DNA/DNA synthesis (complete) Flashcards
What is on the 5’ end of a DNA strand
a free phosphate
What is on the 3’ end of a DNA strand
an OH
In which direction are nucleic acids named
5’ to 3’
are the two strand of a double stranded DNA parallel or antiparallel
antiparallel
what kind of bonds exist between bases that are on opposite DNA strands
hydrogen bonds
The DNA helix is right or left handed
right
What is the shape of the pyramidines
a six carbon ring
what is the shape of the purines
a six carbon ring bound to a five carbon ring
Which bases are pyrimidines
Cytosine
Thymine
Uracil
Which bases are purines
Adenine
Guanine
What is the structure of cytosine
a pyrimidine with -NH2
What is the structure of Thymine
a pyrimidine with -CH3
What is the structure of Uracil
a pyrimidine without -NH2 or -CH3
What is the structure of Adenine
the purine without the carbonyl
what is the structure of guanine
purine with the carbonyl
What is a nucleoside
a sugar and a base
what is a nucleotide
a sugar, base and phosphate group
What are the three parts of a nucleotide
sugar
base
phosphate group
how many phosphates can be on a nucleotide
0-3 (nucleoside if it has 0)
What is the difference between the sugar of DNA and RNA
the c-2 location has an OH in RNA
the c-2 location just has an H in DNA
Which of the Bases (A, T, G, C, U) bind together
A–T (in DNA)
C–G
A–U (in RNA)
how many hydrogen bonds are between A–T
two
how many hydrogen bonds are between C–G
three
what kind of bonds connect nucleotides together
phosphodiester bonds
which part of DNA is hydrophilic, which part is hydrophobic
the backbone (sugar and phosphate) is hydrophilic the bases are hydrophobic
What are the two types of Grooves in DNA
major and minor
why are major and minor grooves significant
because enzymes likely enter and act upon the DNA through the major grooves
Where is the new phosphodiester bond created when two nucleotides bind together
it is formed between the phosphate group off of the 5-C of one nucleotide, to the 3-C of the next
which base pairs are harder to separate A–T or C–G
C–G because they have one more H bond between them
what three things can denature DNA
- Heat
- pH changes
- DNA replication
What did Hershey and Chase discover
that it was the DNA, not the protein, that held the genes
What are histones
proteins that help condense DNA into chromosomes
What did Meselson and Stahl discover
that DNA synthesis is semi conservative
what does it mean that DNA synthesis is semi conservative
That for each generation of DNA made, there is one new strand and one old strand.
at the replication fork is DNA synthesis bidirectional
yes
What are the two types of strands in DNA synthesis
a leading strand
a lagging strand
in which direction is DNA synthesized
5’ to 3’
does DNA synthesis require a primer
yes
does DNA synthesis have high or low processivity
high
is DNA synthesis fairly accurate (doesn’t make many mistakes)
It is very very accurate
What are the 7 enzymes used in DNA synthesis
- DNA-A
- DNA helicase
- Single stranded DNA binding protein
- Topoisomerase
- primase
- DNA polymerase
- ligase
What is the function of DNA-A
it creates the replication bubble, begins to denature DNA
What is the function of helicase
to continue to denature DNA (after DNA-A), unzips the double stranded DNA
What is the function of single stranded DNA binding protein
to make sure that the two single strands of DNA in the replication fork done reanneal
What is the function of Topoisomerase
to release the tension on the DNA coil that is caused by helicase unwinding the double strand (it cuts, untwists, and puts the strands back together)
What is the function of primase
it lays down an RNA primer so that DNA polymerase can do it’s work
what is the function of DNA polymerase
replicates DNA (brings the Bases into place and forms a new DNA strand)
what is the function of ligase
links unconneced strands of the new DNA together
What are the different types of DNA polymerase we talked about
DNA polymerase 1
DNA polymerase 3
What does DNA polymerase 1 do
- removes RNA primer and puts DNA in it’s place
- proofreading
- regular polymerase activity
What does DNA polymerase 3 do
- Most of the polymerase activity is done with #3
2. it also does proofreading
Why does DNA polymerase 3 do most of the DNA synthesizing
because it is the fastest, and the most processive
what does processivity measure
how many nucleotides can be added before the enzyme dissociates
what are the two sites of DNA polymerase 1
polymerase active site Exonuclease site (proofreading)
what are the two ways DNA polymerase can remove bases
5’–>3’ removes RNA primers
3’–>5’ removes misincorporated bases
What are the differences between the leading and lagging strand
leading strand:
one long molecule
single RNA primer
adds 5’–>3’ moving toward the replication fork
lagging strand:
many short (okazaki) fragments
many RNA primers
adds 5’ –>3’ moving away from the replication fork
