Chapter 15 Flashcards
Why did most biologists back up hypothesis that genes are made of proteins?
proteins seemed complex enough to contain a lot of info due to their limitless variation in structure and function
, thousands of chemical rxns occurred in cells involving proteins and amount of info required to specify and coordinate rxns were compelling
is it protein or DNA that enters cells to direct production of new viruses?
Viral genes consist of DNA
Where is OH and Phosphate group attached in DNA?
5’ has phosphate, 3’ has OH
how does DNA backbone link?
phosphodiester bond between an OH and PO4
How does each strand of DNA have directionality?
It has directionality or polarity because OH group is on 3’ and PO4 group is on 5’
What are purines?
Adenine and Guanine, two ringed nitrogenous bases
What are pyrimidines?
Cytosine, Thymine, and Uracil, one rigned nitrogenous bases
why is DNA antiparallel
each DNA strand runs in opposite directions, it is double helix spiral that twist around each other
what is complementary base pairing?
only certain bases will fit together snugly in pairs within helix, hydrogen bonds form between A and T, C and G
How is a double-helical molecule of Dna stabilized?
By complementary base pairing and by hydrophobic interactions between bases inside helix
What is semiconservative replication in DNA?
Parental strands are separated and used as template strands for the synthesis of a new daughter strand
genome
entire completement of DNA
what does DNA synthesis involve?
condensation/dehydration reaction that forms a phosphodiester bond between 3’ and 5’ on an incoming deoxyribonucleoside triphosphate monomer (dNTP)
what is DNA Polymerase?
polymerizes deoxyribonucleotide monomers into DNA, catalyzes DNA synthesis
why can DNA Polymerase only work in one direction and what direction is that?
DNA polymerase can only add deoxyribonucleotides to the 3’ end because of the presence of an OH group. DNA synthesis always proceeds in the 5’ to 3’ direction.
DNA Polymerase reads 3’ to 5’ to make 5’ to 3’
yes
Where is RNA primer located on lagging strand? on leading strand?
RNA primer located right by replication fork in lagging strand, RNA primer located away from replication fork in leading strand
How does DNA synthesis get energy?
potential energy of deoxyribonucleoside monomers is first raised by reactions that add two PO4 groups to form deoxyribose triphosphates
high potential energy due to close proximity of PO4 groups make it possible for phosphodiester bonds in a growing DNA strand to form
where do replication bubbles form?
origins of replication (ori)
where does active DNa synthesis take place?
at the replication forks of each replication bubble
what is a replication fork?
Y shaped region where parental DNA double helix is separated into single strands and copied
what does it mean by DNA synthesis is bidirectional?
DNA synthesis occurs in both directions at the same time, replication bubbles grow in two directions as DNA replication proceeds
how are the proteins that initiate DNA replication controlled?
by cell-cycle regulatory proteins
what does DNA helicase do?
breaks hydrogen bonds between base pairs in that location and opens double helix, causing the two strands of DNA to separate at the replication fork
what do single-strand DNA-Binding proteins ( SSBPs) do?
attaches to separate strands to prevent them from snapping back into a double helix
why is DNA topoisomerase needed to relieve stress/tension?
topoisomerase eases stress because the unwinding of DNA strands at replication fork creates twists farther down helix, leading it to coil on itself as untwisting continues from other side if not prevented
what does DNA topisomerase do?
cuts DNA, allows it to unwind, and rejoins it ahead of the advancing replication fork
what is a RNA primer?
RNA strand about a dozen nucleotides long that forms complementary base pairs with DNA template strand, provides DNA polymerase with a 3’ OH that can be linked to a dNTP to form a phosphodiester bond
what are RNA Polymerases?
class of enzymes that catalyze polymerization of ribonucleotides into RNA
why must an RNA polymerase act before the DNA Polymerase?
only RNA polymerases can initiate
what is initiation?
putting first nucleotide in place
elongation
attaching second nucleotide to the first, third to second, etc.
leading strand
continuous strand of DNA synthesized towards replication fork that proceeds straightforward
lagging strand
discontinuous strand synthesized away from replication fork
Discontinuous Replication Hypothesis
primase adds new RNA primers for lagging strands as moving replication fork opens, DNA polymerase uses primers to make short DNA fragments, later on joined together by ligase
how does DNA Ligase work?
catalyzes formation of phosphodiester bonds between adjacent fragments
What is the replisome?
replication of two strands is done by a single enzyme complex, all enzymes work together as they follow helicase along the dna
Synthesis at the replication fork occurs in three steps:
- Helicase opens double helix, SSBPs stabilize exposed single strands, topoisomerase removes twists downstream the fork
- DNA polymerase makes new leading strand
- DNA polymerase makes lagging strand okazaki fragments, later on joined by ligase
what is a telomere?
region at the end of a eukaryotic chromosome
why is DNA polymerase unable to add DNA near the end of a chromosome?
cannot make DNA without a primer, single-stranded part of DNA is left single stranded and eventually degrades, leading to chromosome shortening
how do telomeres solve the end replication problem?
telomeres had no genes and is a sequence repeated over and over again. If DNA replication leads to shorter and shorter daughter strands, telomeres will ensure dispensable repeat DNA is lost and not important genes
how does telomerase solve end replication problem?
telomerase replenishes telomere repeats before chromosome gets too short
how does telomerase work?
end is unreplicated, telomerase extends unreplicated end, telomerase repeats activity, extended single-strand DNA acts as template
where is active telomerase primarily found?
in cells of reproductive organs, specifically in cells that eventually undergo meiosis and produce gametes
why is activated telomerase in somatic cells not a good thing?
if telomerase was mistakenly activated in somatic cells, telomeres will fail to shorten, allowing cell to keep dividing and contribute to uncontrolled growth and cancer
why do bacterial cells not need telomerase?
DNA is circular and has no end, can’t be shortened
why does telomerase need a built-in template?
cannot use the existing DNA as a guide for adding telomere repeats. The DNA at the end of the chromosome is incomplete and has a single-stranded overhang that cannot be copied by the normal DNA polymerase.
How does DNA polymerase know it made a mistake?
DNA Polymerase’s active site can discriminate wrong shapes from incorrect base pairing and will add more only when previous base pair is correct, removing mismatched nucleotide by a subunit
what is mismatch repair?
form of error correction that occurs after DNA synthesis is complete
why is UV light bad?
causes covalent bond between adjacent pyrimidine bases within a DNA strand, creating a kink in DNA structure that stalls and blocks DNA replication
how do nucleotide excision repair systems work?
proteins detect errors, enzymes remove kinks and other types of damages that distort DNA helix, DNA polymerase replaces damaged parts with correct newly synthesized DNA, and DNA ligase links
three types of DNA repair
proofreading during replication, mismatch repair immediately after replication, nucleotide excision repair occuring before or after replication
is long telomeres detrimental to healthy cells?
yes, long telomeres recruit DNA repair enzymes that are needed elsewhere, like in important genes, leading to longer telomeres being more susceptible to DNA damage
why is DNA repair halted during mitosis?
it would result in damaged chromosomes
