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1

Water as the reference acid with a generic base, B:.

W t th f b ith i id HA

OH

H

BHOH

water as an acid,donates a proton

t

Hydroxide is the conjugate base of water

Acid / Base chemistry is crucial for living organisms (pH control and acid/base catalysis)

Chapter 2: Protein Structure and Function

Kb and pKb

B

Ka = Keq[H2O] =[H+][A: ]

[HA]Keq =

[H+][A: ][HA][H2O]

[H2O] 55.5 M

pK = -(log K) (by definition)

T = 300 Kassumptions

Water as the reference base with a generic acid HA.

AH OH

H

AH

water asa base,accepts a proton

Hydronium ion is the conjugate acid of waterCurved arrows emphasize electron movement.

l (K ) l [H+] l [A: ]

Ka and pKa

OH

H

1

pK (log K) (by definition)

G = 1.4 pKa 1 pKa (kcal/mole) G = 5.8 pKa 6 pKa (kj/mole)

R = 8.4 joule/(mol-K)R = 2.0 cal/(mol-K)

G = - 2.3RT logKa = 2.3RT (-log Ka) = 2.3RT (pKa)

G = (constant)(pKa)G = H - T S

G = free energyH bond energiesS probabilities (randomness)

Also true.

Keq = 10-G

2.3 RT

-log (Ka) = -log [H+] - log [A: ][HA]

pKa = pH - log [A: ][HA]

when [A: ] = [HA]pKa = pH

p(x) = -log (x)

YH Y

stronger acid & base

YH

Y

HB

PEweaker acid

HB Y+ -

weaker acid & base(more stable)

TS

HB

stronger base

G =endergonic

Weak acids (RCO2H, ROH, RSH, RNH3+, H3PO4, H2PO4-1, HPO4

-2, H2CO3, HCO3-1, etc.)

B

B

G = 1.4 pKa 1 pKa (kcal/mole)

G = 5.8 pKa 6 pKa (kj/mole)

HB A+ -

The equilibrium shifts towards the weaker conjugate acid and base (away from the stronger acid and base). Weaker is more stable (think "less reactive").

YH

POR = progress of reaction

Strong acids (HCl HBr HI H2SO4 HNO3 etc )

B

2

AH AHB

stronger acid & base

AH

A

stronger acid

weaker acid & base(more stable)

TS

HB

weaker base

G =

PE potential energy

POR = progress of reaction

exergonic

Strong acids (HCl, HBr, HI, H2SO4, HNO3, etc.)

BB

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NH3

O

HO

pKa=2.35

pKa=9.78

H H

NH3

O

HO

pKa=9.74

pKa=2.29

CH H

NH3

O

HO

pKa=9.87

pKa=2.35

H3C HH3C CH3

NH3

O

HO

pKa=9.74

pKa=2.33

CH2

CHH3C

CH

H

leucineL

valineVal

alanineAla

glycine = name Gly = 3 letter code

G 1 l d

Amino Acids with Nonpolar "R" groups (have two pKa's), All aa C chiral centers are S except cysteine (because of the sulfur)

NH3

O

HO

pKa=9.76

pKa=2.32

C HCH2

CH3

H3C

CH3 LeuL

isoleucineIleI

ValV

AlaA G = 1 letter code

pKa=2.16

pKa=9.18

H2N

O

HO

pKa=10.65

pKa=1.95

pKa=9.44

pKa=2.43

prolineProP

trytophanTrpW

phenylalaninePheF

NH3

O

HO

CH2

H

NH3

O

HO

CH2

H

NH

H

H

2S

3S

body pH 7.4

3

I

NH3

O

HO

pKa=9.74

pKa=2.33

CH2

CH2

SH

methionineMetM

PWF

H3C

CHH3N C

O

OH

R

Ka1

pKa1

CHH3N C

O

O

R

Ka2

pKa2

CHH2N C

O

O

R

Some amino acids have an additional pKa.

Our bodies need 20 amino acids to make our proteins (maybe 22 with some selenium variations).

