Nuclei Acids Flashcards
Structure of DNA
- DNA is double-stranded
- DNA molecules twist as regular intervals to form helix
- Nitrogen bases are closely packed together & phosphate forms an outer backbone on the outside.
purines
A + G
pyrimidines
C + T - 1 carbon-nitrogen ring
DNA replication
Helicase
DNA Gyrase
Single Stranded binding (ssb) protein
DNA primase
DNA polymerase III
DNA Polymerase I
DNA Ligase
Helicase
Unwinds the DNA and breaks the hydrogen bond in the base to separate double-stranded DNA
DNA Gyrase
Reduces tension and strain during unwinding by relaxing the positive super coils
Single Stranded binding (ssb) protein
- Binds to the DNA strands to prevent strands from re-annealing
- Stops it from being digested by nuclease
- Gets dislodged when new complementary strands by DNA polymerase III
DNA primase
- Generates short RNA primer (10-15 nuceolides) on each template strand
- RNA primer provides an initiation point of DNA polymerase III to extend it
DNA polymerase III
- Free nucleotides align opposite their complementary base
- attaches to a 3’ of primer and covalently joins the free nucleotide together in a 5’ -> 3’ direction
-> leading strand - towards replication fork and synthesize continuously
-> logging strand - away from the replication fork & synthesize in parts
DNA polymerase 1
Lagging strand has multiple RNA primase and it removes them to replace with DNA nucleotides
DNA ligase
Joins Okazaki fragments to form continuous strands. Done by covalently joining sugar-phosphate backbone with a phosphodiester bond
Okazaki Fragments
DNA polymerase cannot initiate replication and can only add nucleotides to an existing strand
-> Add to 3’ end of a primer
-> uses energy released to form a phosphodiester bond
Lagging Strand (Okazaki fragments)
- moving away from the helicase meaning It returns to copy a new strand
- copied as short fragments
- Primers replaced with the DNA bases and joined together by a combination of DNA polymerase 1 & DNA ligase
What is the most widely used method for DNA sequencing
Dideoxynucelotides
lacks the 3’-hydroxyl group necessary for forming a phosphodiester bond which prevents elongation and terminates replication
Non-coding DNA
Satellite DNA - repeating sequencing of DNA
Telomeres - protect against deterioration during replication
Introns - Remove by RNA splicing prior to the formation fo MRNA
Non-coding RNA genes - RNA molecules not translated into protein
Gene regulatory sequences - involved in the process of transcription
Nucleosomes
Help to supercoil the DNA, resulting in a greatly compacted structure that gives more sufficient storage.
Protects from DNA damage
Organisation of Eukaryotic DNA
3 sections of genes
Promoter
Coding Sequence
Terminator
Promoter
- responsible for the initiation of transcription
- Binding site of RNA polymerase
Coding sequence
- After RNA binds to the promoter DNA strand will unwind and separate
- Region of DNA that is transcribed by RNA polymerase is the coding sequence
Terminator
Transcription will continue until it reaches the terminator sequence
anti-sense (template strand) VS sense
there are two polynucleotide strands, but only one is transcribed into DNA
anti-sense
- transcribed into RNA
- complementary to the RNA sequence and is the DNA version of the anticodon sequence
sense
- not transcribed into the RNA
- DNA version of RNA sequence (identical swap T & U)
transcription
DNA sequence is copied into a complementary RNA sequence by RNA polymerase
what does RNA polymerase do in transcription
binds the NTPs together which will release two phosphates
Free nucleotides in transcription
exist as nucleotide triphosphate (NTPs) and line up oppositely to complimentary pairs
In what direction does binding occur
5’ -> 3’ direction
Transcription Processes
- Initiation
- Elongation
- Termination
Initiation
RNA polymerase binds to the promoter causing the unwinding and separating DNA strands
Elongation
RNA polymerase moves along coding sequnce
Termination
RNA polymerase reaches the terminator. DNA rewinds
Messenger RNA (mRNA)
carry the genetic information needed to make proteins. They carry the information from the DNA in the nucleus of the cell to the cytoplasm where the proteins are made.
mRNA (capping)
addition of the methyl group to 5’ end
protect against degradation
allows transcript to be recognized by the cells translation material
mRNA (polyadenylation)
Addition for a long chain of adenine nucleotides
Improved stability of RNA transcript
mRNA (spicing)
non coding sequence called introns - removed before forming mature RNA
coding sequence called exons - fused together when introns removed
alternative splicing
exons also removed causing different polypeptides from a single genetic sequence
Gene Expression
the process by which the information encoded in a gene is turned into a function
includes
- Transcription factor
- Regulatory Protein
Transcription factor
- Form complex with RNA polymerase at the promoter
- Cannot be initiated without these factors so their levels regulate gene expression
Regulatory Protein
Binds to DNA sequences outside of promoter and interacts with transcription factors
Activator Protein - Bind to enhancer sites and increases rate of transcription
Repressor protein - binds to silencer sequence and decreases the rate of transcription
Control element
DNA sequence that the regulatory protein binds to
Regulatory protein - binds to distal control
Transcription factor - binds to proximal
Epigenetics
study in change in phenotype as a result of variation
ribosomes
consist of a large subunit
large subunit - contains mRNA binding site
small subunit - contains three tRNA binding sites (E, P, A)
Translation (tRNA)
folds into a cloverleaf structure with four key regions
- acceptor stem carries an amino acid
- anticodon associates with mRNA codon
- T arm associated with ribosomes
- D arm associates with the tRNA activating enzyme. (add amino acid to acceptor stem)
Binding in the tRNA
an amino acid binds to a specific amino acid
- Enzyme binds ATP to amino acid to form amino acid AMP complex
- Amino Acid is now coupled to tRNA and AMP is released. This means tRNA can now be used
tRNA how it works
- tRNA activating enzyme
- Enzyme binds to ATP and a specific amino acid
- Amino acid ATP complex is formed and a specific tRNA molecule is recruited
- the tRNA is bound to the amino acid and AMP is released
- Charged tRNA is introduced
Translation steps
- Initiation
- Elongation
- Translocation
- Termination
Initiation
assembly of three components that carry out the process
- Ribosomes subunit binds to the 5’-end of the mRNA and moves along it until it reaches the start codon
then : tRNA bind to the codon via its anticodon
then : large ribosomal subunit aligns itself to the tRNA molecule at the p site and forms a complex with the small subunit
Elongation
- second tRNA pains with next codon in the A site
- amino acid in P attaches to amino acid in A covalently
- tRNA in p site now has no amino acid but A site carries peptide chain
Translocation
- Ribosomes move along mRNA strand
- tRNA with no amino acid moves to E sire and is released while the molecule carrying peptide chain moves to p site
- another tRNA molecule attaches to next codon and is now occupied in A site
Termination
disassembly of the components and release of a polypeptide chain
continues until a stop codon is reached
- release factor signalling for translation to stop
- polypeptide is released and ribosome disassembles into 2 independent subunits
polysomes
is a group of ribosomes translating an mRNA sequence simultaneously
