L1 - Structure of DNA Flashcards
Briefly describe what DNA is?
- DNA is a nucleic acid
- A macromolecule
- Made up of 2 polynucleotide chains
What sub-units are polynucleotides made up of?
Nucleotides
What components make up a DNA nucleotide?
- 5’ carbon sugar called 2-deoxyribose - a stable sugar
- Nitrogenous base
- Phosphate group attached to the 5’ end of 2-deoxyribose
Name the 4 different nitrogenous bases and their complementary base pairs
A for adenine
T for thymine
G for guanine
C for cytosine
A with T
G with C
* must always write full names not shorthand
Name the bond which attaches the nitrogenous base to 2-deoxyribose in DNA?
What is the purpose of this bond?
N-glycosidic bond
Gives stability to 2-deoxyribose and the nitrogenous base
What term is used to describe the combination of 2-deoxyribose and a nitrogenous base?
Nucleoside
When does a nucleoside become a nucleotide?
When a phosphate is bound to the 5’ carbon on 2-deoxyribose by a phosphodiester bond
Describe the terms 5’ prime end and 3’ prime end in relation to DNA
- Successive nucleotides bond together by phosphodiester bonds to form a DNA strand
- The phosphate is at the 5’ end
- The free hydroxyl group is at the 3’ end
- 2-deoxyribose determines the orientation
What term is used to describe the relation between 2 DNA strands?
- DNA strands run anti-parallel to each other
- DNA strands are complementary to each other
- The second strand runs in the 5’ to 3’ direction but with a different orientation
What type of bonding is between nitrogenous bases? Why is this beneficial?
Hydrogen bonding
Allows stability of the 2 polynucleotide chains running ani-parallel
How many hydrogen bonds are between each complementary base pair?
Guanine and cytosine have 3 bonds
Adenine and thymine have 2 bonds
Which bases are purines and pyrimidines?
A and G = purine (2 carbon ring)
T and C = pyrimidine (1 carbon ring)
What is the key advantage of having the purine and pyrimidine structure?
- Even though they are different bases, they take up the same spacial area in the nucleus
- Compact to allow more DNA in the nucleus
What is a benefit towards DNA structure, as a result of hydrogen bonding?
- Allows a twist (helix) to the anti-parallel structure
- Forms the DNA double helix
- Allows the information needed in the nucleus to be compacted, to allow the DNA to be unwound to carry out eukaryotic functions
Why is a double helix able to form?
- The phosphate groups are on the outside with the nitrogenous bases in the centre
- Provides stability and flexibility
What two areas form on a DNA double helix?
What are their functions?
- Major and minor grooves
- Allows eukaryotic processes to be carried out
- Some sequences of DNA can only be exposed though these grooves
- Aids transcription factors or replication machinery to bind
What reaction is involved in nucleotides bonding to subsequent nucleotides?
- Condensation reaction
- Removal of water molecule
- Forms a 3’ 5’ phosphodiester bond
*need all of this info to gain full marks
Define DNA replication
When a cell divides, both daughter cells must receive a complete set of genes, so the DNA molecules (chromosomes) must replicate accurately before division
Where is DNA found in prokaryotes?
The entire genome is on one circular chromosome
Describe the process of asexual reproduction in a prokaryote
1) Entire genome is on one circular chromosome
2) The chromosome replicates once to produce two chromosomes that are identical (except for rare mutations)
3) Two identical daughter chromosomes move towards opposite end of the cell, towards the poles
4) Process of partitioning - cell divides the daughter chromosomes into singular daughter cells when partitioned
When does DNA replicate in eukaryotic cells?
DNA replicates in the S phase of the cell cycle
When are genes expressed in the cell cycle?
- Occurs in G1 and G2 and occasionally in the S phase (these are only genes not highly expressed)
- Silent or temp. silent genes ate replicated late in the cycle as they may be needed later on
What are the general features of eukaryotic DNA replication?
- DNA replication is semi-conservative
- Bi-directional process
- Proceeds from a specific point called the origin
- Proceeds in the 5’-3’ direction
- Occurs with a high degree of fidelity
- Multi-enzymatic process
What does semi-conservative mean in DNA replication?
From the parent double strand, one of each of those double strands is used to form the new daughter strand, by acting as a template and complementary base pairing
What is the role of enzyme helicase in replication?
- Unwinds the double helix of DNA ready for replication
- By disrupting the H bonds between complementary base pairs creating a replication fork of two strands running in antiparallel directions.
- This occurs at specific regions (origins of replication),
What are SSBP? What are their functions?
- Single-stranded binding protein
- Keep the replication fork open, bind and stabilise the single strand of DNA to keep it unwound
- 2 of these are present
What is the purpose of an RNA primer?
Allows DNA polymerase to attach to the primer and begin the process of replication
What enzyme is needed to synthesise an RNA primer?