NH3

O

HO

pKa=9.10

pKa=2.09

C H

NH3

O

HO

pKa=9.21

pKa=2.19

H2C HH3C OH

threonineTh

serineSer

pKa=2.1

pKa=8.84

asparagineAsn

NH3

O

HO

CH2

HO

Amino Acids with Polar "R" groups

OH

NH3

O

HO

pKa=10.25

pKa=2.19

H2C H

cysteineCys

SH

pK =8 33pKa13 pK 13

H

2S

3R

body pH 7.4

ThrT

SerS

pKa=9.13

pKa=2.17

glutamineGlnQ

AsnN

NH2

NH3

O

HO

CH2

CH2

H

O

H2N

CysC

pKa=2.20pKa=9.11

tyrosineTyr

NH3

O

HO

CH2

H

HO

pKa=10.13

pKa=8.33

NH3

O

HO

CH2

S

H

cystine = 2 x cysteine

SCH2

NH3

HHO

pKa 13 pKa13pKa15

pKa15

dimer

4

Qy

Ycystine = 2 x cysteinewith disulfide linkageO

pKa=2.1H3PO4 H2PO4

pKa=7.2HPO4

pKa=12.4PO4

-2 -3

pKa=6.4H2CO3 HCO3

pKa=10.3CO3

-2

Other relevant biological pKa values

phosphoric acid carbonic acid

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NH3

O

HO

pKa=2.19

H2C H

cysteine SH

pKa=1.99pKa=9.90 pKa=9.47

pKa=2.10NH3

O

HO

CH2

HO

NH3

O

HO

CH2C

HHO

Amino Acids with Charged "R" groups (have three pKa's)

pKa=4.07

pKa=9.18

pKa=2.16 NH3

O

HO

CH2C

HH2C

pKa=10.79

pKa=10.25body pH 7.4

yCysC

pKa=8.33

Nonessential AAsAlanineArginineAsparagineAspartic acidCysteineGlutamic acidGlutamineGlycineProline

Essential AAsHistidineIsoleucineLeucineLysineMethioninePhenylalanineThreonineTryptophanValine

glutamic acidGluE

asparatic acidAspD

OH

H2O

pKa=3.90 lysineLysK

CH2CH2H3N

pKa=8.99pKa=1.82

NH3

O

HO

CH2CH

HH2C

pKa=12.48pKa=1.80

pKa=9.33

NH3

O

HO

CH2

H

H

H2N

5

SerineTyrosineSelenocysteineOrnithine

arginineArgR

H2NH

H2N

histidineHisH

pKa=6.04N

NH

H

All amino acids are "S" absolute conf iguration at the C position, except cysteine (because the sulfur atom changes the order of

priorities). Isoleucine (3S) and theonine (3R) have a second chiral center. These are the starting points for our body's proteins. Their

pKa's can change in an actual protein invironment due to nearby hydrophobic, hydrophilic and/or ionic groups.

pH = pKa+ log

Henderson-Hasselbach Equationextracellular blood pH 7.4

intracellular 6.8stomach 1.5 - 3.5

small intestines 8.5What do the amino acids look like?

[A ][HA]

CR

O

OHC

R

O

O

NH3R

NH2R

1100

pH = 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

pKa = pH when [HA] = [A: ]

pKa2 pKa9.4

[A ][HA]

7.4 = 2 + log [A ][HA]

[A ][HA]

= (7.4 - 2) = 5.4log

= 105.4 = 2.5x105 = 250,000 / 1

7.4 = 9.4 + log

= (7.4 - 9.4) = -2.0log

= 10-2.0 = 1 / 100

[A][HA+]

[A][HA+]

[A][HA+]

250,0001

CR

O

OHC

R

O

O2 5001

asparatic acid

pKa4

pK =10 79lysine

NH3R

NH2R

12,500

Typical aa carboxylicacid ionization constant

Typical aa ammoniumacid ionization constant

pKa10.8

6

[A ][HA]

7.4 = 4 + log [A ][HA]

[A ][HA]

= (7.4 - 4) = 3.4log

= 103.4 = 2.5x103 = 2,500 / 1

2,5001andglutamic acid(second pKa)

pKa 10.79(third pKa) 7.4 = 10.8 + log

= (7.4 - 10.8) = -3.4log

= 10-3.4 = 1 / 2,500

[A][HA+]

