1. 2 Ester (functional group, acid + alcohol) Handout 2-9 top A trigyceride (fat)
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Transcript of 1. 2 Ester (functional group, acid + alcohol) Handout 2-9 top A trigyceride (fat)
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Ester (functional group, acid + alcohol)}
Handout 2-9 top A trigyceride (fat)
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cis
C C| |
HH
HH| |
| || C C| |
HH|| ||
- 2H
X
Free rotation about single bonds
No free rotationabout double bonds
cis
Solid fats
Oils
Effect of fatty acid structure on physical properties
trans
cis
Free rotation about single bonds
No free rotation about double bonds
C C|
|H
H
||
|
|
X
trans
Unsaturated fatty acid
Saturated fatty acid
Hydrogenation of oil to solidify it
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Fatglobule
Nuc.
Adipocyte (fat storage cell)
Adipose tissue
Fat is a good compact source of energy, about twice the calories as starch, pound for pound.
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[HO]
[HO]
Handout 2-9
Phospholipids:
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O ||
HO-P-O-
|
O-
Phosphoric acid(phosphate ion)
+ R-OH
an alcohol(hydroxyl)
O ||R-O-P-OH |
O-
a phosphoester
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If R=another alcohol:a phospho-diester
If R=H, phosphatydic acid
}HO
HO
Handout 2-9
HO –CH2CH2N+H3
(alcohol = ethanolamine) phophatydyl ethanolamine
(2 FAs implied)
x y
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HOHHOH
Phosphate head
2 fatty acid tails each
Biological membranes are phospholipid bilayers
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Incidentally, note the functional groups we have met so far:
HydroxylAmineAmideCarboxylCarbonylAldehydeKetoneEster: Carboxylic acid ester
PhosphoesterPhosphodiester
And:
Glycosidic bondsC=C double bonds (cis and trans)
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Amino acids (the monomer of proteins)
PROTEINS
R = ONE of 20 CHEMICAL GROUPS
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At pH 7, ,most amino acids are zwitterions (charged, but electrically neutral)
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Equilibrium state of the carboxyl group lies far towards the ionized molecule at pH7
+H+
pH7
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+OH- ( = -H+)
+H+
pH:Net charge:
50-50 charged-uncharged at ~ pH9 (=the pK)
50-50 charged-uncharged at ~ pH2.5 (=the pK)
R OH | /+H3N - C – C=O
| H
R O-
| /
H2N - C – C=O
| H
R O-
| /+H3N - C – C=O
| H
1+1
11-1
70
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Numbering (lettering) amino acids
alpha-carbon
alpha-carboxyl (attached to the α-carbon)alpha-amino
β
γδ
ε
ε-amino group
The 2 amino groups and the carboxyl are assumed to be charged (understood)even if unwritten.
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Sho
wn
unch
arge
d (a
s on
exa
ms)
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18
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H+ H+
~10% charged at pH7 guanido +1
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Ball and stick physical model of an amino acid
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Amino acids in 3 dimensions
• Asymmetric carbon (4 different groups attached)
• Stereoisomers• Rotate polarized light• Optical isomers • Non-superimposable• Mirror images
• L and D forms
From Sadava text
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Mannose
A
B
C
D
Any compound
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Condensation of amino acids to form a polypeptide(must be catalyzed)
dehydration again
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Parts of a polypeptide chain
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Handout 3-3
The backbone is monotonous It is the side chains that provide the variety
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“Polypeptides” vs. “proteins”
• Polypeptide = amino acids connected in a linear chain (polymer)
• Protein = a polypeptide or several associated polypeptides (discussed later)
• Often used synonymously
• Peptide (as opposed to polypeptide) is smaller, even 2 AAs (dipeptide)
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(Without showing the R-groups)
The backbone is monotonous
It is the side chains that provide the variety
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Proteins do most of the jobs in the cell
E.g., egg albumin, hemoglobin, keratin, estrogen receptor,immunoglobulins (antibodies), enzymes (e.g., beta-galactosidase)
Each is a polymer or assemblage of polymers made up of amino acidsEach particular protein polymer (polypeptide) has a unique sequence of amino acids . . . . and an English name.Each molecule of a particular protein has the same sequence of amino acids.
E.g., met-ala-leu-leu-arg-glu-leu-val- . . . .
How is this sequence determined?
