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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?
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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
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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
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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
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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)
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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.
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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
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#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
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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.
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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
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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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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.
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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
24
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
25
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.