Proteins AP Biology

AP Biology

Proteins

Multipurpose molecules 2008-2009

Proteins

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Most structurally & functionally diverse group (100,000 different proteins?)

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Function: involved in almost everything

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enzymes (pepsin, DNA polymerase)

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structure (keratin, collagen, silk) hair, skin, nails, feathers, horns

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carriers & transport (hemoglobin, aquaporins, membrane proteins AP Biology

Functions continued

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cell communication

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signals (insulin, adrenalin & other hormones)

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Receptors in membranes defense (antibodies – immunoglobulins)

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movement (actin & myosin in muscle, tubulin in microtubules)

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storage (bean seed proteins, milk casein, eggs-albumin) AP Biology

Proteins

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Structure – they contain C, H, O, N H 2 O and sometimes P &/or S

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monomer =

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amino acids 20 different amino acids

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polymer =

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polypeptide protein can be one or more polypeptide chains

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large & complex molecules (Ex. Hemoglobin is C 3032 H 4811 O 872 N 780 S 8 Fe 4 ) complex 3-D shape hemoglobin AP Biology growth hormones

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Amino acids Structure

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central carbon

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amino group (base)

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carboxyl group (acid) H H — N — | H | R

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R group (side chain)

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variable group

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different for each amino acid

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confers unique chemical properties to each amino acid O || C —OH Oh, I get it! amino = NH 2 acid = COOH AP Biology

Kinds of R groups Nonpolar

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nonpolar & hydrophobic AP Biology Why are these nonpolar & hydrophobic?

Polar

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polar or charged & hydrophilic AP Biology Why are these polar & hydrophillic?

Review of R groups

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Non-polar ex. R is -CH 3 or –(CH 2 ) n CH 3

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Polar (uncharged) ex. R is –OH, -SH

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Polar, + charge ex. R is –NH 2 which becomes –NH 3 +

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Polar, - charge ex. R is –COOH which becomes –COO

-

AP Biology

R- groups or side chains Determine the properties of the amino acids

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-NH 2 accepts H+ and is therefore BASIC

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-COOH donates H+ and is therefore ACIDIC

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Non-polar groups are hydrophobic Where in a protein would they be found?

On the inside (away from the water) AP Biology

Building proteins

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Peptide bonds

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covalent bond between NH 2 (amine) of one amino acid & COOH (carboxyl ) of another

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C –N bond dehydration synthesis H 2 O AP Biology peptide bond

Building proteins

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Polypeptide chains have direction

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N-terminus = NH 2 end

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C-terminus = COOH end

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repeated sequence (N-C-C) is the polypeptide backbone

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can only grow in one direction AP Biology

Protein structure & function

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Function depends on structure

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3-D structure (fibrous, globular)

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twisted, folded, coiled into unique shape pepsin hemoglobin AP Biology collagen

Levels of structure

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Primary Secondary Tertiary Quartenary – not all proteins AP Biology

Primary (1 °) structure

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Order of amino acids in chain

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determined by gene (DNA)

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slight change in amino acid sequence (caused by DNA mutation ) can affect protein’s structure & its function

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even just one amino acid change can make all the difference!

AP Biology lysozyme: enzyme in tears & mucus that kills bacteria

Sickle cell anemia Just 1 out of 146 amino acids! AP Biology I’m hydrophilic! But I’m hydrophobic!

Primary structure

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Is held together by peptide bonds (which are covalent)

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Primary structure can only be broken by hydrolysis (digestion)

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Determines all other levels of structure AP Biology

Question  

There are 20 different amino acids How many possible sequences could a protein have that is 100 amino acids long?

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20 100 DNA determines the correct sequence AP Biology

Secondary (2 °) structure

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“ Local folding ” interactions between nearby amino acids

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Held by H bonds

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weak bonds between H (from NH 2 and O (from COOH) Two kinds of secondary structure

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Alpha helix

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-pleated sheet AP Biology

AP Biology

Alpha Helix Wool has alpha helices AP Biology

Beta pleated sheet Silk has beta pleated sheets AP Biology

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Tertiary (3 °) structure “ Whole molecule bending and folding ”

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interactions between R groups of distant amino acids

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Gives protein its 3D shape

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Held by 4 kinds of interactions or bonds AP Biology

1 . H bonds – between H and O usually 2. Ionic bonds – between positive and negative groups( -COOH- and -NH 3 +) Also called salt bridges 3. Disulfide bonds – Strong (covalent) bonds between sulfhydral groups (-S---S-) 4. Hydrophobic interactions cytoplasm is water-based.

Non-polar amino acids cluster away from water *VanderWaals ’ Interactions AP Biology

Quaternary (4 °) structure

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More than one polypeptide chain together bonded

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only then does polypeptide become functional protein

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Not all proteins have this hemoglobin

Fibrous or Globular AP Biology

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http://www.youtube.com/watch?v=lijQ3 a8yUYQ AP Biology

Bonds involved in protein structure AP Biology

Which bonds do you see?

AP Biology

Protein structure (review) 1 ° amino acid sequence peptide bonds determined by DNA AP Biology 2 ° H bonds R groups hydrophobic interactions disulfide bridges (H & ionic bonds) 3 ° 4 ° multiple polypeptides

Shape Protein shape allows the protein to function

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Ex. An enzyme must fit its substrate A hormone must fit its receptor Even minor changes in shape can affect its work AP Biology

Chaperonin proteins

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Guide protein folding

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provide shelter for folding polypeptides

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keep the new protein segregated from cytoplasmic influences

2005-2006

AP Biology

Protein models

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Protein structure visualized by

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X-ray crystallography

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extrapolating from amino acid sequence

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computer modelling AP Biology lysozyme

2005-2006

Protein denaturation

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Unfolding a protein In Biology, size doesn’t matter, SHAPE matters!

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conditions that disrupt H bonds, ionic bonds, disulfide bridges

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temperature pH

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Salinity Heavy metals alter 2 ° & 3° structure (3-D shape)

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destroys functionality AP Biology

Change in Temperature

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Heat disrupts the H + bonds and other weak links AP Biology

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Why do we cook meat?

To denature the proteins to make it easier to chew.

AP Biology

Change in pH

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Adding acids increases the amount of H+ in the solution

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The H+ are attracted to negative parts of protein and disrupt the original attractions Ex. sour milk AP Biology

Heavy metals

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Arsenic, lead, mercury, etc. are poisonous because

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They disrupt the salt bridges by attaching to the –COO-

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This changes the shape of proteins and they don’t work!

Arsenic poisoning

AP Biology

Stirring – mechanical

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Weak bonds (attractions) can be changed by stirring or whipping

Whipped cream from heavy cream Meringue from egg white

AP Biology

Alcohol denatures bacterial proteins It interferes with the H bonds AP Biology

Oxidation-reduction

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Perms cause oxidation and reduction of disulfide bonds AP Biology

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What would happen if you moved a protein from water and put it in an organic (non-polar) solvent?

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The non-polar amino acids would move to the outside of the protein, changing its shape AP Biology