68 terms

Biology Chapter 15- DNA and the Gene: Synthesis and Repair


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What question did the Hershey-Chase Experiment Settle?
whether genes are made of DNA or proteins
What did Hershey and Chase use in their experiment?
T2 infections that attach to host cell and leace infectious capsids behind

the capsids eventually conduct the production of new viruses
Why did Hershey and Chase use the T2
because it is made primarily of DNA and protein, by testing the capsid they could determine what is left behind for reduction of infection
What two biochemical factors aided Hershey and Chase in their experiment?
Proteins contain sulfur but no phosphorous

DNA contains phorphorous but no sulfur

they grew the T2 viruses in presence of radioactive Sulfur 35 which radioactive proteins and radioactive phosphate 2 which produced radioactive DNA
How did the radioacitve labeling aid Hershey and Chase?
they allowed each radio active virus to infect an e coli cell and then tested the E.coli cell to see which radioactive capsids where in the cell
Radioactive DNA found in the cells.

Viral genes consist of DNA
what is DNA made up of? (3)
Deoxyribose sugar
Phosphate Group
Nitrogeneous Bases
How are monomer held together to create polymers in DNA?
Phosphodiester Bond

Bxt hydroxyl group on 3' and phosphate on 5'
Two Main Features of the Primary Structure of DNA
1. backbone made up of sugar and phosphate

2. A series of nitrogenous bases that project from backbone
Polarity of DNA?
One end 5' has phostphate (parital pos.) while the 3' has -OH (parital neg.)
Secondary Structure of DNA?
To strands line up antiparallel (5' -- 3' and 3'--5')
The complementary Nitrogenous bases (ATGC) form H-bond and twist into double helix
What is the Semi-Conservative Hypothesis?
Old parental DNA separates and each is used as a template for synthesis of new daughter cell

Each daughter cell consists of one old and one new DNA strand
What is the Conservative Replication Hypothesis?
Nitrogeneous bases temporarily turn away from eachother and serve as template for synthesis of entirely new double helix

intact parent and entirely new daughter
What is the Dispersive Hypothesis?
Parental strands are cut and crossed over with new strands to form a mixture of newly synthesized pieces assembled piece by piece.
The Meselson-Stahl Experiment
Grew E.coli cells in the presence of N15 (heavier) first and then N14 to determine which hypothesis was correct

they then used the parent strands density and the daughter cell density of the strands to determine which isotopes where present and whether there was a mixture or pure.
Conclusion of Meselson-Stahl Experiment?
Semi-conservative is correct hypothesis
What is DNA polymerase?
Enzyme that makes many units of DNA - synthesizes DNA strands by reading one base and adding a new one. Also has a proof-reading function to check for errors.
In what direction does DNA synthesis take place?
5' --> 3'
what provides the energy fro DNA synthesis?
dNTP or triphosphates
What is the origin of replication?
a replication bubble that forms at a specific sequence of bases
what does it mean to say that DNA synthesis is bidirectional?
occurs in both directions as the same time, thus the replication bubbles grow in two directions as DNA replication proceeds
What is the replication fork?
the Y shaped region where the parent-DNA double helix is split into two single strands and copied
What is DNA helicase?
the enzyme that breaks the h-bond bxt the two strands of DNA to "unzip" double helix
what are SSBPs (single strand DNA binding proteins)
single stand DNA binding proteins attach to separated strands and prevent them from snapping back into double helix
What is topisomerase?
enzyme that cuts DNA and allows it to unwind and rejoins it ahead of the advancing replication fork. Relieves tension
What is primer?
a strand of few nucleotides long that is binded to the template strand
what does a primer provide?
provides DNA polymerase with a free 3' hydroxyl (-OH) group that can combine with an incoming deoxyribonucleotide to form a phosphodiester bond.
what is primase?
enzyme that synthesis short RNA primer FOR DNA polymerase
what is RNA polymerase?
Transcription enzyme that links RNA nucleotides together
What is the sliding clamp?
ring structure that holds DNA polymerase in place during strand extension
what is the leading strand?
continuous strand
leads into the replication fork and synthesized continously
The lagging strand?
the strand that is synthesized in the direction away from the replication fork (discontinous)
The discontinuous replication hypothesis?
Primase syntheisis new RNA primers for the lagging strands as the moving rep. fork opens single stranded regions of DNA,

DNA polymerase uses these primers to synthesize short, lagging strand DNA fragments that are linked together into a continuous strand
What are Okazaki Fragments?
(100-200 bases long in Eukaryotes)

attacher to RNA primer, a relatively short fragment of DNA synthesized on the lagging strand during DNA replication.
What is the job of DNA polymerase 1?
removes RNA primer from fragment on lagging strandand replaces them with DNA
What is DNA ligase? (STAPLER)
enzyme that catalyzes the formation of phosphodiester bond bxt the adjacent fragments

