Lecture 1 - DNA Flashcards
revision
what are the components of DNA
- its a nucleic acid
-a macromolecule made up of 2 polynucleotide chains - nucleotides consist of deoxyribose, a nitrogen containing base (adenine, thymine, guanine or cytosine), a phosphate group
- the base is connected to carbon 1
-the 3’ carbons hydroxyl group will join to the adjacent nucleotide
what makes up a nucleoside?
sugar and base
whats the bond that connects the sugar and base
N-glycosidic bond
what do phosphodiester bonds do
connect adjacent nucleotides, to create the sugar phosphate backbone
what bond connects the bases of opposite strands and how many of these bonds
-hydrogen bonds
-A and T have 2
-C and G have 3
what bases connect with which?
adenine and thymine
cytosine and guanine
which bases are pyrimidines and which are purines?
-adenine and guanine are purines
-thymine and cytosine are pyrimidines
is DNA a right or left handed helix?
right
what is important about the grooves in DNA?
-some proteins need to interact with the DNA and the bases and some cases need to pull apart bases and these grooved provide access to the DNA and bases
How do nucleotides join together?
- a condensation reaction, which eliminates water
-this creates a 3’,5’ phosphodiester bond
why is DNA replication important in cell division?
when a cell divides, both daughter cells must receive a complete set of genes, so the DNA molecules (chromosomes) must replicate accurately before division
what happens in asexual reproduction?
1- the entire genome is on one circular chromosome = DNA molecule
2-the chromosome replicates once to produce two chromosomes that are identical (except for rare chromosomes)
3-the two identical daughter chromosomes move toward opposite end of the cell
4-when the cell divides the daughter chromosomes are partitioned one to each daughter cell
why does replication need to be accurate?
so the daughter cell ends up with two copies of the genome, identical or near identical to the parent
what happens in M phase in the cell cycle?
mitosis and cytokinesis
what happens in G1 and G2?
transcription of genes
what happens in S phase?
it depends where the genes are in the genome and how the replication process is going as to whether transcription can occur in those genes or not
is DNA replication semi-conservative?
yes
where do each strand come from in DNA replication
one from the parent and one is a new strand
what strand determines the sequence of the newly synthesised strand
the template strand
which end of the molecule do the nucleotides add onto
3’ end
is DNA parallel or anti-parallel?
anti-parallel
what happens in DNA replication?
1-the strands separate
2-a new strand is made using each old strand as a template according to the rules of base pairing
what direction does DNA synthesis occur in?
5’ to 3’ direction
what does helicase do in replication?
unwinds double helical DNA, giving all other proteins required access to the template
what do single binding proteins do?
help maintain single strands of DNA and keep the DNA unwound
what does primase do?
adds ribonucleoside triphosphates to synthesise an RNA primer
differences between RNA and DNA
-RNA is single stranded, DNA is double stranded
-RNA has ribose but DNA has deoxyribose
-RNA has uracil instead of thymine
can DNA synthesis start on its own
no
what happens when an RNA primer is added
it creates a 3’ end which the DNA polymerase can start adding to
what does DNA polymerase do, and what does it require?
-it proceeds in a 5’ to 3’ direction
-adds 1000 bases/second to the growing chain
-requires all 4 dNTP’s deoxyribonucleotides
-must have a template and a primer
-has proof reading activity
what do exonucleases do?
removes nucleotides from the end of the DNA strand; different enzymes work 5’ to 3’ or 3’ to 5’
(removes the RNA primer and then fills the space in with DNA)
what does ligase do?
ligase joins ends of single DNA strands by making new phosphate bonds
what does it mean by DNA polymerase having proof reading activity?
it can detect if there are errors and could remove the wrong nucleotide and correct it with the right one
Process of DNA replication
-DNA is unwound by helicase
-Ssbp bind to the DNA to keep the strands separate
-a replication bubble is where the 2 strands are pulled apart, and then DNA replication will proceed in both directions
-primase lays downs the primer
-DNA polymerase starts adding nucleotides
-DNA polymerase will extend and produce DNA from this 3’ end of this primer
-when the DNA arrives at the RNA primase it needs to be removed and then a polymerase fills in the gap
-the ligase then joins the two pieces together
what are origins of replication
places in the genome where replication starts
what does gyrase do?
-gyrase is a topoisomerase
-it relaxes supercoils produced when the molecule is twisted during replication
-also facilitates unwinding at beginning of replication
what does telomerase do
uses a short RNA template to add short DNA repeats to the short ends of linear chromosomes when the last primer is removed using RNA template
why is telomerase important
protects our chromosomes
what happens to telomerase over time and how does it effect the genome
it shortens over time and after multiple divisions and this process makes the genome more vulnerable
- exceptions to this are stem cells
which enzyme removes supercoiling in the replicating DNA ahead of the replication fork?
topoisomerase