[A][HA+]

[A][HA+]

H3PO4 H2PO4

pKa=7.2

HPO4

pKa=12.4

PO4-2 -3

pKa2.1

H2PO4 HPO4-2

1.61.0ratio =1 200,000 1100,000

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pKa = pH when [HA] = [A: ]

histidineHisH

R

NH

pKa6 R

N K 12 48

R

NH

H2N

H2N

arginine7.4 = 12.5 + log [A]

[HA+][A]

1126,000

R

NH

HN

H2N

pH = pKa+ log

Henderson-Hasselbach Equation

extracellular blood pH 7.4 intracellular 6.8

stomach 1.5 - 3.5small intestines 8.5

What do the amino acids look like?[A ][HA]

pH = 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

pKa12.5

Important acid/base catalystand binds with metals

pKa=6.04(second pKa)

N

NH

N

NH

[A ][HA]

7.4 = 6 + log

[A ][HA]

= (7.4 - 6) = 1.4log

= 101.4 = 2.5x101 = 25 / 1

pKa=12.48(third pKa)

= (7.4 - 12.5) = -5.1log

= 10-5.1 = 1 / 126,000

[A][HA+]

[A][HA+]

pKa=10.1(third pKa)

tyrosine

7.4 = 10.1 + log

= (7.4 - 10.1) = -2.7log

= 10-2.7 = 1 / 500

[A][HA+]

[A][HA+]

[A][HA+]

1500

OH O

[A][HA+]

1 25

Any amino acid pKa value can be shifted, left or right by its enzyme environment. More hydrophobic regions will favor the neutral forms (RCO2H, RNH2). A nearby opposite charge will favor the ionic form (nearby

pKa10.1

R R

7

pKa=6.4

H2CO3 HCO3

pKa=10.3

CO3-2

HCO3

RSH

RS

7.4 = 8.3 + log

= (7.4 - 8.3) = -0.9log

= 10-0.9 = 1 / 8

[A][HA+]

[A][HA+]

8 1R

OH

RO

7.4 = 13 + log

= (7.4 - 13) = -5.6log

= 10-5.6 = 1 / 340,000

[A][HA+]

[A][HA+]

340,000 1

pKa=8.33(second pKa)

cysteine

pKa13(third pKa)

serinethreonine

[A ][HA]

[A ][HA]

charge will favor the ionic form (nearbypositive favors negative and vice versa). An open environment that allows access to water is similar to the reference aqueous values (obtained in water). It is therefore hard to determine the form of a functional group (ionic or neutral) in a particular region of a protein without knowing something about its structure.

pKa8 pKa13

101 1800

pH = pKa+ log

Henderson-Hasselbach Equation extracellular blood pH 7.4 intracellular 6.8

stomach 1.5 - 3.5small intestines 8.5

What do the amino acids look like?

[A ][HA]

NH3 NH2

pH = 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14

C

O

C

Oasparatic acidand

pKa4 Typical aa ammoniumacid ionization constant

pKa = pH when [HA] = [A: ]

pKa9.4

3R

NH2R

1100

CR OH

CR O

2,5001

glutamic acid(second pKa)

pKa5ratio = 250/1

pKa6ratio = 25/1

pKa8.4ratio = 1/10

pKa7.4ratio = 1/1

pKa10.4ratio = 1/1,000

pKa11.4ratio = 1/10,000

pKa9.4ratio = 1/100

pKa5ratio = 2500/1

If Ka gets smaller: 10-2 10-4

pKa gets ??? larger 2 4

O O O

8

pKa4.9 pKa12.8

pKa25.7

pKa12.3

pKa29.8

pKa17.6

pKa210.7Compare to reference, pKa getsa. Higher b. Lower c. No change

CH2

H C

O

OH

reference = pKa4.7

CH2

R C

O

OH CH2

C C

O

OH CH2

H3N C

O

OH

O

HOCH2

H3NH2C

NH3

CH2N NH2

HNR

pKa12.8

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What happens to the pKa when...

There is nearby negative charge?

CR

O

OC

R

O

O

pKa?a. pKa is higherb. pKa is similarc. pKa is lower

H

There is a hydrophobic pocket?

