lecture 6: discovery of DNA and DNA replication Flashcards
what is the monomer of nucleic acid?
nucleotides
what are the polymers of nucleic acid?
DNA and RNA
what are the monomers linked by in nucleic acids?
phosphodiester bonds
what are the functions of DNA and RNA respectively
DNA: info storage
RNA: transmission of info (transcription/translation)
what does DNA stand for?
deoxyribonucleic acid
what does RNA stand for?
ribonucleic acid
what are the types of RNA?
rRNA (ribosomal RNA)
tRNA (transfer RNA)
mRNA (messenger RNA)
what are the characteristics of DNA?
-contains genes which code for protein synthesis
-double stranded
what are the characteristics of RNA?
-functions in the synthesis of proteins
-single stranded
what are the 2 different types of nitrogenous bases that can be contained in nucleotides?
-pyrimidines
-purines
what is the difference between a pyrimidine and a purine?
-pyrimidine: 6-membered ring made of carbon and nitrogen
-purine: 5-membered ring fused to a 6-membered ring (both rings made of carbon and nitrogen)
which nitrogenous bases are pyrimidines?
-Cytosine,
- thymine (DNA)
-Uracil (RNA)
which nitrogenous bases are purines?
adenine and guanine
what are the components of nucleotides?
-nitrogen containing bases
-pentose sugar
-phosphate group
what is the pentose sugar for DNA?
deoxyribose
what is the pentose sugar for RNA?
ribose
what is the difference between ribose and deoxyribose?
deoxyribose lacks an oxygen on carbon 2
what does a nucleic acid look like?
what are the base pairing rules in DNA? how many bonds are between each?
C=G (3 bonds)
A=T (2 bonds)
what are the pairing rules between RNA and DNA?
all the same as base pairing rules, except for A will pair with U on RNA (cause RNA doesn’t have Thymine)
Which Pentoses are these?
true or false, purines bind with purines, and pyrimidines bind with pyrimidines?
false. strands are complementary. purines bind with pyrimidines
with which bonds are DNA strands held together by?
H bonds between nitrogenous bases
what do we mean by saying that DNA strands are antiparallel?
oen strand runs from 5’ to 3’, and the other runs from 3’ to 5’
how many bases are there per turn of the helix?
10
how are phosphodiester bonds formed?
by linking the phosphate of ones nucleotide to the pentose of the next
which part of the nucleic acid is forming bonds to make the DNA helix?
nitrogenous bases
which part of the nucleic acid is forming the backbone of the DNA helix?
pentose sugar and phosphate group
how is DNA packaged?
in chromatin
what is chromatin?
DNA wrapped around histone proteins
what are histones?
small proteins rich in the positively charged (basic) amino acids arginine and lysine
why does DNA bind so tightly to histone proteins?
because DNA is negatively charged (because of the phosphate group), therefore it binds tightly to the positively charged histones
what is the difference between eukaryotic and prokaryotic DNA?
what year did Frederick Griffith make his discovery in?
1928
what did Frederick Griffith discover?
that information is stored in a molecule, and that it can be transferred between organisms (did not know that it was DNA at the time)
what experiment did Frederick Griffith conduct?
studied 2 strains of streptococcus pneumonia, smooth (S) (deadly) and rough (R) (harmless). he then injected all of these inside the mice and saw what happened.
in what year did Avery, McCarty and Macleod make their discovery?
1944
what did Avery, McCarty and Macleod’s experiment consists of?
the experiment had a goal to show that between protein, RNA and DNA, DNA is the one that transfers genetic information.
what were the results of Avery, McCarty and Macleod’s experiment?
in what year did Hershey and chase make their discovery?
1952
what question did Hershey and chase have when conducting their experiment?
what contains the information to make new viruses?
what is a bacteriophage
-virus that infects bacteria
-consists of protein and DNA
-infected cells manufacture viruses
what did Hershey and chase’s experiment consist of?
E-coli were infected with T2 bacteriophage which contained radio labelled proteins (35S) or radio labelled DNA (32P)
-cells were placed in a blender to separate phages from bacteria and then the mixture was centrifuged
what are the three hypothesis for the DNA replication models
-conservative
-semi-conservative
-dispersive model
what is the conservative model for DNA replication
what is the semi-conservative model for DNA replication
what is the dispersive model for DNA replication
what was the question for the meselson and stahl experiment?
they wanted to see how DNA replicates itself (with which model)
how did they do the meselson and stahl experiment?
E.coli were grown in a heavy nitrogen (15N) environment, then switched to a media with lighter nitrogen (14N). all the newly synthesizes DNA will incorporate 14N. therefore, the newly synthesized DNA will be less dense (higher in the tube)
what are the 2 time intervals at which the DNA is replicated during the Meselson and Stahl experiment?
