Bio 2- Chapter 3

binding of 2 complimentary DNA strands

separation of 2 complimentary DNA strands

1 circular chromosome; 10^6 bp
twist 2 sides of the circle around each other, creating supercoils

Humans: 46 chromosomes- 23 from each parent; 10^9bp

wrap DNA around histone proteins

nucleosome: DNA wrapped around 8 histones
chromatin: fully packed DNA

DNA--transcription--> RNA --translation--> protein

1. info in DNA is copied into mRNA in nucleus
2. mRNA travels to cytoplasm & encounters ribosome
3. ribosome synthesizes polypeptides

codon= 3 nucleotides
4^3= 64 possible codons

AUG=methionine

UAG, UAA, UGA= nonsense codons

more than 1 codon will code for same amino acid

mistakes in replication of genome during cell division

chance chemical malformations

environmental agents

1. point mutation
2. insertion mutation
3. deletion mutation

1. transitions: substitution of pyrimidine by another pyrimidine or a purine by another purine

2. transversions: substitution of pyrimidine for purine or vice versa

*missense: 1 amino acid replace by another
*nonsense: stop codon replaces regular codon causing truncated protein
*silent: 1 codon changes to another, but results in same amino acid

addition of 1 or more extra nucleotides to DNA sequence

can cause frame shift mutation

removal of nucleotides from DNA sequence

can cause frame shift mutation

duplication of DNA
occurs during S (Synthesis) phase in interphase of cell cycle

elongation occurs in the 5' to 3' direction

coupled reaction of removing/hydrolyzing pyrophosphate (P2O7^-4) from each bp added to the chain

enzyme that drives DNA replication
can't start replication though. needs a primer/template

begins DNA replication and DNA pol elongates chain

enzyme that uses ATP to unwind and separate DNA strands
begins unwinding @ origin of replication

enzymes that cut 1 or both strands and unwrap the helix to release excess tension

strand that elongates continuously

strand that elongates in fragments--> okazaki fragments

all RNA primers are replaced by DNA and the fragments are joined by this enzyme

theta replication
3 DNA polymerases
1. DNA pol 3: fast and accurate elongation of leading strand. proof reads and corrects mistakes
2. DNA pol II: unknown
3. DNA pol I: same as III, but slower. main job is proofreading and repair w/ 3'-5' exonuclease activity

RNA pol I--> rRNA
RNA pol II--> mRNA
RNA pol III--> tRNA

Remember: I, II, III = r, m, t

carries genetic info from nucleus to cytoplasm

monocistronic- 1 strand makes 1 protein; eukaryotes

polycistronic- 1 strand makes many proteins; prokaryotes

provide catalytic function of the ribosome

translates genetic code

carries amino acids from cytoplasm to ribosome to be added to growing polypeptide

principle site of regulation of gene expression
involves template-driven polymerization, so RNA is complementary (no primer required)
driven by removal/hydrolysis of pyrophosphate from added nucleotides
no proofreading
begins @ start site

sequence on chromosome that activates RNA pol

same sequence as transcript

complementary to transcript

all types of RNA are made by the same RNA polymerase

sigma factor in RNA pol increases RNA pol's ability to recognize promoters and decreases its affinity for DNA.

2 primary sequences in every bacterial promoter:
1. Pribnow box @ -10 (TATA)
2. -35 sequence

anabolic enzymes
default is on

catabolic enzymes
default is off

1. DNA encoding a piece of mRNA that codes for 3 enzymes needed for lactose catabolism
enzymes; z, y, and A

2. there are 2 regulatory sequences:
1. Promoter (p)
2. operator (o)

process:
repressor protein sits on operator and prevents RNA pol from binding to promoter and transcribing z, y, and A genes. When lactose is present, it binds to repressor, changing it so that it can no longer bind to operator. Transcription of z, y, and A proceeds. mRNA is transcribed to the 3 enzymes that catabolize lactose

prokaryotes: free in the cytosol, so transcription & translation occur @ the same time

eukaryotes: transcribed and modified in the nucleus, then transported across nuclear membrane for translation in cytosol. NOT simultaneous

proks: mRNA is ready to be translated. no proofreading

euks: mRNA is modified extensively before translation
splicing-- removing introns and joining exons
*introns: intervening sequences
*exons: protein coding regions

5' cap-- methylated guanine, essential for translation

3' poly-A tail-- prevents digestion of mRNA by exonucleases

produced by RNA pol III

stem and loop structure stabilized by H bonds b/w bases on neighboring segments of RNA chain.

dihydrouridine

specific base pairing b/w mRNA codon and tRNA anticodon. amino acid is attached to tRNA @ amino acid receptor site.

amino acid attachment is accomplished through reaction coupling of breaking the amino acetyl-tRNA bong that provides the energy needed to form peptide bond in tRNA loading.

amino acetyl-tRNA synthetase enzyme specific to each amino acid ensures that the right amino acid is loaded.

larger proteins

1. A-site: amino acetyl-tRNA site
where each new tRNA delivers its amino acid

2. P-site: peptidyl-tRNA site
growing polypeptide chains location during translation

3. E-site: exit-tRNA site
where empty tRNA sits before release from ribosome

prokaryotes: 70s ribosome --> 50s + 30s
eukaryotes: 80s ribosome --> 60s + 40s

while mRNA is being made, ribosomes bind to Shine-Delgarno (-10 bp) sequence and being translation

initiatied by formation of 70s initiation complex--> powered by GTP hydrolysis

initiated tRNA: fMet-tRNA

termination occurs when stop codon appears in A-site and a release factor enters the A-site after.

tRNA loading: 2 ATP per 1 anticodon

initiation: 1ATP

A-site binding: 1ATP per amino acid (not counting starting amino acid)

translocation: 1 ATP per amino acid = A-site binding

50 amino acid example:
tRNA loading= 2ATP x 50aa= 100ATP
initiation= 1ATP
A-site binding= 1ATP x 49aa= 49ATP
Translocation= 1ATP x 49aa= 49ATP

Total: 100+1+49+49= 199ATP

1. triglyceride--> most common. stored in adypocytes (fat cells).
structure: glycerole backbone w/ 3 fatty acid chains

2. phospholipids: amphipathic (polar & nonpolar)
structure: glycerol backbone= 1 phosphate group (hydrophobic- nonpolar) & 2 fatty acid chains (hydrophillic- polar)

3. cholesterol: no efficiently used in the body. functions in the cell membrane, as a precursor to bile, and a precursor for steroids

Arginine: arg-- basic
Asparagine: asp-- acidic
Cysteine: cys-- neutral
Glutamic acid: glu-- A
Glutamine: gln-- N
Histidine: his-- B
Lysine: lys-- B
Serine: ser-- N
Threonine: thr-- N
Tryptophan: trp-- N
Tyrosine: tyr-- N

Alanine: ala -- neutral
Glycine: gly-- N
Isoleucine: ile-- N
Methionine: met-- N
Leucine: leu-- N
Phenyl alanine: phe-- N
Proline: pro-- N
Valine: val-- N