(joins the okazaki fragments in a continous strand)
What is the job of DNA polymerase 111
to extend the okazaki fragment on the lagging strand
extends the leading strand
What is the job of the sliding clamp?
holds the DNA polymerase in place during strand extension
What is the replisome?
the large macromolecular machine made up of the all the enzymes used in DNA synthesis
What occurs after DNA polymerase completes okazaki fragment synthesis?
it is released from the DNA and reassembles on the most recently made RNA primer.
Is the replication of the ends of linear chromosomes the same as the rest of the DNA?
no, there is a specialized DNA replication enzyme that has been subject of intense research
What is the region at the end of linear eukaryotic chromosome called?
What is the First step that occurs during replication of telomeres?
the replication fork reaches the end of a linear chromosome

DNA polymerase synthesizes the leading strand all the way to the end of the parent DNA template and leads to a double stranded DNAmolecule
What is the second step that occurs during replication of telomeres?
on the lagging strand, primase adds RNA primer close to the tip of the chromosome
What is the Thrid step that occurs during replication of telomeres?
DNA polymerase synthesizes the final okazaki fragment on lagging strand and an enzyme that degrades ribonucleotides removes RNA primer
What is the four step that occurs during replication of telomeres?
DNA polymerase is unable to add DNA near the tip of the chromosome because it cannot synthesize DNA without a primer
what is the result of DNA polymerase is unable to add DNA near the tip of the chromosome because it cannot synthesize DNA without a primer?
single stranded toward end of 3' end of DNA on lagging strand stays unreplicated and eventually gets degraded?
What is a result of the degradation of single stranded DNA toward end of 3' end on lagging strand stays unreplicated and eventually gets degraded
the chromesome would shorten about 50-100 bases every time it replicated and the DNA lifespan decreases.
What is telomerase?
extraordinary catalyst that catalyzes the synthesis of DNA from the RNA template contains it

What are telomeres made up of?
Not genes, but short stretches of bases that are repeated over and over
What is the telomere humans?
What is the function of telomerase?
adds DNA onto the end of a chromosome to prevent it from getting shorter
Step One in Telomerase Process "overhang"
The unreplicated segment of the telomere at the 3' end of the template for the lagging strand forms a single-stranded "overhang"
Step Two in Telomerase Process "binding"
telomerse binds to the "overhang" and begins DNA synthesis
The template for this synthesis comes from a portion of RNA held within telomerase
Step Three in Telomersase Process "catalyze"
synthesizes DNA in the 5' -> 3' direction and catalyzes repeated additions of the same short DNA sequence to the end of the growing single strand
Step Four in Telomerase Process "DNA Polymerase"
the normal DNA polymerase use the lengthened strand as a template to synthesize a complementary strand.

Lagging strand is slightly longer than it orginally was
Telomerase Regulation occurs in which cells
gamete cells and a few (limited) somatic cells
What does longer telomere length allow for in cells?
more cell divisions (longer cell life)
The dark side to telomerase activity?
it can allow for the continuous division of cancerous cells
how many nucleotides make up an amino acid during DNA synthesis?
What occurs bxt deoxynucleotides on the template and new incoming deoxynucleotides in DNA synthesis?
Hydrogen Bonding
How is DNA polymerase selective about the bases they add to growing strand?
1. complementary base pairing (A-T and C-G)
2. the correct pairings have distinct shapes
Does DNA ploymerase III correct its own mistakes?
Yes, it serves as a proof reader, using its e subunit if a mismatched pair occurs DNA polymerase acts as a 3' -->5' exonuclease and then adds correct base
What is a mismatched pair?
occurs when mismatched bases are corrected after DNA synthesis is complete

play a key role in cancer devleopment and progression
What is nucleotide Excision Repair?
a repair system for damaged cause by ultraviolet light

Fixes thymine dimers and many other types of damage

One enzyme Recognizes kink in DNA helix and another enzyme removes a short single strand of DNA containing the defective sequence
What cause thymine dimers and kink in the structure?
UV light cause pyrimidines next to one in same strand of DNA another to covalently bond.
What is Xeroderma Pigmentosum? (CLEAVER)
Autosomal recessive syndrome of defective nucleotide excision repair causing increased skin cancers
Steps in Nucleotide Exicision Repair
1. Error Detection
2. Enzyme excises a stretch of nucletides that includes damage
3.DNA polymerase fills in gaps 5' --> 3'
4. DNA ligase links new and old nucleotides