DNA replication and gene expression

for a molecule to serve as the genetic material, it must be able to

replicate; passing on to offspring

store information; stable, long lasting

express information; should be able to be converted into another usable form

allow variation by mutation; gives rise to new traits and characteristics

DNA possess all four of these characteristics

structure of DNA

made of deoxyribonucleotides: 5 carbon sugar (deoxyribose) + phosphate + nitrogenous base (A,T,G,C) —> nucleotide

phosphodiester covalent bonds form the sugar/phosphate backbone of each strand

double-helix: two strands are anti-parallel and complementary; held together by hydrogen bonds; A/T form 2 H-bonds and G/C form 3 H-bonds

what problem will arise if the two strands of DNA are parallel to each other

phosphates repel one another on 5’ end, no double strand

genes

a sequence of DNA that codes for a functional product; within each piece of DNA there are many

in eukaryotes, there are ___ between the __

introns (noncoding sequence); exons (coding sequence)

within the cells, DNA form a complex with protein —> chromosomes

archaea: a single circular chromosome packaged around histone proteins

eukarya: multiple linear chromosomes packaged around histone proteins

bacteria: a single circular chromosome packaged by histone-like proteins

genome

where all the genetic information of an organism constitutes

plasmids

DNA molecules that replicate independently of chromosome

not essential but beneficial

transposable elements

segment of DNA that can move from one site to another site on the same or a different DNA molecule; incorporate into other DNA molecules

central dogma

DNA—> RNA—> proteins

replication, transcription, translation

DNA replication

DNA is duplicated; semi-conservative process; each time the dsDNA is copied, each coy carries on strand of the original molecule and one newly-made strand

bacteria dna replication

initiation: begins at the origins of replication (oric) (only one); 245 bp. AT rich

DNAa protein binds to oriC; generate 1 replication bubble and 2 replication forks

DNAb ( a helices) is recruited with DNAc ( a helices loader); helices unwinds the dsDNA, replication is bidirectional

single-stranded DNA binding proteins recruited to help keep the DNA unwound

DNAG (a primase) is recruited to lay down initial RNA primers needed for DNA polymerases III to work

what is the purpose of the primers

provide free 3’OH

eukarya dna replication

eukaryal replication initiation: multiple origins of replication on each chromosome, chromosomes are much larger, so they need multiple starting points for replication; very similar to process in bacteria, just using different proteins; studied in yeast

bacteria dna replication

elongation: bidirectional

once the replication fork forms, DNA pol. III adds nucleotides to the initial RNA primers

a continuous leading strand and a discontinuous lagging strand (forming Okazaki fragments) are formed

this process is virtually identical in both bacteria and eukarya (with different proteins)

what is the direction of synthesis

5’ —> 3’

replisome

complex of multiple proteins involved in replication

ter sequences

locate on the opposite side of the oriC

tus proteins

bind to ter sequence to block the faster of the two replication forks

RNA

the produce of transcription

transcription

only one strand of DNA is transcribed by RNA polymerase for any gene

genes are present on both strands of DNA, but at different locations

RNA polymerase is the main enzyme that carries out RNA synthesis

RNA polymerase recognizes DNA sites called promoters

initiation and elongation

the basic process of transcription starts at a promoter

RNA polymerase separates the DNA and lays down a complementary strand of RNA

RNA pol reads the template strand of DNA

RNA is the same sequence as the coding strand of DNA

initiation and elongation of bacteria

sigma factor bound to RNA pol core enzyme direct the combined holoenzyme to a promoter

different sigma factors can direct core RNA pol. enzyme to different genes as needed

once RNA pol is situated, sigma factor dissociates —> transcription proceeds

initiation and elongation in eukarya

individual transcription factor proteins associate with promoter regions first

RNA pol. is then recruited to the transcription factor/DNA complex

this binding initiates the unwinding of the DNA and the start of the actual transcription process

more complex, depends on which type of RNA pol ( I, II, or III) is doing the transcription

RNA modified after transcription

• 5’cap added; allow ribosome to recognize the RNA

• polyA tail added; protect RNA from degradation

• introns spliced out, exons joined together by spliceosome (snRNA + proteins)

initiation and elongation in bacteria

rhodependent: a rhododendron protein follows RNA pol. and pops it off the DNA when it reaches a termination sequence (require ATP)

rhoindependent: the DNA sequence transcribed forms an RNA hairpin loop structure that causes the RNA pol. to dissociate from the DNA; happens spontaneously

translation

sythesis of proteins from mRNA

proteins are made up of amino acids (central carbon attached to a hydrogen atom, an amino group, a carboxyl group and an R group)

peptide bond connect the amino acids

genetic code

codon: a triplet of nucleic acid bases encodes a single amino acid

specific codons for starting and stopping translation:

• start codon: AUG

• stop codon: UAA, UAG, UGA

open reading frame

a strong of codons beginning with the start codon and ending right before the stop codon

degeneracy and redundancy of genetic code

20 amino acids; 64 acids possible codons, 61 code for amino acids

more than one codon may code for the same amino acid

one codon cannot code for more than one amino acid

key players: mRNA, t RNAs, and ribosomes

transfer RNA: at least one tRNA per amino acid; bring amino acid to ribosome

has anticodon sequence that temporarily base pairs with mRNA codon during translation

tRNA and amino acid brought together by animoacyl-tRNA synthestases ; ATP is required to attach amino acid to tRNA

incorrect amino acid could result in a faulty or nonfunctioning protein

ribosomes

site of protein synthesis

combination of rRNA and protein

thousands of ribosomes per cell

ribosomes subunits

30 S and 50 S for bacteria (70S)

ribosome initiation

two ribosomal subunits assemble with mRNA; begins at AUG

in bacteria, the ribosome recognizes the Shine-Dalgaro sequence that is localizes upstream of AUG

in eukaryotes, the ribosome recognizes the 5’ cap, searches for the Kodak sequence which contains the start codon

ribosome elongation

amino acids are brought to the ribosome by the tRNA and are added to the growing polypeptide

lengthen the chain of amino acids to build the protein

ribosome termination

occurs when ribosome reaches a stop codon

release factor recognize stop codon and cause complex to come apart

ribosome subunits dissociate

subunits free to form new initiation complex and repeat process

replication/transcription/translation in archaea

not well understood but shows some similarities to bacteria and eukarya

only one RNA polymerase but resembles a simplified version of eukaryotic transcription

are proteins fully active after translation

no, proteins must be folded, processed, and transported

folding

newly synthesizes proteins are available for folding and modification

the folding depend on a number of interactions between the amino acids in the primary structure

proteins must fold into their secondary structure (H-bonds) and tertiary structure (R group interactions)

some proteins require assembly of multiple subunits to form a quaternary structure

molecular chaperones

• proteins identified in all three domains of life

• they assist in correct folding/refoolding of polypeptide sequences

• originally referred to as heat shock proteins because they appear after exposure of cells to heat

processing

many proteins are further modified after initial translation ( in a process termed post-translational modification)

these modifications can include phosphorylation or glycosylation steps, modifying the final protein structure

transport

proteins that carefully formed and functional need other be directed to the proper location

the basic steps are the locating/transport process are similar in each domain

signal peptides (short amino acid sequences near the beginning of the protein) act as a zip code to direct the protein to the correct location

once the protein is properly located, the single peptide os often cleaves