@Agathe-Zhu 2015-08-15T07:19:38.000000Z 字数 3671 阅读 2224

Secret of Life - Week 2 (Lecture 3-5)

MOOC Biology Course_note

Lecture 3. Protein and Protein Structure

1. Protein: Primary Structure

H2N-CH(R)-CO[OH H]2N-CH(R')-COO == H2N-CHR-CO-NH-CHR'-COOH
* NH2:Amino
* R: Side chain
* COO: Carboxyl
* CO-NH: Peptide bond

Double or more peptide bonds cannot Rotate freely(partial double bonds character)

2. Category of amino acides

20 amino acides into 3 groups

a. Polar, Uncharged

R	Name	Short for three	Short for one
-CH2OH	Serine	Ser	S
-CH(CH3)OH	Threonine	Thr	T
CHO-NH2	Asparagine	Asn	N
CH2-CHO-NH2	Glutamine	Glu	Q

b. Polar, (-)charged at pH 7

R	Name	Short for three	Short for one
CH2-COO	Aspartic acid	Asp	D
CH2-CH2-COO	Glutamic acid	Glu	E

c. Polar, (+)charged at pH 7

R	Name	Short for three	Short for one
(CH2)4-NH3	Lysine	Lys	K
(CH2)3-NH(NH2)+-NH2	Arginine	Arg	R
	Histidine	His	H

d. Hydrophobic

R	Name	Short for three	Short for one
-CH3	Alanine	Ala	A
-CH(CH3)2	Valine	Val	V
-CH2-CH2-S-CH3	Methionine	Met	M
CH2-CH(CH3)2	Leucine	Leu	L
CH(CH3)-CH2-CH3	Isoleucine	Ile	I
-CH2-Phenyl	Phenylalamine	Phe	F
-CH2-Phenyl-OH	Tyrosine	Tyr	Y
	Tryptophan	Trp	W

e. Special

R	Name	Short for three	Short for one
-H	Glycine	Gly	G
-CH2-SH	Cysteine	Cys	C
Ring	Proline	Pro	P

-S=S-: Disulfide bond

Problem of protein folding:
1. Varied possiblities of amino acid composition
2. Proteins changes according to environment (not physically/chemically perfect)

3. Proteins' Secondary structure

The proteins' secondary structure was found by neglecting the side chains by Linus Paulin.

Alpha Helix: 3.7 amino acids per turn
Beta Sheets
Loops

Alpha helix and Beta sheets are stablized by hydrogen bonds between C=O and N-H of the polypeptide.

4. Proteins' Tertiary and Quarternary structure

Tertiary structure: Alpha helix and Beta sheets combine together

Quaternary structure: Different proteins combine together by certain bonds like hydrogen bonds formed by Cystein (S=S)

Lecture 4. Enzymes and other amazing machines

1. Design a Protein

Object	Solution	Explanation
Situated in the outer membrane of bacteria	Beta Barrel	Non-polar parts inside to get contact with phospholipid tails
Make through 600-unit Molecules	Hole
Make through non-charged molecules	(+)&(-) charged amino acides	Get away charged molecules

2. Enzyme: Triose Phosphate Isomerase (TIM)

Reactant		Intermediate		Product
Glyceraldehyde-3-Phosphate		Cis-enediol		Dihydroxylacetone phosphate
G3P				DHAP
CHO-CHOH-CH2-PO3^2-	=>	COH=CO-CH2-PO3^2-	=>	CH2OH-CO-CH2-PO3^2-
High free energy		Extremely high		Low

So enzyme helps getting through the energy obstacle from G3P to cis-enediol by changing activation barrier.

Target of TIM:
1. Stablize the trasition step
- His95 (+ charged) give one H⁺ to oxygen in the end and grab another H⁺ from hydroxy
- Glu165 (- charged) grab H from the second Carbon
2. Prevent losing the phosphate
- Hydrogen bonds stablize the phosphate in the end by loop

Limitation: Diffusion of substrate => catalyse effeciently => Perfect

Lecture 5. Biochemical Pathways

1. Energetic reaction

Reaction depends on:
1. Free energy $\Delta$ G₀^'
2. Concentration of composition

For reaction A --> B:
$\Delta G = \Delta G_0^{'} + RTln\frac{[A]}{[B]}$

R: Constant which depends on temperature
T: Temperature in Kelvin

if:
$\Delta$ G < 0, reaction runs forward/favorable
$\Delta$ G > 0, reaction runs backward/unfavorable

2. Logical tricks of pathways

If A --> B is unfavorable, there may be two tricks:
1. Direct coupled reactions, ex: coupled to th ehydrolysis of ATP (ATP --> ADP, $\Delta$ G << 0)
2. Indirect coupled reaction, ex: A--> B --> C

3. Glycolysis

Glycolysis

4. Reaction Regulation

Feedback inhibition, ex: product combines with enzyme witch activates precedent reactions(Allosteric regulation)
Feddforward activation, ex: substrate combines with activate enzymes