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Primary (1o) Structure = the sequence of the amino acids in the polypeptide chain
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Determining the sequence
One way: use an enzyme: (an old method, but useful for teaching)
identify,
e.g., …. arg-leu-leu-val-gly-ala-gly-phe-trp-lys-glu-asp-ser
…. arg-leu-leu-val-gly-ala-gly-phe-trp-lys-glu-asp +
…. arg-leu-leu-val-gly-ala-gly-phe-trp-lys-glu +
Carboxypeptidase: hydrolyzes the peptide bond
ser
asp
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(-) (+)
AA mixture (ala, glu, lys
METHODS . . .
Anode Cathode
Note: The cathode is negative in an electrophoresis apparatus even though it is positive in a battery (voltaic cell)
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A paper electrophoresis apparatus
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AAs applied at lower end
Side view
Handout 3-4
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“Rf”
0.82
0.69
0.45
0.27
0.11
After stopping the paper chromatography and staining for the amino acids:
1.00“front” =
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Paper chromatography apparatus
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N C
Trypsin (lys, arg)
Chymotrypsin (trp, tyr, phe)
The order of the subpeptides is unknown.The sequence is reconstructed by noting the overlap between differently produced subpeptides
(1)
(2)
Sequence overlap
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N C
Trypsin (lys, arg)
Chymotrypsin (trp, tyr, phe)
The order of the subpeptides is unknown.The sequence is reconstructed by noting the overlap between differently produced subpeptides
(1)
(2)
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Sub-peptides
Fingerprinting a protein: analysis of the sub-peptides
(without breaking them down to their constituent amino acids)
Application to sickle cell disease(Vernon Ingram, 1960’s)
Hemoglobin protein
No further digestion to amino acids; left as sub-peptides
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Oligopeptides behave as a composite of their constituent amino acids
Net charge = -1: moves toward the anode in paper electrophoresesFairly hydrophobic (~5/6): expected to move moderately well in paper chromatography
Nomenclature: ala-tyr-glu-pro-val-trp or AYEPVW or alanyl-tyrosyl-glutamyl-prolyl-valyl-tryptophan
+
-
-
E.g.:
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In fingerprinting, these spots containpeptides, not amino acidsThe mixture of
all sub-peptides formed
------glutamate----- (normal)
------valine------(sickle)
More hydrophobic
More hydrophilic
Negativelycharged
Positivelycharged
Negativelycharged
Positivelycharged
Negativelycharged
Positivelycharged
Less negatively charged,More hydrophobic
Hb
trypsin
Protein fingerprinting
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Every different polypeptide has a different primary structure (sequence).Every polypeptide will have different arrangement of spots after fingerprinting.
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• Molecule #1: N-met-leu-ala-asp-val-val-lys-....
• Molecule #2: N-met-leu-ala-asp-val-val-lys-...
• Molecule #3: N-met-leu-ala-asp-val-val-lys-...
• Molecule #4: N-met-leu-ala-asp-val-val-lys-... etc.
3-dimensional structure of proteins
One given purified polypeptide
clothesline . . .
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Information for proper exact folding(How does a polypeptide fold correctly?)
Predicting protein 3-dimensional structure
Determining protein 3-dimensional structure
Where is the information for choosing the correct folded structure?
Is it being provided by another source (e.g, a scaffold) or does it reside in the primary structure itself?
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Denature by heat
Cool, renature?
Tangle, gel.Probably due to non-productivehydrophobic interactions
XToo long to sort out
“Renaturation” of a hard-boiled egg
ovalbuminCool, entangled
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urea
chaotropic agent
used at very high concentrations (e.g., 7 M)
gentler, gradual denaturation, renaturation
O||
N-C-N
H
H
H
H
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+ urea, denature
-urea, renature
??
“Renaturation” of pure ribonuclease after urea
“native” ribonucleaseactive enzyme
compact
denatured ribonucleaseinactive enzyme
random coil
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Now dialyze out the urea
Slow denaturation of ribonuclease by urea
O ||Urea = H2N-C—NH2
Macromolecules (protein here) cannot permeate bag material
Small molecules (H20, urea) can.Urea will move from areas of high concentrationto areas of low concentration
Ribonuclease in the bag is denatured
RENATURESRibonuclease
in the absence of any other material
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PRIMARY STRUCTURE DETERMINES TERTIARY STRUCTURE.
Christian Anfinsen:
+ urea, denatures
- urea, renatures
“The Anfinsen Experiment”