CR

O

O

pKa? a. pKa is higherb. pKa is similarc. pKa is lower

CR

O

OH

R H

R H

R H

R H

R H R H

R H

R H

R H

R H

There is nearby positive charge?

9

There is nearby positive charge?

CR

O

O

pKa?a. pKa is higherb. pKa is similarc. pKa is lower

CR

O

OH

What happens to the pKa when...

There is nearby negative charge?

a. pKa is higherb. pKa is similarc. pKa is lower

pKa?

NH3R

NH2R

There is a hydrophobic pocket?

a. pKa is higherb. pKa is similarc. pKa is lower

pKa?

R H

R H

R H

R H

R H R H

R H

R H

R H

R H

NH3R

NH2R

There is nearby positive charge?

10

pKa?

a. pKa is higherb. pKa is similarc. pKa is lower

NH3R

NH2R

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C

O

N

H

RC

NC

H

O

R

H R

C

O

N

H

RC

NC

H

O

R

H Rresonance

Because of resonance of the nitrogen lone pair with the C=O the amide bonds are planar. This is called the peptide bond. S = single bond conformation (trans or cis)

R C

O

N R

R C

O

N R

resonance

HO H

C

O

N

H

CC

NC

H

O

C

H R

S trans conformation is favored 1000/1 over S cis.

C

O

N

C

HC

NC

H

O

C

H R

S cis

RH

C

N

R H

R

H

R H

NR

H

R

N

H

R

H O

N R

steric crowding

1 000 to 1

H H

11

C

H R

flatC

R H

flat flatC

H R

flat

C

R H

flat

H

The flat shape of the amide bond limits possible conformations of proteins.

1,000.............................................to......................................................1

Cα-Cα distance when trans is 3.8 A and when cis 2.9 A (more crowded).

180o

Ramachandran Plot

C HO

N

R

H

= xo

CONHR

H

HROC

N

0o

-180o

= alpha helix

= beta pleated sheets

NH

C

C O

C

R

N

R

H H

R

= 180o

= yo

x

RHN

R

H

NRHO

= xo

R = yo

12

180o0o-180o

Original outlines in f (phi) and y (psi) space proposed by G.N. Ramachandran in 1963. Solid lines enclose region allowed by hard-sphere bumps at standard radii; dashed lines show region allowed with reduced radii; dotted lines add region allowed when the tau angle (N-Calpha-C) is relaxed slightly.

R

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OHNR

S trans favored over S cis 3/1 in proline(also depends on tensions in the protein chain)

Proline is unusual in that both trans and cis conformations are possible. It is referred to as a disrupter of normal protein patterns ( helices and pleated sheets).

C

O

NCN

C

C

O

H

HC

O

NCN

C

OC

H

H

H

RNH

H

S transS cis

3 1

Normally, this is an H

13

R3

N

R2

C

OR1

R2

N

R3

C

OR1

crowded alsocrowded

Normally, R2 is an H

Proteins are polymers. Less than 40 amino acids are considered peptides. Their specific spatial conformations are controlled by ionic interactions, hydrogen bonding, dispersion forces and disulfide linkages. The most common ways to determine their 3D structure are X-ray crystallography and NMR spectroscopy. The amino end is referred to as the N-terminus and the carboxyl end is referred to as the C-terminus. Counting residues always starts at the N-terminus (-NH3

+) and finishes at the C-terminus (-CO2--). The primary structure of a protein is determined

by the gene sequence in DNA, as transcribed to the RNA, as tranlated into the protein (with the possibility of post translational modifications, which cannot be determined from the DNA

C

O

NC

CN

C

H

CN

H3C H H2C H

N

Primary protein structure = the linear order of amino acids.

C

O

NC

CN

C

H

C

C

R H H2C H

N

OH SHalanine

serine cysteine

possibility of post translational modifications, which cannot be determined from the DNA sequence).