Primase
Describe the role of primase and a primer
- Adds ribonucleoside triphosphates to synthesise a primer (primase)
- Binds to the initiation point of the 3’ - 5’ parent chain (primase)
- Runs in the 5’-3’ direction (primase)
- DNA polymerase will attach to the primer
What is the role of DNA polymerase? What direction does it move along the DNA strand?
- Attaches to the primer and adds nitrogenous bases to the base on the template strand, so the base pairs are complementary
- 5’ to 3’ direction
How many bases per second does DNA polymerase add?
1000/sec
How many nitrogenous bases are required by DNA polymerase?
All 4 dNTPs (deoxyribonucleotides)
What two factors are key for DNA polymerase to act?
Template strand and a primer
What key function can DNA polymerase carry out?
- Proof reading
- Able to ‘check over’ previous bases which have undergone complementary base pairing
- Ensures fidelity in the replication process
What is the function of exonucleases?
Remove nucleotides from the end of a DNA strand
Work in a 5’ to 3’ or 3’ to 5’ direction
What is the function of ligase?
Joins the ends of single DNA strands by forming new phosphodiester bonds
What is the function of alpha polymerase?
Synthesises the RNA primer, initiation of DNA synthesis and the lagging strand
What is the function of beta polymerase?
Repair DNA
What is the function of gamma polymerase?
Replicate mitochondrial DNA
What is the function of delta polymerase?
Synthesise the leading strand, filling DNA gaps after removal of primer
What is the function of epsilon polymerase?
Repair of DNA
Which forms of DNA polymerase are also able to act as exonucleases? In which direction?
Gamma, delta, and epsilon
All in the 3’ to 5’ direction
What are the 3 stages of DNA replication?
Initiation
Elongation
Termination
Briefly describe the process of DNA replication
1) Helicase unwinds and unzips the DNA double helix by breaking H bonds between complementary bases
2) Single-stranded binding proteins will bind to each of the parent strands - keep the replication fork open
3) Primase acts to allow a primer to attach to each strand of DNA, in a 5’ to 3’ direction, using the 3’ to 5’ parental strand as a template
4) Elongation - the DNA polymerase attaches to the RNA primer and will lay down complementary bases according to the parent template strand in a 5’ to 3’ direction
5) This occurs on both strands
6) The exonuclease will come in and remove the RNA primer, recognising that the RNA primer has ribose and uracil, and so is not part of DNA
7) DNA polymerase proof reads and fills any gaps on the replicated strands
8) Ligase uses condensation reactions to reform the sugar-phosphate backbone between nucleotides through 3’5’ phosphodiester bonds
What is the leading strand?
The continuous strand. DNA polymerase can always add complementary bases, and continue replication, as it is in the 5’ to 3’ direction
What is the lagging strand?
Not continuous. Has to wait for the helicase to break the H bonds between bases, and for the RNA primer to be activated on the strand, to allow DNA polymerase to carry out replication
What are the small replicated DNA fragments on the lagging strand known as?
Okazaki fragments
How is DNA replicated on the lagging strand?
- A primer is added using primase, with DNA polymerase able to add free nucleotides which are complementary.
- Process has to happen in a 5’ -3’ direction
- Use of multiple primers and okazaki fragments
- Same process after with exonucleases and ligase
How many origins of replication are there in prokaryotes? Why?
One
Due to the small size
How many origins of replication are there in a eukaryote? Why?
Multiple
Large genome so needs to be a faster process
Draw a diagram of how origin points result in a continuum two daughter strands
Why does this happen?
Due to the process of replication being bi-directional
How long does replication take in eukaryotes?
8 hrs
How long is a full cell cycle for a specialised, differentiated cell?
16-18 hrs
What are found at the ends of the new daughter cells, and how do they form?
- Telomeres
- There isn’t a proceeding 3’ -OH when the RNA primer is removed at the 5’ end. There is a gap which has to be filled, because this causes a loss of genetic information in that region
What are telomeres rich in?
They are G:C rich and attached to the end of the genome
Why are telomeres so important?
Highly conserved
Serves an important function in protecting the sequence of DNA
Are telomeres involved in coding?
They are a non-protein coding region
Simply a series of bases for protecting the genome and ending the termination sequence
What is the function of gyrase?
A topoisomerase which relaxes supercoil produced when the molecule is twisted during replication. Also facilitates unwinding at the beginning of replication
What is the function of telomerase?
- Makes and replicated the telomeres
- Uses a short RNA template to add short DNA repeats to the short end of linear chromosomes when the last primer is removed using RNA template
What happens to telomeres as you age?
- Become shorter after every replication by 10-15 bases
- Increases the risk of age related diseases because the genome is not as well protected
What is the human telomere sequence?
TTAGGG/ AATCCC repeats
Where can the enzymes involved in replication also be used?
- PCR
- Making recombinant DNA
- Detecting mutations at the molecular level
