DNA: Structure and function, replication Flashcards
- Bond found between two nucleotides
- Reaction to form the bond
- Phosphodiester bond
- Produced during condensation
Primary structure of DNA
- Sequence of nucleotides
- Order of mononucleotides
3’ end of the nucleotide
Free 3-OH group
5’ end of the nucleotide
Free 5-phosphate group
2 bound mononucleotides
Dinucleotide
3-10 bound mononucleotides
Oligonucleotide
11-100 bound mononucleotides
Polynucleotide
>100 bound mononucleotides
Nucleic acid (DNA/RNA)
Structure of RNA
Similar to DNA:
- Ribose instead of deoxyribose
- Uracil instead of Thymine
Secondary structure of DNA
- 2 antiparallel strands
- 3’ end of one meets 5’ end of the other
Chargaff-rule
Number of purine bases = Number of pyrimidine bases
in double-stranded DNA
Number of H-bonds between: Adenine-Thymine
2
Number of H-bonds between: Guanine-Cytosine
3
Denaturing of DNA
- Heating
- H-bonds broken
- DNA becomes single-stranded
Renaturation of DNA
- Cooling
- Double-stranded structure rearranges
The melting point of DNA
When half of the total DNA becomes single-stranded
- Dependent on:
- Types of bases
- More G-C pairs = higher melting point
The alpha-helix form of DNA is its…structure
Tertiary
Who discovered the tertiary structure of DNA?
- Franklin & Wilkins
- Watson and Krick
Is the DNA double helix left-handed or right-handed?
Right-handed
How many nucleotides in the tertiary DNA chain contribute to 1 turn of the helix?
10
On DNA, where do transcription factors bind?
In the major & minor groove
Minor groove on DNA
The distance between two DNA strands
Major groove of DNA
The distance between two turns of DNA
What are the varieties of DNA double helix?
- A-DNA
- B-DNA
- Z-DNA
B-DNA structure
Based on the Watson-Wrick model
A-DNA
- Decreased humidity
- Increased salt concentration
- Frequent turns in the strand
Quarternary structure of DNA
- Superhelix
- Found in prokaryotes
What are the three forms of DNA superhelix
- Relaxed
- Positive superhelix
- Negative superhelix
Relaxed superhelix form
Double helix is loose
Positive superhelix form
Double helix is spirally twisted
Negative superhelix form
Double helix is twisted in the opposite direction
Out of the positive and negative superhelix forms of DNA, which is the most transcriptionally active?
Negative superhelix
Topoisomerases
- Enzymes
- Form the relaxed superhelix structure
How does Topoisomerase I form a relaxed superhelix
- Splits and ligates one DNA strand
- No energy is required
How does Topoisomerase II form a relaxed superhelix
- Splits and ligates both DNA strands
- Requires ATP
An alternative name for topoisomerase II
DNA gyrase
How many chromosomes do prokaryotes have?
1
DNA is organised into the form of…
Chromosomes
Prokaryotic chromosome structure
- Double-stranded
- Circular
Histone
- Alkaline protein
- High isoelectric point
- Positive charge
Why is DNA is attracted to histones?
- Histone: positive charge
- DNA: Negative charge
- Strong ionic interaction
The composition of histone octamers
Pairs of core histones:
- H2A
- H2B
- H3
- H4
Histone H1
Fixes and strengthens DNA binding on the histone octamer
Structure of a nucleosome
Regularly repeating unit:
Histone octamer + DNA + histone H1
The effect of histone modifications
- Histones can be modified covalently
- Nucleosome therefore changes
- Transcription is altered
Which modifications of histones are possible?
- Acetylation
- Methylation
- Phosphorylation
What is the acetylation histone modification?
Binding of acetyl groups
What is the methylation histone modification?
Binding of methyl groups
What is the phosphorylation histone modification?
Binding of phosphate groups
The makeup of chromosomes
Nucleosomes → Chromatine → Chromatids → Chromosome
What is a gene?
- A unit of heredity
- The region of DNA coding:
- A protein
- An RNA molecule
Amino acids are coded by…
Nucleotide/base triplets
1 amino acid → Base triplets of DNA = 1 code
The reading frame in the genetic code system is
- Universal (for each organism)
- Confluent (commaless)
- Non-overlapping sequence
A triplet code can make a genetic code for how many different combinations?
64 (43 = 64)
Steps of the central dogma
- DNA code from base triplets
- Transcription
- tRNA transports amino acids → ribosomes
- Translation
Transcription
- mRNA synthesis
- mRNA base triplets = Codon
Base triplets of tRNA
Anticodon
Translation
Protein synthesis in the ribosome
DNA replication
Reduplication of DNA
- Forwarding genetic information during cell division
What is the structure of DNA during replication?
The double helix is split into two single strands
Acts as a template
Describe the semi-conservative theory of DNA replication
- Produced double helix is composed of:
- 1 parental strand
- 1 newly synthesised strand
The three phases of DNA replication
- Initiation
- Elongation
- Termination
Where does DNA replication of prokaryotes initiate?