20 mins and 40 mins
when is DNA replication happening in the cell cycle?
S phase of interphase
what are the key players in DNA replication?
-helicase
-DNA polymerase
-primase
-ligase
what does helicase do?
-unwinds DN strand by breaking hydrogen bonds
what does DNA polymerase do?
-synthesizes DNA by catalyzing the formation of phosphodiester bonds between nucleotides
-uses parental strand as template (adds complementary nucleotides)
-makes DNA in the 5’ to 3’ direction (links 5’ phosphate group of new nucleotide to 3’- OH group of growing strand
-reads the template strand from 3’ to 5’
what does primase do?
-makes short RNA primer
-An RNA polymerase that synthesizes an RNA primer on the template strand
-required because DNA polymerase can only add a nucleotide to a free 3’ OH group
what do single-stranded binding proteins do?
stabilize single stranded DNA, so that it stays unwrapped after helicase unwraps it
what does ligase do?
-glues together nicks in DNA sugar-phosphate backbone (forms phosphodiester bonds)
-needed after RNA primers are replaced by DNA and for Okazaki fragments
what does DNA replication in a prokaryotic cell look like?
what does DNA replication in a eukaryotic cell look like?
how does DNA polymerase get its energy?
from the hydrolysis of 2 phosphates off of the incoming nucleotide. the free nucleotides in the cell are nucleotide triphosphate, so 2 of them need to come off in order to be a monomer of the DNA
what is the first step of DNA replication? what happens?
-initiation
-helicases bind to the origins of replication and begin unwinding DNA to form a replication bubble (2 replication forks)
-single stranded binding proteins bind to the single stranded DNA
what is the second step of DNA replication? what happens during this step?
-primase makes a complementary RNA primer
-DNA polymerase synthesizes a new strand of DNA using the parental strand as a template
how many nucleotides is in the RNA primer?
5-10 nucleotides
true or false, DNA replication occurs in both directions
true
which strand is the leading strand? what is the direction of it?
-continuous DNA synthesis
-DNA polymerase is synthesizing DNA in the same direction as DNA unwinding
-only needs one RNA primer
-the template of the leading strand is in the 3’ to 5’ direction (if we’re going from left to right)
which strand is the lagging strand? what is the direction of it?
-discontinuous DNA synthesis (Okazaki fragments)
-DNA polymerase must synthesize DNA in the opposite direction of DNA unwinding
-requires multiple RNA primers
-the template strand is in the 3’ to 5’ direction (if going to the left)
true or false, the primer made by primate is DNA
false, it is RNA
what happens during DNA replication for the leading strand? (overview)
what happens during DNA replication for the lagging strand? (overview)
true or false, DNA polymerase has a very low error rate
true
why does DNA polymerase have a very low error rate
-it proofreads each added nucleotide
-if there is an incorrect match DNA polymerase can fix it
-DNA polymerase will remove incorrect nucleotide and resume synthesis
-errors not caught by DNA polymerase can be repaired by mismatch repair
what is nucleotide excision repair?
-corrects errors/changes in already synthesized DNA
-a nuclease remove changed nucleotides
-DNA polymerase fills in gap and DNA ligase glues together backbone
what can changes to DNA be caused by?
-chemicals
-radioactivity, X-rays and UV light
why does each replication end in a shorter DNA strand?
-removal of RNA primer from beginning of lagging strand leaves a gap and a free 5’ phosphate end, and since there’s no free 3’ end, DNA polymerase cant fill the gap
why cant the gap caused by the removal of the first/last primer be fixed by DNA polymerase?
-because it can only add DNA to 3’-OH end, and the end of where the primase was is 5’ for the beginning primase on the lagging strand. remember that each synthesized strand is half lagging and half leading, therefore both full strands will have a hanging end
what are the consequences of the shortening of DNA over time?
-can result in the deletion of genes
-limiting factor in life span of cell
why do prokaryotes not need telomeres?
because they are circular, therefore there is no start/end to the segment, and telomeres are needed for the beginning of the segment of the lagging strand
what are telomeres?
repeats of noncoding nucleotide sequences
what is the pattern for telomeres?
TTAGGG-AATCCC
which enzyme are telomeres synthesized by?
telomerase (RNA and protein)
where is telomerase active?
-in germ cells and stem cells (not in somatic cells) (made before we develop)
true or false, telomeres lengthen as we age
false, they shorten
how can telomeres be visualized?
by fluorescence microscopy
how many origins of replication are there in prokaryotic and eukaryotic cells?
prokaryotic: one
eukaryotic: hundreds
What does the loss of DNA due to the lagging strand look like over time
what is the difference between nucleotide excision and mismatch repair?
-excision: corrects changes i
