in a row, children of carrier have an expanded number of repeats

Bases repeated: CGG, CAG, CTG, GCC, GAA

What happens with intercalating agents

insertion between DNA bases cause frameshifts leading to insertion of a random base pair or deletion of base pair

What happens with base analogs

Analogs are chemicaly alike to DNA bases and pair with A and G. Can turen A to T site to G to C site after replication

What is the affect of hydroxylation

addition of a hydroxyl (OH) group , adds OH to C, now C pairs with A instead of G

What are the effects of alkylating agents

addion of ethyl or methyl groups , changes G to pair with T

What is the purpose of the Ames Test and what does it not tell us

detect if a chemical is a mutagen but does not tell us how much DNA damage it cost

In the Ames test what shows if something is a mutage

if a high number of reventants (auxotrops → prototrophs) are present after incubation

What does Base excision repair remove

damaged bases and single strand breaks w

what does nucleotide excision repair do

detects and removes DNA lesions/ distortion, ex: thymine dimers

What does DNA mismatch repair do

detects and repairs base mismatches and short insertions and deletions

What are the repair mechanisms for double strand breaks

Homologous recomombination (only S/G2 phase) and Nonhomolgous end joining

What is an example of a deaminatting agent

nitrous acid (HNO2)

what is an example of a intercalating agent

ethidum bromide, proflavine, acridine orange

what is an example of a base analog

5-bromouracil (5-BU)

What is an example of a hydroxylating/oxidizing agent

hydroxyl radicals (.OH), ROS

what is an example of a alkylating agent

EMS, MMS, nitrogen mustards

What mutagen/DNA damage(s) use base excision repair as a repair mechnanism

Nitrous acid (deamination), Hydroxyl radicals/ROS, and EMS/MMS (alkylation)

what mutagen/DNA damage(s) use nucleotide exsion repair as a repair mechanism

UV light and intercalating agents( ethidum bromide, proflavine)

What mutagen/DNA damage(s) use mismatch repair as a repair mechanism

replicaiton error

what mutagen/DNA damage(s) use HR or NHEJ as a repair mechanism

X-rays/ionizing radiation , double strand breaks

what are complementation test used for

determine if two mutations are on the same genes

what do supplementation test used for

determing the order of genes in a biochemical pathway

What makes up an amino acid

amino group, carboxyl group, r group, and h

where are the amino acids linked by peptide bonds

between the carboxylic groups

what establishes the reading frame

the start codon

what is the start codon and the amino acid it codes for

AUG and Met

what are the stop codons

UAG, UAA, UGA

what is the product of transcription called

the transcript

what is required for transcription initation in prokaryotes

RNA polymerase and promoters

What is the role of RNA polymerase in the initation of transcrtiption in prokayotes

bind to the promoter sequence near the beginning of the of the gene and starts transcription, locally unwinds the double helix

What happens in elongation of transcription

RNA polymerase addes nucleoties in 5’ → 3’ direction, moves downstream the DNA

what happens at termination of transcription

terminators (rna sequences) signal the end of transcription and RNA polymerase falls off of DNA, RNA transcript is released

why is transcription different in eukaryotes

Eukaryotic genes have enhancers that are required for transcription, genes are transcribed by pol II

what is need to make mature mRNA in eukaryotes

5’ G methylated cap, poly- a tail, splicing of inrons

What are the differernt sites were spicing occurs in an intron

splice donor (GU beginning of intron), branch site (A in the middle of intron), and Splice acceptor (AG end of intron)a

what catalyzes slicing

the spliceosome is the machinge that cuts the extra pieces out and stiches pieces together, only assembled for splicing

what is envolved in translation

mRNA, tRNA, and ribosomes

what are the diffent function of the small and large ribosome subunit

small: bind to mRNA

large: has peptidyl transferase activity, catalyzes the formation of peptide bonds

how do tRNAs help with translation

have anticodons that bind to mRNA, brings correct amino acid to codon

what is the wobble position

5’ end of tRNAs anticodon , recognizes more than one codon

What happens in translation initation of prokaryotes

ribosomes bines to Shin-Dalgarno box and AUG, fMet-tRNA position in p-site, large subunit binds

what happens in translation initiation of eukaryotes

small ribosoms subunit binds to methylated 5’ cap, then migratges to the first AUG codon, initator tRNA caries Met

what happens in translation elongation

addition of amino acids to c-terminus of polypeptide, charged tRNAs ushered into A site by proteins called elongation factors

what happens in translation termination

release factors recognize and bind to the stop codons, release of ribosomal subunits, mRNA, and polypeptide

how many reading frames do each double stranded region have

6

what is an open reading frame

an region of DNA with no stop codons so translation can continue

how do mutations in non-coding regions alter gene expression

they have an effect on regulatory sequences

What are the types of loss of funtion mutations and what is the common dominance pattern

amorphic (null) and hypomorphic, these mutations are usually recessive to wildtype

what happens with a amorphic mutation

the gene has no function

what happens with a hypomorphic mutation

there is reduced levels of production of normal progein or it is less efficient