H3N C

O

O

N-terminus(#1)

C-terminus(#n)

14

HO H CH2H H HO H CH2 H

HOphenylalanine tyrosine

Possible variety = (20)n

n=1 (20 choices)n=2 (400 choices)n=3 (8,000 choices)n=4 (160,000 choices)n=100 (20100 choices)

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Secondary structure refers to highly regular local sub‐structures on the actual polypeptide backbone chain. Two main types of secondary structure, are alpha helices and beta pleated sheets. In 1951 Linus Pauling suggested both alpha helices and beta sheets as a way of maximizing all the hydrogen bond donors and acceptors in the peptide backbone. 

15

β‐pleated sheets can be parallel or anti‐parallel.

16

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#1#n #1 #n

C

O

O

NH3C

O

O

H3N

17

#1#1 #n #n

C

O

O

H3NC

O

O

H3N

Tertiary Structure

Tertiary structure refers to the three‐dimensional structure of monomeric and multimeric protein molecules. The alpha‐helices and beta pleated‐sheets are folded into a compact globular structures The folding is

-pleated sheets

globular structures. The folding is partly driven by the non‐specific hydrophobic interactions, the burial of hydrophobic residues from water, but the structure is stable only when the parts of a protein domain are locked into place by specific tertiary interactions, such as salt bridges, hydrogen bonds, and the tight 

-heliz

18

packing of side chains and disulfide bonds. The disulfide bonds are extremely rare in cytosolic proteins, since the cytosol (intracellular fluid) is generally a reducing environment. NADH can reduce the disulfide bond to 2 thiols.

random strands

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Quaternary structure refers to the three‐dimensional structure of a multi‐subunit protein and how the subunits fit together. The quaternary structure is stabilized by the same non‐covalent interactions and disulfide bonds as the tertiary structure. Complexes of two or more polypeptides are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, a tetramer if it contains four subunits, etc. The subunits are frequently related to one another by symmetry operations, such as a 2‐fold axis in a dimer. Multimers made up of identical subunits are referred to with a prefix of "homo‐" (e.g. a homotetramer) and those made up of different subunits are referred to with a prefix of "hetero‐", for example, a heterotetramer, such as the two alpha and two beta chains of hemoglobinthe two alpha and two beta chains of hemoglobin.

19

N

H

H

H hydrogenbond

H2C

CH2arginine

NNH

H

O

H

hydrogenbond

threoninehistidine

Forces of interaction (strength)1. covalent (disulfides)2. ionic3. hydrogen bonds4. dispersion forces4. pi stacking (similar)

H

OH

H

H

OH

H

OH

H

O

H

Protein

CH

CH3

CH3

CH3

HC

CH3

H2C

CH3

H2C

CH

H3C

CH3

dispersionforces

leucine

isoleucine

alanine

valine

phenylalanine

S

Scysteine

cysteine

CH2

H2C

SH3C

methionine

dispersion

dispersionforces

CH

H3C

H3C

CH3

dispersionforces

alanine

valine

N

H

H

Hi i

OH

OP

O

O

O

phosphorylatedserine

H2CN

H

CN N

H H

HH

arginine

ionicbond

polar forces are morecommon on the outside

H

O

H

H

O

H

H

OH

tyrosine

lysine

ammoniumions

20

pi stacking

phenylalanine

phenylalanine

HN

pforces

tryptophan

CO

O

ionicbond

common on the outsidewhere they can interactwith water (hydrophilic)

nonpolar forces are more common on theinside where they can avoid water(hydrophobic)

H

OH

H

OH

carboxylateions

NH

C

H2NNH2

arginine H

OH

H

OH

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11

One possible way disulfide bonds can form involves cytochrome P-450s and oxygen, (previous topic). There are other possibilities too.

H

SR

sulfursubstrate

(1e-)

H

SR

sulfursubstrate

S

HR

O

sulfoxidesFe +4

O

Fe +4

OFe +3

(nitrogen too)cytochromeP-450

BH

S

HR

OH

RS

HBsulfoxides

SR

OH

B

B H

B H

B O

H H

S

S

R

R

water

disulfides

S

HR

O

A second way to make disulfide bonds uses lipoamide.

