Feb 13

Genetics, February 13, 2009
Genetics: Analysis of Genes and Genomes, Chapter 10 and 11. Protein folding; gene regulation 1
I. Codon redundancy and the “wobble hypothesis”
a. More than one codon per amino acid
b. “wobble hypothesis”: first two bases in codon binding with first two bases in anticodons making them the most important.
c. EF-1α/ EF-2 + GTP to bind to paired tRNAs, catalyze peptide bond formation
II. Polysomes/polyribosomes
a. In prokaryotes, transcription and translation are coupled processes
b. In bacteria, mRNA can begin translation while undergoing transcription
c. Polyribosome: a single mRNA being translated by more than one ribosome simultaneously
III. Protein folding
a. Protein structures
i. Primary: sequence of amino acids in protein
ii. Secondary: shapes of sub-parts within a protein
1. Alpha-helices: shape caused by H-bonds between adjacent amino acids
2. Beta-sheets: H-bonds formed between amino acids that are distant from each other on the chain
iii. Tertiary: how alpha-helices and beta-sheets interact with each other in a single polypeptide chain
iv. Quaternary: how separate folding polypeptide chains interact to form protein with multiple subunits
b. Factors (interactions) that influence folding:
i. Hydrogen bonds: H-bonds form between amino acids; cause alpha-helices or beta-sheets
ii. Covalent bonds: Some amino acids can covalently bind with each other
iii. Hydrophobic interactions: hydrophobic amino acid residues cluster on inside of protein, away from aqueous environment
*huge importance in determining shape of polypeptide chain*
c. Environmental conditions that influence folding
i. Temperature:
1. protein shape dependent on temperature correct protein combination at normal temperature for organisms
2. Can cool protein to lower temperature than normal; won’t affect shape
ii. Osmolarity
1. Concentration of water in aqueous environment influences folding
2. Ex: under high salt conditions, hydrophobic amino acids move toward outside of the protein; Compared to the protein’s shape in low salt/ high water
iii. pH
1. high and low pH both denature proteins like high temps do
a. ideal pH for cells =7.0
b. ideal ph for proteins = 7.0
d. chaperone proteins and chaperonions:
Most proteins spontaneously fold into correct conformations. But some large polypeptides and proteins with lots of hydrophobic amino acid residues need help chaperone proteins
i. Chaperones: hydrophobic amino acids in chaperone transiently bind hydrophobes amino acids in new polypeptide; then chaperone proteins use ATP  ADP to detach new polypeptide amino acids from chaperone refold into right shape
ii. Chaperonions: large, barrel-shaped chaperone proteins that take in large hydrophobic polypeptides and provide ideal environment for folding inside barrel
a. Lots of chaperonions associated with heat shock of cells

IV. Gene regulation checkpoints
a. Transcriptional regulation
i. Promoter sequences on DNA interaction with RNA polymerase
b. RNA processing
i. 5’ capping; splicing out introns
c. Translational control
i. Programmed ribosomal frameshifting
d. RNA degradation
i. RNAi- double- stranded RNAs match mRNA  that mRNA chewed up by enzymes
e. Post-translational control: modifications made to protein after translation
i. Ex: addition of carbohydrates
ii. Phosphorylation of proteins (Addition of phosphate)
f. DNA rearrangements: recombination of DNA segments prior to transcription

V. Gene regulation checkpoints
a. Transcriptional activators:
i. Proteins that bind to DNA activating transcription
ii. Common shapes:
1. Zinc fingers
2. Helix-turn-helix
3. Leucine zipper
iii. All transcriptional activators have + charge at least in the area that interacts with DNA
b. Transcriptional enhancers/ silencers.
i. Enhancers: Sequence of DNA bases that transcription-related proteins (transcriptional activators) bind to
1. Lots of variability is sequences
2. Are typically upstream of site for a particular gene start site, but can be downstream in introns… pretty much anywhere in close proximity of gene
ii. Silencers:
1. Sequences of DNA bases that proteins bind to prohibiting transcription from occurring
2. Are typically upstream of site but can be anywhere in close proximity
c. Basal transcription factors
Proteins required for the transcription of all genes.
i. TFIID : a complex of several polypeptides
1. TBP (TATA-box binding protein) subunits
2. TAFs (TBP- associated factors)
ii. TFIIA, TFIIB, TFIIE, TFIIF, TFIIH
iii. RNA polymerase: enzymes recruited by other factors to transcribe
d. Chromatin-remodeling
i. Chromatin: DNA wound around proteins
ii. DNA strand displacement from histones, other proteins its wound around
iii. done by chromatin-remodeling proteins
iv. uses ATP for energy
e. Epigenetic regulation/imprinting
i. Epigenetics: heritable change in regulation of gene expression
ii. Epigenetic changes can be explained by the differences in chromatin-remodeling
f. Methylation of certain genes also can explain epigenetic changes
i. Methylation of cytosine and guanine on genes that aren’t transcribed, “CpG” islands, c followed by g, lots of methylation of C on genes that aren’t transcribed
ii. Ex: x-inactivation in mammalian females

Here is a video that shows the different protein structures and how protein bind and fold to get there shape
http://www.youtube.com/watch?v=lijQ3a8yUYQ

I found this article interesting about epigenetic changes in monzygomatic twins
http://schizophreniabulletin.oxfordjournals.org/cgi/reprint/29/1/169

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