Exam 3

Gregor Mendel

priest who discovered teh principles of genetics, traits are passed on from generations

Miescher

discovered that DNA is a substance separate from others (protiens, etc)

Erwin Chargoff

discovered DNA composition and their relative proportions. Guanine and cystosine in equal amounts, adenine and thymine in equal amounts

Rosalind Franklin and Maurice Wilkins

Discovered structure of DNA, showed its double stranded

Watson, Crick, Wilkins

used x-ray diffraction and chrystalogoraphy to determine the actual structure of DNA using physical and chemical information

Fred Griffin

discovered transformation when trying to find a vaccine for streptococcus pneumonia, living cells could take up substnace from dead cells that changes gene expression (DNA)

Avery, MacLeod, McCarty

discovered that DNA alone is a transforming particle (responsible for transformation)

Hershey and Chase

DNA is the genetic material in T2 bacteriophage

Centra Dogma

DNA is replicated into two daughter strands. DNA is transcribed to RNA, then RNA is translated to proteins

what are the two bases of DNA/RNA

purine and pyrimidine

what are the two sugars of DNA/RNA

deoxyribose and ribose

what is a base and a sugar

nucleoside or deoxynucleoside

what is a base sugar and phosphoric acid

nucleotide or deoxynucleotide

what are the purines

adendine and guanine

what are the pyrimidines

cytosine, thymine, uracil

sugar phosphate backbone

phosphodiester linkage covalently binds the 3’OH of one sugar to the phophate on the 5’C of another

Structure of DNA strands

double stranded helix, complementary and anti-parallel

what does it mean that dna is complementary

ability to identify second strand from first, always follows base pairing rules because hydrogen bonding can only occur between the correct pairs

what does it mean that DNA strands are anti-parallel

they face in opposite directions, sugar-phosphate backbone makes it so one end has a phosphate tail and one end has a sugar tail, the two strands are opposite so the 5’ phophate tail of one faces the 3’OH tail of another and vis versa

what pairs with adenine (DNA)

thymine

What pairs with Guanine (DNA)

cytosine

major groove vs minor groove

base pairing occurs at an angle so the sugar phosphat backbone of each strand is closer on one side than the opposite, creating two groves

what groove is the most biologically important, location of most modification of DNA

major grove

structural differences of RNA

single strand, uses uracil instead of thymine, uses riobose instead of deoxyribose

organization of prokaryotic DNA in cell

circular, supercoiled, non-membrane bound

what are the supercoils of prokaryotic DNA held together by

histone like proteins

organization of eucaryotic DNA

linear, membrane bound, held together by histones

what is a nucleosome

histones associated with DNA

what does semiconservative mean

after replicaiton, each new copy of DNA contains one old strand and one new strand

what is the replication bubble

area of DNA that is being replicated

what is the replication fork

location were replication process takes place

DnaA

proteins bind to DnaA box in OriC region to open up double strands

Helicase (DnaB)

unwinds the double stranded DNA

DNA gyrase

introduces negative supercoiling to minimize over-twisting of DNA

what inhibits DNA gyrase

novobiocin and ciprofloxacin

DNA primase

synthesizes short complementary RNA primers (10 nucleotides)

what is a primosome

primase with accessory proteins

which enzyme/protein is a DNA dependent RNA polymerase

DNA primase

single stranded binding proteins

attach to each strand to keep them from reannealing (base pairs rejoining)

DNA polymerase 3 function

synthesizes complimentary DNA at the 3’OH end in a continuous process (leading strand)

what is the replisome

dna polymerase 3 with all of its accessory proteins

structure of DNA polymerase 3

core enzyme with polymerase activity and a epsilon subunit with 3’ to 5’ proofreading ability

limitation of dna polymerase 3

adds nucleotides to pre-existing 3’OH ends only, needs pre existing 3’OH ends to begin DNA synthesis, needs a template strand

