DNA and Protein Synthesis

molecular structure of DNA

• double helix

• phosphate group

• deoxyribose (sugar)

• nitrogenous base sticking out to the side

DNA backbone structure

covalent bond between a phosphate group and deoxyribose

purines

• adenine (A)

• guanine (G)

• double ring structure

pyrimidines

• thymine (T)

• cytosine (C)

• single ring structure

rule of base pairing

• only C and G can form a triple hydrogen bond with each other

• only A and T can form a double hydrogen bond with each other

• amount of cytosine = thymine, amount of guanine = adenine

• double ringed base has to be attached to a single ringed base

antiparallelism

• strands run in opposite directions

• 5’ tail, 3’ tail

• problem: can only easily add onto the 5’ end

when does DNA replication occur?

S phase

DNA replication

• two original strands are used as a template for new DNA based on the rules of base pairing

• results in 2 identical molecules of DNA

conservative model

the two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix (comes back together)

semiconservative model

• the two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand

• actual model

• ½ original, ½ new strand

steps of DNA replication

• initiation: unwinding of DNA helix at the origin of replication

• elongation: new strands are synthesized by DNA polymerase from the template strands

• leading strand synthesis: continuous synthesis on the strand towards the replication fork

• lagging strand synthesis: discontinuous synthesis, producing Okazaki fragments away from the fork

• termination: complete synthesis and separation of the newly formed DNA strands.

DNA helicase

enzyme that breaks the hdrogen bonds between nucleotides and splits “unzips” the helix into 2 parts

lagging strand

• replicates discontinuously forming short Okazaki fragments

  • can’t add onto 5’ end

• runs 5’ to 3’ away from the fork

leading strand

• replicates continuously

• can easily add onto 5’ end

• runs 5’ to 3’ towards the fork

• smooth process because helicase moving in same direction (reading 5’ - 3)

primase

an enzyme that synthesizes a short RNA primer to provide a starting point for DNA synthesis during replication

DNA polymer I (DNA pol I)

enzyme responsible for removing RNA primers and filling in the gaps with DNA nucleotides, proofreading and correcting

DNA polymer III (DNA pol III)

enzyme responsible for synthesizing new DNA strands during replication, working in conjunction with the leading and lagging strands

topoisomerase

relieves the strain from winding up the DNA, makes it more flexible and easier to work with

single-strand binding protein

prevents the original strands from re-bonding

proofreading in prokaryotes

no proofreading mechanism allows for more variation due to higher mutation rates

mismatch repair

a cellular mechanism that detects and rectifies errors made during DNA replication, maintains accuracy of genetic information

nucleotide excision repair

• nuclease cuts out the damaged DNA strand at two points, damaged section is removed

  • DNA polymerase fills in the section with repair synthesis

telomere

• tiny caps on the end of DNA strands

• repeated DNA base sequence that is non-coding

• protect the coding DNA as every time the DNA is replicated it gets a little bit shorter

telomerase

• enzymes that prevents DNA from becoming shorter

• protect telomere

ligase

enzyme that joins DNA fragments by forming covalent bonds, sealing nicks and linking Okazaki fragments

protein synthesis - transcription

a segment of DNA is taken and a complementary mRNA is formed

protein synthesis - translation

codons are translated into a chain of amino acids (polypeptide)

protein synthesis - ribosome

• made up of a large and small subunit

• UTR helps mRNA bind to the small subunit

• P site (polypeptide) contains tRNA with developing polypeptide

• A site (arrival) is where the next tRNA will arrive and enter the ribosome

• E site (exit) is where tRNA sits right before it leaves during translation

building a polypeptide - initiation

• mRNA binds to small subunit

• start codon (AUG) signals amino acids and forms a hydrogen bond with codon

• utilizing energy from GTP, large ribosomal subunit sandwiches mRNA and small subunit

• E site empty, A site empty, P site with codon

building a phosphate - elongation

• assembly line of workers bring amino acids over one at a time

• translation has occurred a few times

• P site growing polypeptide chain

• tRNA carrying a new amino acid enters A site and bonds polypeptide chain to the new amino acid

building a polypeptide - termination

• tRNA that was in the P site is now in the A site, tRNA that was in the E site exits

• A site now empty and ready to accept another tRNA

• termination occurs from stop codons (UGA, UAA, UAG) that signal ribosomes to stop translating and for the polypeptide chain to be released

polyribosome

different ribosomes translate the same mRNA molecule to produce polypeptides at the same time, allows cells to produce a lot of a protein at once

ribosomes in the cytoplasm

• proteins will be used in the cell

• all ribosomes start in cytoplasm

ribosomes in the rough ER

• proteins will be secreted outside of the cell, be used in the cell membrane, or become a lysosome or peroxisome

• signal peptide signals the cell that the protein is needed outside of the cell, and should move over to the ER

• translocation complex opens up and as translation occurs the polypeptide starts to enter the lumen of the ER as its being made

silent mutation

• one base changes, but the amino acid coded for stays the same

• no change in amino acid sequence → no change In protein

missense mutation

changes a single amino acid

nonsense mutation

• amino acid coded for changes to premature stop codons instead of another amino acid

• causes polypeptides being much shorter than they should be

frameshift mutation

• base is inserted and all bases shift to the right

• can also occur when a base is deleted and all bases are shifted in opposite directions, as well as every amino acid that follows that interaction