DNA Structure Flashcards
What is the definition of nucleotides?
- building blocks of nucleic acids formed of phosphates, ribose/deoxyribose and nitrogenous base
What is the definition of nucleic acids?
- a polymer (long repeating chain) of nucleotides
What is the definition of deoxyribonucleic acid?
- usually a double helix made up of two chains of deoxyribonucleotides
What is the definition of ribonucleic acid (RNA)?
- usually a single-stranded chain of ribonucleotides
What are the building blocks of a nucleotide?
- 3 phosphate groups (PO4, PO4, PO4,)
- a central sugar ring (either ribose in RNA or deoxyribose in DNA)
- a base
The structure of ribose and deoxyribose is almost identical with just one difference - what is this and due to this what happens?
- Ribose sugar has a hydroxyl (OH) group at position 2
- whereas deoxyribose sugar has a hydrogen (H) atom at position 2
= due to this deoxyribose sugar is more stable than ribose sugar
The core bases differ between DNA and RNA.
What bases does DNA have?
- Guanine (G)
- Cytosine (C)
- Adenine (A)
- Thymine (T)
What bases does RNA have?
- Guanine (G)
- Cytosine (C)
- Adenine (A)
- uracil (U) - T will be transcribed as U from DNA to RNA
What is the bonding of the nucleotides like in DNA and RNA?
- each nucleotide is covalently bonded through phosphodiester bonds
What gives DNA directionality?
- forms nucleic acids (polymer)
- there is a free 5 end
- there is a free 3 end
There is a second major difference between DNA and RNA (in terms of strands) - What is this?
- DNA is double stranded
- RNA is single stranded (mostly)
- RNA can from complementary bonds like DNA
In DNA bonding what base pair bonding is stronger?
- G:C bonding is stronger than A:T
How many hydrogen bonds is between thymine and adenine?
- 2 hydrogen bonds
How many hydrogen bonds are between cytosine and guanine?
- 3 hydrogen bonds
What does the difference in hydrogen bonds mean for DNA?
- means DNA in a double strand can be easily unwound
What does the bonding of the bases in DNA have implications for?
- Has implication in primer design for PCR
What helps from the DNA double helix structure?
- complementary hydrogen bonds
What components make up the DNA double helix structure?
- sugar-phosphate backbone
- complementary bases
- hydrogen bond between them
How long is the DNA for a mammalian genome?
- 2 metres long
How big is the nucleus of DNA?
- 6-10 microns in diameter
- (so there needs to be a way to fit the 2 meter DNA into the nucleus)
How is the DNA organised in order to fit its 2 meter DNA into its nucleus?
- To help organise and compact it, genomic DNA is packaged around specific proteins = histones
What do histones function as?
- as a histone octamer
What are the 4 types of histone subunits?
- Histone H2A
- Histone H2B
- Histone H3
- Histone H4
How many of each histone subunit do you need to make the barrel in which DNA wraps?
- 2x Histone H2A
- 2x Histone H2B
- 2x Histone H3
- 2x Histone H4
All octamer histones are what type of charge?
- positively charged
How many base pairs of DNA are wrapped around the octamer?
- 147 base pairs
The 147 base pairs of DNA wrapped around the octamer forms what?
- a nucleosome
There are linker DNA between nucleosomes - how many base pairs does this DNA contain?
- 10-80 base pairs
What makes it so easy for DNA to wrap around an octamer?
- that a octamer is positively charged whereas DNA is negatively charged
What leads to the formation of 6 histone octamer rings?
- H1 histone binds ton each nucleosome
- interactions between H1 histone then leads to the formation of 6 histone octamer rings
How can 6 histone octamer rings aid DNA?
- they condense DNA further
How is DNA further coiled to make chromosomes
- the nucleosomes and histones make up chromatin
- this chromatin then makes the solenoid fibres which can be used to make chromosomes
The condensed nature of chromatin is variable - what does this impact?
- impacts gene expression
What else can impact gene expression?
- Addition of methyl groups and acyl groups to histones can impact chromatin and gene expression
What are histone tails?
- Histone tails are proteins that are parts of the histone octamers
We can either add methyl and acyl groups or take them away.
what needs to be done to add and what needs to be done to take them away?
- To add them we use writer enzymes such as methyltransferase
- To remove them we use eraser enzymes such as deacylase
Why is DNA packaging important?
- We examine it for drug targets against parasites
- Can also be used to help understand and target cancer
What does DNA need to do in order to produce more cells and offspring?
- reproduce/ replication
What is the most important enzyme in DNA replication?
- DNA polymerase
What does the directional nature of DNA mean for replication?
- means replication moves from 5’ to 3’ end
- starts with origin of replication
What creates replication forks in DNA?
- helicases = enzymes that aid in the unwinding of the DNA
What is primase?
- enzyme that synthesize short RNA sequences called primers
What is DNA polymerase?
- enzymes that synthesize new new DNA strands
DNA replication occurs in different ways for each strand.
how does it occur in the leading strand?
- there is continuous replication moving towards the fork
How does replication occur in the lagging strand of DNA?
- moves away from the fork and makes discontinuous fragments of DNA
What does DNA unzipping and replication lead to?
- supercoiling downstream in the original dsDNA
What is the enzyme that prevents supercoiling?
- DNA gyrase (topoisomerase)
DNA gyrase proteins differ between prokaryotes and eukaryotes - What do quinolones (an antibiotic) target?
- target the bacterial DNA gyrases
What does PCR stand for?
- polymer chain reaction
What is PCR?
- an amplification technique of DNA
What can PCR be used in?
- genetic disease determination
- allelic determination for breeding programmes
- detection of pathogens
What does PCR rely on the use of?
- Template DNA
- Free dNTPs (4 nucleotides)
- 2 specific primers
- Taq Polymerase
- Buffer
What are the free dNTPs?
- dATP
- dGTP
- dCTP
- dTTP
What are the primers needed for PCR?
- short single stranded DNA = complementary to region of amplification
What is Taq polymerase and what does it allow for?
- extremophiles
- allows DNA synthesis only at high temperatures
What does buffer do in PRCs?
- helps enzyme work correctly have the right amount of salt and pH so the enzymes work
Describe the process of PCR:
- start off with a long piece of double stranded DNA
- Heat the DNA (94’c) to separate the two strands of DNA and denature
- cool the DNA (60’c) to allow the primers to anneal - because there are millions of copies of the primer they will numerically out-complete the longer pieces of DNA
- Heat the DNA (72’c) to allow DNA polymerization (extension)
- repeat
PCRs using specific primers can be used to determine what?
- infections (species, strain etc,)
PCR can be run on what on what in order to separate it by size and visual?
- agarose gel