21

H

SR

S

SR

B

BH

S

SR

H

S

RH

SR

B

BH

S

SR

H

S

R

HS

R

lipoamide

disulfidessulfoxides

thiol

FADFADH2

The hormone, oxytocin, is released by the pituitary gland, located in the hypothalamus. The functions f i i l d l b di ilk

Vasopressin has two primary functions in the body: to retain water and to constrict blood vessels.  It is synthesized in the hypothalamus and stored in vesicles at the posterior pituitary, where it is released into the bloodstream.  It is thought to have an important role in social behavior and has a very short half‐life between 16–24 minutes.

of oxytocin include maternal bonding, milk production, uterine contractions during labor, sexual pleasure, reduced fear, and love.

22

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Insulin has 3 disulfide bonds (lots of post translational modification)

23

GLUT4 containing vesicles fuse to the membrane to allow glucose into the cell.

Diabetes mellitus (DM), commonly referred to as diabetes, is a group of metabolic diseases in which there are high blood sugar levels over a prolonged period. Symptoms of high blood sugar include frequent urination, increased thirst, and increased hunger. If left untreated, diabetes can cause many complications. Acute complications include diabetic ketoacidosis and nonketotic hyperosmolar coma. Serious long-term complications include cardiovascular disease, stroke, chronic kidney failure, foot ulcers, and damage to the eyes.

Diabetes is due to either the pancreas not producing enough insulin or the cells of the body not responding properly to the insulin produced. There are three main types of diabetes mellitus:

Type 1 DM results from the pancreas's failure to produce enough insulin. This form was previously referred to as "insulin-dependent diabetes mellitus" or "juvenile diabetes". The cause is unknown.

Type 2 DM begins with insulin resistance, a condition in which cells fail to respond to insulin properly. As the disease progresses a lack of insulin may also develop. This form was previously referred to as "non insulin-dependent diabetes mellitus" or "adult-onset diabetes". The primary cause is excessive body weight and not enough exercise.

Gestational diabetes, is the third main form and occurs when pregnant women without a previous history of diabetes develop high blood-sugar levels. It increases the risk of pre-eclampsia (high

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y p g g p p ( gblood pressure, protein in urine), depression, and requiring a Caesarean section. Prevention is by maintaining a healthy weight and exercising before pregnancy. Gestational diabetes is a treated with a diabetic diet, exercise, and possibly insulin injections. Most women are able to manage their blood sugar with a diet and exercise. Breastfeeding is recommended as soon as possible after birth.

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Prevention and treatment involve a healthy diet, physical exercise, maintaining a normal body weight, and avoiding use of tobacco. Control of blood pressure and maintaining proper foot care are important for people with the disease.

Type 1 DM must be managed with insulin injections. Type 2 DM may be treated with medications with or without insulin Insulin and some oral medications can cause low blood

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medications with or without insulin. Insulin and some oral medications can cause low blood sugar. Weight loss surgery in those with obesity is sometimes an effective measure in those with type 2 DM. Gestational diabetes usually resolves after the birth of the baby.

As of 2015, an estimated 415 million people have diabetes worldwide, with type 2 DM making up about 90% of the cases. This represents 8.3% of the adult population, with equal rates in both women and men. From 2012 to 2015, diabetes is estimated to have resulted in 1.5 to 5.0 million deaths each year. Diabetes at least doubles a person's risk of death. The number of people with diabetes is expected to rise to 592 million by 2035. The global economic cost of diabetes in 2014 was estimated to be $612 billion USD. In the United States, diabetes cost $245 billion in 2012

The amino‐acid sequence of a protein determines its native conformation and it folds spontaneously during or after biosynthesis.  The process also depends on the solvent (water or lipid bilayer), the concentration of salts, the pH, the temperature, the presence of cofactors and of molecular chaperones.

Minimizing the number of hydrophobic side‐chains exposed to water is an important driving force in protein folding (maximizing entropy of water).  Formation of intramolecular hydrogen bonds is another important contribution to protein stability, more so in a hydrophobic core than H‐bonds exposed to the aqueous environment.  

Chaperone assisted folding is often

Many, many, many decisions (interactions) lead to localized minima, which leads to an overall structure

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Chaperone‐assisted folding is often necessary in the crowded intracellular environment.

Aggregated misfolded proteins are associated with prion‐related illnesses such as mad cow disease, amyloid‐related illnesses such as Alzheimer's disease, Huntington's and Parkinson's disease. 

