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MOLECULES

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H2N-CH-C-OHO

R

Monomer

E.g. protein

Monomer vs polymer

amino acid monomerR is a side group

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H2N-CH-C-OH

O

The 20 amino acids found in proteins each have different side chains, R

R RRR R

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Each amino acid has at least one carboxyl group

X CO

OHAt cell pH, the carboxyls dissociate to form carboxylate ions

CO

OHX + H

+C

O

OX

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Proteins are the working language of biology

The 20 amino acids found in proteins are the alphabet

Let's start with the letter AA

Alanine, Ala, A

All the common amino acids have 3-letterand 1-letter abbreviations

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C HH3NR

Note asymmetry around the carbon(all 4 side groups are different)

Most amino acids have D- and L- isomers*

*But only L-amino acidsare present in typical proteins

COO

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Glycine, Gly, G is unusual

R group is a second H-atom

Hence, no asymmetry round

C HH3N

carbon

COO

No L- and D- isomers

H

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Classes of amino acid R-groups

C HH3N

COO

R group Polar, uncharged

CH2OHe.g. Serine, Ser, S

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Classes of amino acid R-groups

C HH3N

COO

R group* is negatively charged

CH2e.g. Aspartic acid, Asp, D

COO

*An additional -COO- group

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Classes of amino acid R-groups

C HH3N

COO

R group positively charged

(CH2) 4 e.g. Lysine, Lys, K

NH3

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C HH3N

COO

R group hydrophobic

CH3

e.g. Alanine, Ala, A

C HH3N

COO

CH2

OHTyrosine, Tyr, Y

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Glycine, Gly, G (mentioned before)

The "baby" (smallest) of the amino acids

No special hydrophilic or hydrophobic character

C HH3N

COO

H

"Special" amino acids

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C HH3N

COO

"Special" amino acids

CH2

SH

Cysteine, Cys, C

Important in forming disulfide (S-S)crosslinks within a protein

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-S-S-

A protein with two disulfide bonds

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CH2SH

HS

CH2

C

C of Cys

of cysteine

S

CH2

C of cysteine

CH2S

C of cysteine

2H

DISULFIDE BOND

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Special amino acids Proline. This amino acid produces a “kink” in a polypeptide

COOHCCH2

CH2H2CHN

Proline, Pro, P

Pro is an imino acid (not, strictly speaking, an amino acid

+H3N-

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Forming a peptide bond between 2 amino acids

R2

C C-O -O

+H3N

+

C

R1

H3N+OC

R1

C C-O -O

H3N+

C

R2

C-O -O

N

H

H20

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C

R 1

H 3 N+OC C

R 2

C-O-

O

N

H

A dipeptide. All peptides and proteins have:

carboxyl endan amino end

C-terminalN-terminal end

and a

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Polypeptide structure

Polypeptide structure

Primary Secondary Tertiary Quaternary

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1. Primary structure1. Primary structure

Amino acid sequenceDisulfide crosslinking within the polypeptide

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1. Primary structure: portion of

-chain of human hemoglobin

1. Primary structure: portion of

-chain of human hemoglobin

Val His Leu Thr Pro Glu Glu Lys

Tyr Arg bla bla bla bla bla bla bla bla bla bla

1 2 3 4 5 6 7 8

140 141

N-terminus

C-terminus

aa substitution; Val instead of Glu at position 6 is found in the disease sickle cell anemia

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2. Secondary stucture of a protein

2. Secondary stucture of a protein

The folding of portions (domains) of the protein to form:-helices-pleated sheets

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Secondary structure: -helix

3.6 aa's per turn

Hydrogen bonding

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Secondary structure: -pleated sheet

Edge view

R R R R

R R R

Polypeptide chains

H-bond

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Overall folding of: helices-pleated sheets and–the regions between them

3. Tertiary structure of protein

3. Tertiary structure of protein

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4. Quaternary structure of protein

4. Quaternary structure of protein

Ordering of several different polypeptide strands to form a functional protein complex

e.g. Hemoglobin