Lecture 2 Flashcards
telomere
The ends of a eukaryotic chromosome
semi-conservative replication of DNA
the method of DNA replication where the new molecule of DNA has one strand which comes from the parent molecule and one strand which is newly synthesised.
complementary base pairing
nucleotides or nucleotide sequences that are able to base pair. For example, G and C are complementary as are A and T.
pyrimidine
one of the two types of nitrogenous base compounds found in nucleotides. The pyrimidine bases in DNA are cytosine and thymine
purine
one of the two types of nitrogenous base compounds found in nucleotides. The purine bases in DNA are guanine and adenine.
polynucleotide
a polymer consisting of nucleotide subunits.
phosphodiester bond
the chemical bond that links the adjacent nucleotides in a polynucleotide.
5’ (PO4) end
the end of the polynucleotide that terminates with a phosphate attached to the 5’- carbon of the sugar.
3’ (OH) end
the end of a polynucleotide which terminates with a hydroxyl group attached to the 3’- carbon of the sugar.
leading/ lagging strand
the leading strand is that which is synthesized continuously, whereas the lagging strand is synthesized in a discontinuous fashion during DNA replication.
Okazaki fragment
one of the RNA-primed short segments of DNA synthesized during replication of the lagging strand of the double helix.
DNA helicase
an enzyme that uses energy from ATP to unwind the DNA
topoisomerase
gyrase
an enzyme which can relax DNA by cutting and reforming the polynucleotide backbones
single-strand binding protein
one of the proteins that attaches to single stranded regions of DNA and prevents the reformation of base pairs, particularly in the region of the replication fork.
primase
an enzyme which synthesises the RNA primer
DNA polymerase I
enzyme which adds nucleotides to gaps when primers removed
DNA polymerase III
main polymerase which adds nucleotdes to template in a complementary way
RNA primer
sequence of RNA to make a stretch of double stranded DNA on which the DNA pol III can work
ligase
enzyme which joins sequences of DNA
What is euchromatin?
on- active (open) chromatin
- unmethylated cytosines
- acetylated histones
- can be transcribed and replicated
What is heterochromatin?
off- silent (condensed) chromatin
- methylated cytosines
- deacetylated histones
- acetyl group CHCH3
- can’t be replicated in this form
When can we see chromosomes?
only in mitosis and meiosis
Where are chromosomes in prokaryotes and eukarytoes?
- prokaryotes: cytosol
- eukarytoes: nucleus
What is a chromosome made of?
- DNA and protein
- may consist of one or two DNA molecules, depending on the cell stage in the cell cycle
- when two DNA molecules- called sister chromatids
What are the 3 components of DNA for its stability and function and how do they achieve it?
telomeres
- structural stability, replication, positioning
- the end bit of a chromosome
- needs to be intact for chromosome to be stable, if not- stick together
centromeres
- essential for segregation at cell division
- holds chromatids together
origins of replication
- DNA replication start point
What is the end sequence of a telomere in humans and how many times is it repeated?
TTAGGG
2500x
How does a telomere protect end of a chromosome?
thanks to the repetition by looping or recruiting proteins
What is the issue with replicating telomeres?
- leading strand replication easy, lagging- issues
- lagging- at the end not enough space for a primer so a little bit gets lost- that’s why we lose the ends of our chromosomes gradually=though to be involved in aging as older people have shorter telomeres
Which cells have telomerase?
-gametes, most other cells do not have it!
What is telomerase?
-protein with RNA sequence complimentary to the end telomere sequence TTAGGG that binds to the lagging strand so the replication of the lagging strand can be completed in its entirety
How many bases from the telomere do we lose each round of replication?
50-200 bases
What happens when the genes on ends of chromosomes are lost (due to telomere shortening)?
-cell dies
What is a possible reason why cancer cells live for so long (immortal)?
- have telomerase and don’t lose the ends of their telomeres
diploid
two of each type of chromosome
two similar chromosomes = homologous
haploid
one copy of each chromosome
What is chromatin?
DNA and protein
- basically uncondensed chromosome
- visible most of the time (not in M)
What is a nucleosome?
-basic unit of chromatin, in eukaryotes, oackaging unit
How many histones does a nucleosome have?
-8
What is the function of histone H1?
-linker, keeps the histones and DNA rolled, clamps DNA to the core
What are the functions of histones H2A, H2B, H3 and H4?
-structural histones
How is gene transcription affected when nucleosomes are coiled?
- then unavailable for transcription
- packaging= influences gene expression (if too tightly coiled)
What are the strands of DNA?
-strands are complementary and antiparallel 5’-3’ 3’- 5’
What binds A and T and C and G together?
-hydrogen bonds
How many hydrogen bonds are there in C and G?
3
How many hydrogen bonds are there in A and T?
2
What 3 components does a nucleotide compose of?
- deoxyribose sugar
- phosphate group(with sugar- Phosphodiester bond)
- nitrogenous base= A,C,G,T,(U-in RNA)
Which are the purines and how many C rings do they have?
A and G
2 C
Which are the pyramidines and how many C rings do they have?
C and T
1 C
Why do we have both pyramidines and purines?
-balance the molecule, always have 1C and 2C so it stays the same width
Are there equal proportions of A,T,C and G in an organism’s DNA?
-no, humans AT rich
When does DNA replication take place?
- S stage
In which stages is the DNA in its replicated form?
-S, G2 and beginning of M
What are the differences in DNA replication in eukaryotes and prokaryotes?
prokaryotes
- only one point of origin O goes to terminus T
- fork movement, goes in both directions (as DNA is not packaged)
eukaryotes- several points of origin due to size of DNA, both directions, faster replication (bases per minute)
What does helicase do in DNA replication?
separate strands of DNA- disrupt the hydrogen bonds along the molecule
What do single stranded binding proteins do in DNA replication?
keep the bases open so replication can proceed(bases unstable when open, tend to shut)
What does primase do in DNA replication?
constructs a bit of double-stranded RNA acting as a primer for Polymerase III
What does polymerase III do in DNA replication?
constructs DNA in 5’- 3’direction and can add bases only to in that direction (3’ OH end – the growing strand) -works for leading strand= continuously replicated
Which strand needs more primers?
-lagging, non-continuous replication
What are the replicated fragments on the lagging strand?
-Okazaki fragments
What does DNA Topoisomerase do in DNA replication?
keeps the uncoiled DNA from getting coiled, creates nicks in DNA to do this
What does DNA Polymerase I do in DNA replication?
gets rid of the RNA primers, fills in the missing nucleotides
What does ligase do in DNA replication?
joins the Okazaki fragments so it’s continuous
What is the function of the clamp?
donut-shaped protein complex, next to Polymerase III, keeps the polymerase in the DNA, without it the polymerase would need to constantly re-attach itself, only for polymerase III not I- that only stays on for a short time, clamp not needed. Increases efficiency of replication
How many bases are there in Okazaki fragments in eukaryotes and prokaryotes?
eukaryotes 100-200 bases
prokaryotes 1000 bases
Are there different enzymes in DNA replication in prokaryotes and eukaryotes?
yes
different DNA polymerases
- prokaryotes- DNA polymerase III
- eukaryotes- many (alpha, beta, epsilon) polymerase
