AP Biology

Proteins

AP Biology 2008-2009

Proteins Diverse group

Made of Amino Acids

AP Biology

Proteins  Most structurally & functionally diverse group   Function: involved in almost everything

  Enzymes (pepsin, DNA polymerase)   Structural Support (keratin, collagen)   Transport of substances (hemoglobin, aquaporin)

  Hormones (insulin & other hormones)   Defense (antibodies)   Contraction and Movement (actin & myosin)   Storage (bean seed proteins)

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Proteins  Structure

 monomer = Amino Acid   20 different amino acids

 polymer = Chains of AA   protein can be one or more polypeptide

chains folded & bonded together   large & complex molecules   complex 3-D shape

Rubisco

hemoglobin

growth hormones

H2O

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Amino acids  Structure

 central carbon  amino group  carboxyl group (acid)  R group (side chain)

  variable group   different for each amino acid   confers unique chemical

properties to each amino acid   like 20 different letters of an

alphabet  can make many words (proteins)

—N— H

H

C—OH || O

R

|

—C— |

H

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Effect of different R groups: Nonpolar amino acids

Why are these nonpolar & hydrophobic?

 nonpolar & hydrophobic

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Effect of different R groups: Polar amino acids

 polar or charged & hydrophilic

Why are these polar & hydrophillic?

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Ionizing in cellular waters H+ donors

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Ionizing in cellular waters H+ acceptors

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Sulfur containing amino acids   Form Disulfide bonds

  covalent cross links betweens sulfhydryls   stabilizes 3-D structure

H-S – S-H

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Fig. 7.12 (TEArt) Constant region Variable region Disulfide bond

s

α chain β chain

T Receptor B Receptor

Light chain Light chain α chain

Heavy chains

Plasma membrane

MHC-II

α chain

MHC-I

β-2 microglobulin

S S

s s s

s s s s

s s s s s

s s s s s s

s s s s s s s s

s s s s

s

s s s s s s

s s s s s s

s s

s s s s s s s s s s s s

β chain

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AP Biology

Building proteins  Peptide Bond

 covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another

 C–N bond

peptide bond

dehydration synthesis H2O

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Building proteins  Polypeptide chains have direction

 N-terminus = NH2 end  C-terminus = COOH end   repeated sequence (N-C-C) is the

polypeptide backbone   can only grow in one direction

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Protein structure & function

hemoglobin

 Function depends on structure  3-D structure

  twisted, folded, coiled into unique shape

collagen

pepsin

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Primary (1°) structure  Chain of Amino Acids

 amino acid sequence determined by gene (DNA)

 slight change in amino acid sequence can affect protein’s structure & its function   even just one amino acid change

can make all the difference!

lysozyme: enzyme in tears & mucus that kills bacteria

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Sickle cell anemia

I’m hydrophilic!

But I’m hydrophobic!

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Secondary (2°) structure

  folding along short sections of polypeptide   interactions between

adjacent amino acids  Hydrogen Bonds

 weak bonds between R groups

  forms sections of 3-D structure  Alpha Helix  B Pleated Sheet

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Secondary (2°) structure

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Tertiary (3°) structure   interactions between distant amino acids

 Hydrophobic Interactions  cytoplasm is

water-based  nonpolar amino

acids cluster away from water

 H-Bonds  Disulfide Bonds

 covalent bonds between sulfurs in sulfhydryls (S–H)

 anchors 3-D shape

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Quaternary (4°) structure  Consists of the interactions of two or more

polypeptide chains   only then does polypeptide become

functional protein

collagen = skin & tendons hemoglobin

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Protein structure (review)

amino acid sequence

peptide bonds

1°

determined by DNA R groups

H bonds

R groups hydrophobic interactions

disulfide bridges (H & ionic bonds)

3° multiple

polypeptides hydrophobic interactions

4°

2°

AP Biology 2008-2009

Fig. 5-21d

Abdominal glands of the spider secrete silk fibers

made of a structural protein containing β pleated sheets.

The radiating strands, made of dry silk fibers, maintain

the shape of the web.

The spiral strands (capture strands) are elastic, stretching

in response to wind, rain, and the touch of insects.

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Protein Folding in the Cell   It is hard to predict a protein’s structure

from its primary structure  Most proteins probably go through several

states on their way to a stable structure  Chaperonins are protein molecules that

assist the proper folding of other proteins

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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Fig. 5-24

Hollow cylinder

Cap

Chaperonin (fully assembled)

Polypeptide

Steps of Chaperonin Action:

An unfolded poly- peptide enters the cylinder from one end.

1

2 3 The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comes off, and the properly folded protein is released.

Correctly folded protein

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Protein denaturation  Unfolding a protein

 alter 3-D shape   some proteins can return to their functional

shape after denaturation, many cannot

AP Biology 2008-2009

Let’s build some

Proteins!