2 forms of prokaryotic DNA synthesis

bidirectional and rolling circle

bidirectional replication

2 replication forks move in opposite directions starting at the origin of replication and ending at the ter site

rolling circle replication

nick induced into circular dna, 3’ end grows with DNA synthesis and displaces the other strand, sythesis occurs in the displaced strand

eukaryotic replication

multiple origns of replication traveling in opposite directions on a linear chromosomes

mechanism of chain growth

3’ OH group attacks inner phosphate group of dATP to add to the end of the chain

lagging strand

pre-primed with RNA primers, DNA polymerase 3 moves from 3’-5’ synthesising gaps

DNA polymerase 1

removes RNA primer and replaces it was complimentary DNA

how does DNA polymerase 1 remove RNA primers

with its 5’ to 3’ exonuclease activity

DNA polymerase 3 proof reading ability

epsiolon subunit has 3’ exonuclease activity that removes the wrong base

what does methylase do

add methyl groups to new bases

DNA ligase

seals the nicks in the sugar backbone between bases

what is the ter site

site of termination of dna replication

how does the ter site end replication

has tus proteins that cause the replication complex to fall off

what is the promoter

section of gene that RNA polymerase binds to

leader sequence

codes for a segment of mRNA containing the shine-dalgarno sequence

what is the coding region

section of the DNA gene that will be transfered into amino acids

what is the trailer in DNA transcription

non coding sequence following the coding sequence of a gene before the end of transcription

what is the terminator

sequence located after a non-coding sequence and codes for termination of transcription

what recognizes the shine dalgarno sequence during translation

16s ribosome

structure of promoter region

has sequence 10bp before start site and 35 base pairs before start site

sense strnad

contains coded information

antisense strand

complimentary to the sense strand, begining of gene starts at 3’ end

what direction is mRNA synthesized

5’ to 3’ end

what strand of DNA is transcribed

the antisense strand

what does the promoter of the gene do

directs binding of RNA polymerase

What is the -35 sequence of the promoter

RNA polymerase recognition site

what is the -10 sequence of the promoter

the pribnow box, location of RNA polymerase binding

structure fo coding region

starts at 3’ TAC 5’ of the template strand in order to be transcribed to the start codon for translation

how is rRNA and tRNA transcribed

large transcript created with 16s,23s,5s rRNA and 1-3 tRNA genes

how is the rRNA transcript processed

ribonuclease cuts them out to seperate rRNA and tRNA

what is unusual about prokaryotic rRNA and tRNA transcription

the tRNA and rRNA genes are modified which is unusual in prokaryotes

mutation

changes in teh DNA sequence that are only expressed when replicated

conditional mutation

mutations expressed only under certain enviornmental conditions

example of conditional mutation

bacteria loosing plasmids under high temperatures

biochemical mutations

change of the biochemistry of a cell

what is a prototroph

bacterium that can grow on minimal medium, synthesizing all amino acids and nucleotides from CHNOPS

what is an auxotroph

bacterium that needs a nutrient suppliement (amino acid) to grow

induced mutation

use of agents that increase the mutation frequency

spontaneus mutation

natural mutations caused by errors in replication

what are transposons

insertion of pieces of DNA from other parts of the genome into genes

whats another word for transposons

jumping genes

what are frame shift mutations

addition or deletion of DNA that causes the coding frame to shift

mutagen

agent (chemical or physical) that causes mutation

6 types of mutagens

transition, transversion, base analogs, change in base structure, intercalating agents, mutagens that damage H-bonds

transition

mutation causing a purine-purine or pyrimidine-pyrimidine substitution

transversion

mutation causes purine-pyrimadine or pyrimidine-purine substitution

base analogs

mutagens are strucuturally similar to a base but have different binding properties

what is an example of a base analog

5-bromouracil

change in base structure

mutagen changes the structure of a base to prevent binding

example of mutagen that changes base structures

methyl-nitrosoquanidine

intercalating agents

distort DNA to introduce nucleotide pair insertions or deletions

example of intercalating agent

ethidium bromide binds between two strands of DNA causing distortion

mutagens that damage H-bonds so that pairing does not occur

UV light inducing thymine dimerization

wild type

most common gene form

forward mutation

a mutation of wild type gene leading to a mutant

reverse mutation

second mutation in mutant that occurs and restores the wild type gene form

true reversion/back mutation

second mutation in mutant OF THE SAME NUCLEOTIDE CHANGE that restores wild type gene