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Hydrophobic forces can be important in quaternary structures.

(on the outside)

Hydrophobic surface faces outside toward lipid bilayer, polar channel on the inside. Hydrophobic surface

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H2O OH2

OH2

OH2

OH2

H2O

H2O

H2OH2O

OH2

Hydrophobic surfaces face towards each other to minimize structuring water molecules.

hydroxylation

collagencollagen collagencollagen N

collagencollagen

Fe+3

Post translational modifications of proteins

N-acylation

protein N

H

H S

O

CoA

B

BH

protein N

H B

OB H

SH CoA

acetyl CoA

Not protonated at body pH when an amide.

N

H H

Fe

O

N

H

Fe

O

+4

H

+4

H OH

hydroxyproline 4% of amino acids in animal tissue.proline

Makes stronger interactions with neighbors via H bonds.

carboxylation

NN

O

H

O

O

proteinC

H

H

B

BH

proteinC

H

NN

O

HHO

O

More acidic when acitivated by 2 x C=O. B

BH

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OO O

Osimplified

biotinsimplified

biotin

phosphorylation - turns enzymes on and turns enzymes off.

protein O

H

B

P

O

O

O

O P

O

O

O P

O

O

O ATP

O P

O

O

O P

O

O

O ADP

O P

O

O

O

Mg+2

Mg+2 acyl-like substitution reaction

ADP = leaving groupproteinATP

Does the Mg+2 make ADP a better or poorer leaving group?Can turn on or turn off an enzyme.

serine, threonine or tyrosine

B H

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Enzymes as receptors and transporters Enzymes ‐ life’s catalystsReceptors ‐ life’s communication system  Structural Proteins – life’s  framework

Na+/K+ ATPase (sodium-potassium pump) is an enzyme found in the plasma membrane of all animal cells. The Na+/K+ ATPase enzyme is a solute pump that pumps sodium out of cells while pumping potassium into cells, both against their concentration gradients. (it uses energy from ATP).

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Structural proteins in cell division ‐Microtubules are crucial for cell division.

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O

OH

OHO O

O

OO

O

O

OH

NHO

H

O

Taxol

Paclitaxel is used to treat ovarian, breast, lung, pancreatic and other cancers. Paclitaxel stabilizes the microtubule polymer and stops it from disassembly, preventing cell division. Discovered in 1960s in bark of slow growing Yew tree (> 600 years to grow, 3-6 trees = 1 patient, not sustainable). Precursor later discovered in needles or ornamental Yew tree. Even later, genes were spliced into bacteria to synthesize precursor.

O

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Interphase: Cells may appear inactive during this stage, but they are quite the opposite. This is the longest period of theInterphase: Cells may appear inactive during this stage, but they are quite the opposite. This is the longest period of the complete cell cycle during which DNA replicates, the centrioles divide, and proteins are actively produced.

Prophase: During this first mitotic stage, the nucleolus fades and chromatin (replicated DNA and associated proteins) condenses into chromosomes. Each replicated chromosome comprises two chromatids, both with the same genetic information. Microtubules of the cytoskeleton, responsible for cell shape, motility and attachment to other cells during interphase, disassemble, and the building blocks of these microtubules are used to grow the mitotic spindle from the region of the centrosomes.

Prometaphase: In this stage the nuclear envelope breaks down so there is no longer a recognizable nucleus. Some mitotic spindle fibers elongate from the centrosomes and attach to kinetochores, protein bundles at the centromere region on the chromosomes where sister chromatids are joined. Other spindle fibers elongate but instead of attaching to chromosomes, overlap each other at the cell center.

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Metaphase: Tension applied by the spindle fibers aligns all chromosomes in one plane at the center of the cell.

Anaphase: Spindle fibers shorten, the kinetochores separate, and the chromatids (daughter chromosomes) are pulled apart and begin moving to the cell poles.

Telophase: The daughter chromosomes arrive at the poles and the spindle fibers that have pulled them apart disappear.

Cytokinesis: The spindle fibers not attached to chromosomes begin breaking down until only that portion of overlap is left. It is in this region that a contractile ring cleaves the cell into two daughter cells. Microtubules then reorganize into a new cytoskeleton for the return to interphase.