7. Nucleic Acids Flashcards
7.1 What is a nucleosome?
The structured unit of chromatin fiber
The fiber is wrapped around 8 histone protiens, the ends are linked to an additional H1 protien
Linker DNA connects to next nucleosome
7.1 Nucleosome preperation for nuclear division
To prepare for division, the coiled structure coils again to form a supercoiled chromosome
7.1 What is the order of strands during replication?
Leading strand: Synthesized 5’ to 3’
contineous
Lagging strand 3’ to 5’, in pieces
7.1 What does helicase do?
This enzyme breaks hydrogen bonds between bases and unwinds helix
7.1 What does gyrase do?
Relieves tension stress on DNA when unwinding
7.1 What are single strand binding protiens?
Prevent DNA strands reconnecting
7.1 What does primase do?
Synthesizes RNA primers required by lagging strand
7.1 What does DNA polymerase III do?
Builds complementary strand by adding nucleotides, moves 5’ to 3’
7.1 What does DNA polymerase I do?
Replaces RNA primers with nucleotides
7.1 What does ligase do?
Binds backbones of adjacent okazaki fragments, lagging strand
7.1 What are tandem repeats?
Do not code for protien but repeat over and over again
7.1 Function of tandem repeats
1) Telomere @ end of chromosome to protect
2) Regulates where, when and how protiens are made
3) Provides code to make RNA
4) Might be leftover from viral infections
5) “junk” DNA
7.1 What is VNTRS
Variable Number Tandem Repeat Sequences
number of repeats
Use: DNA profilling
7.1 What are dideoxynucleotides
Lack the ‘3 Hydroxyl group so they can’t form bond with next nucleotide
They also have a florecent marker on the base
7.1 Sanger sequencing
1) 4 PCR mixes are made that contain normal nucleotides (+ replication materials) and one type of dideoxynucluotide (ddA, ddT, ddC or ddG)
2) Within each mix, DNA polymerase III replicates stopping by change when it adds dideoxynucleotide (many strands of DNA with different lengths)
3) The replicated DNA is run through electrophoresis where the shorter pieces make it farther
7.1 What did the Hersey and Chase experiment prove?
Was DNA or protien the genetic material?
Vriuses with radioactive protiens (radiactive sulfur) and viruses with radioactive DNA (radiactive phosphorus) were tested as they infected bacteria
The bacteria and viruses were put into a centerifuge, the viruses beign later remained in supernatant while the bacteria formed a pellet
It was found that the supernatant was radiactive for protien, and the pellet radioactive for DNA
7.2 What is gene expression?
The appearebce in a phenotype attributed to a particular gene
7.2 Why is gene expression regulated?
- To save energy and space
- Response to changing environment
7.2 Types of sequences associated with gene regulation
Promoter-Proximal Sequences: any regulatory sequence in DNA
- Enhancers: DNA codes that increase gene expression
- Silencers: decrease
7.2 What is the role of histone tails?
Histone tails are typically positively charged so they wrap tightly around the negative DNA
7.2 Methylation of Histone Tails
A methyl group is added to the tail which maintains positive chrage, makes DNA more coiled, reduces transcription
Supercoild DNA = heterochromatin
7.2 Acetylation of histone tails
A acetyl group is added to tail which nuetralises charge making DNA less ciled, more transcription
Loosley packed = euchromatin
7.2 How do DNA methylation patterns change?
DNA (rather than histones) can alos be methylated
Nature: influenced by heritability, not genetically pre-determined. DIfferent cell types have different patterns
Nurture: Environmental factors, diet pathogen exposure, may influence level of DNA methylation
7.2 What is a gene?
A sequence of DNA which is transcribed into RNA
7.2 Parts of a gene
Promoter
non-coding sequence responible for intial transcription, binding site for RNA polymerase,
Coding sequence
Termiator:
Once RNA polymerase reaches sequence it stops
7.2 Steps of transcription
Initation: RNA polymerase bind to promoter, causing unwinding and seperation of DNA strands
Elongation: RNA polyerase moves along coding sequence moving in a 5’ to 3’
Termination: RNA polymerase reaches terminantor and enzyme and RNA strand detaches, DNA rewinds
7.2 Eukarotic Modifaction of mRNA
1) Capping: Addition of methyl group to 5’ end of RNA (provides protection and recognization for translation)
2) Polyadenylation: Long chain of adenine nucleotides (poly-A tail) to 3’ end (provides stability)
3) Splicing:
Introns (non-coding sequences) need to be removed, exons are fused together as introns are removed
Alternative splicing: removal of exons (provide different combination of protiens)
7.3 Structure of a ribosome
Ribosomes are made of two subunits
Small: mRNA binding side
Large: three tRNA binding sites EPA
(aminoacyl site) (peptidyl site) (exit site)
These are found free or binding to rER in eukaryotes
7.3 Structure of tRNA, (TADA!)
tRNA (transfer RNA) has four regens
Acceptor stem (3’ - CCA) carries amino acid
Anticodon associates with mRNA codon (via base pairing)
T arm associates with ribosome at binding sites
D arm associated with tRNA activating enzyme (adds amino acid to acceptor stem)
7.3 Steps of translation
1) Initiation:
- Small ribosomal subunit binds to 5’ end of mRNA, moves until start codon (AUG)
- tRNA molecule binds to codon via anticodon
- large subunit aligns with tRNA in P spot
Process:
2) Elongation:
-Second tRNA pairs to codon at A site
-A-acid in P attaches via covalent bond
- tRNA in P is no deacylated (no amino acid)
3) Translocation:
- Ribosome moves by one codon 5’ –> 3’
- deacylated tRNA moves to E site and is released, other tRNA moves to P site
- new tRNA attacges at A site
4) Termination
- once stop codon is reached, a release factor is recruited instead of tRNA molecule
- Polypeptide is released and ribosome disassembles
7.3 Free ribosomes vs bound ribosomes
Free ribosomes: protiens for primary use in cell
Bound ribosomes: syntehsize protiens for lysosomes or to be secreted
7.3 Primary structure of protiens
Linear polypeptide sequence
Bonds: peptide (carboxyl + amine) (OH + H)
7.3 Secondary structure of protiens
Alpha helix or beta-pleated sheet
Bonds: Hydrogen (between carboxyl and hydrogen) netween non-adjacent amino acids
7.3 Tetiary structure
How it coils and forms 3D shape
Bonds: Interaction between R-groups
- hydrogen bonds
- ionic
- Disulfide
- Hydrophobic interactions btwn non-polar groups
7.3 Quaternary structure of protiens
Multiple polypeptides
Bonds:
– hydrogen
- ionic
- Disulfide
- Hydrophobic interactions
Prosthetic Group: a non-protien molecule tightly bound to protien
7.3 tRNA activation
1) A specific synthetase is required for each amino acid
2) The enzyme binds ATP to the amino acid
3) ATP is hydrolysed and the amino acid is covently linked to AMP (1 phosphorus)
4) specific tRNA binds to active site
5) Amino acid is bond to tRNA and AMP is released
7.3 What is a polysome
A group of ribosomes that translate mRNA simultaneously