The replication origo
Replication origo is composed of…
Consensus sequences
DNA-A during prokaryote DNA synthesis
- Proteins recognise replication origo
- DNA-A binds to DNA-A binding sites
DNA-B and DNA-C during prokaryote DNA synthesis
- Bind to a DNA-A protein
-
Helicase activity
- H-bonds split
- Double helix opens
- ‘Replication bubble’ forms
Replication of prokaryotes: Initiation phase (Phase 1)
- Single strand proteins (SSB-proteins) separate the two strands
Which group of the DNA is needed for synthesis in prokaryotes
3’-OH-group
Primer
- Short RNA sequence
- Has a free 3’-OH-group
Synthesis of primers is by…
Primosomes
Primosome
- Protein complex
- Contains Primase
- Contains synthesising primer
Replication of prokaryotes: Elongation phase (Phase 2)
- Continuous & discontinuous synthesis
- The building of nucleotides in new strands
In prokaryotes, where does continuous synthesis occur?
The leading strand
In prokaryotes, where does discontinuous synthesis occur?
The lagging strand
A primer + DNA is known as…
Okazaki-fragment
In prokaryotes, synthesis of the new DNA strand is responsible by…
DNA polymerase III
DNA polymerase synthesises in which direction?
From the 5’ → 3’
The building blocks for new DNA strands
dNTP
(Deoxyribonucleoside triphosphate)
How is dNTP made into nucleotides
dNTP → dNMP + 2Pin
Replication of prokaryotes: Termination phase (Phase 3)
- DNA polymerase III dissociates
- Primers hydrolysed
- DNA polymerase I moves between DNA fragments
- Ligation of new DNA
During prokaryote termination which enzyme will hydrolyse and cut out primers?
DNA polymerase I
During prokaryote termination which enzyme ligates new DNA?
DNA ligase
The function of DNA ligase
- DNA ligase: ATP → AMP + 2Pin
- AMP binds to the activated enzyme
- 5’-end and 3’-end of two fragments
- → Phosphodiester bond
- AMP dissociated from enzyme
Function of topoisomerases
- Strands become tense during replication
- Topoisomerase cuts DNA strand
- DNA rotates to remove coils
- Topoisomerase rejoins the DNA strands
DNA gyrase is a type of…
Topoisomerase
How does DNA polymerase act as a dimer?
Simultaneous replication of two DNA strands
Where are proteins needed for replication organised?
Replisome
The three main differences between eukaryote and prokaryote DNA replication
- Eukaryotes
- Numerous replication origos
- Distinct DNA polymerase names
- Telomeric sequences
List the DNA polymerases of Eukaryotes
- DNA polymerase α
- DNA polymerase β
- DNA polymerase γ
- DNA polymerase δ
The responsibility of DNA polymerase α
Synthesis of new DNA strand
Acts as the equivalent of DNA Polymerase III in prokaryotes
The responsibility of DNA polymerase β
- Repair DNA during replication
- Removes the primer
- Filling of gaps
Acts as the equivalent of DNA Polymerase I & II in prokaryotes
The responsibility of DNA polymerase γ
Replication of mitochondrial DNA
The responsibility of DNA polymerase δ
- Synthesis of new DNA strand
- Requires PCNA protein for operation
Telomeric sequences are used to solve which problem?
- Lagging strand:
- Last primer of the 5’-end cannot be replaced by nucleotides
- Chromosome would be shortened
Telomere
- Extra sequence attached to 3’ end of chromosome
- Telomerase synthesis the telomeric sequences
The process of DNA repair
- UV-specific endonuclease
- Cuts damaged strand
- Damaged/mismatching bases removed and replaced
- DNA polymerase I & II (Prok.)
- DNA polymerase β (Euk.)
- DNA ligase links fragments
Mutation
Heritable change of DNA base sequences
Types of mutation
- Spontaneous mutation
- Induced mutation
- Gametic mutation
- Somatic mutation
- Chromosome mutation
- Gene mutation
Causes of induced mutation
Caused by physical conditions
Gametic mutation
- Mutation in ovum/sperm
- Forwarded onto descendants
Somatic mutation
- In somatic cells
- Causes tumours
Gene mutation
- Mostly point mutation
- Only a single nucleotide is changed
Forms of point mutation
- Substitution mutation
- ‘Frameshift’ mutation:
- Insertion
- Deletion
Substitution mutation
A non-complimentary nucleotide is built into the chain rather than a complimentary nucleotide
Varieties of substitution mutation
- Missense mutation
- Nonsense mutation
- Silent/samesense mutation
Missense mutation
Mutated base sequence → Different amino acid produced
Nonsense mutation
Mutated base → Stop code produced → Translation halts → Produced protein is shorter
Silent/samesense mutation
Mutated base → Same amino acid is produced
Insertion
Extra nucleotides introduced into the DNA
Deletion
Nucleotides missing from the DNA
Thymine dimer formation
- UV radiation → covalent bonds between pyrimidine bases
- Replication and transcription affected
- Mutagenic process → Melanoma
Sickle-cell anaemia
- Missense substitution mutation
- β-globin gene affected
- Change from Glutamine → Valine production
- Change is haemoglobin solubility
