Proteins
AP Biology
Proteins
Multipurpose
molecules
AP Biology
2008-2009
Proteins
 Most structurally & functionally diverse
group (100,000 different proteins?)
 Function: involved in almost everything
enzymes (pepsin, DNA polymerase)
 structure (keratin, collagen, silk)
hair, skin, nails, feathers, horns
 carriers & transport (hemoglobin,
aquaporins, membrane proteins

AP Biology
Functions continued
cell communication
 signals (insulin, adrenalin & other
hormones)
 Receptors in membranes
 defense (antibodies – immunoglobulins)
 movement (actin & myosin in muscle,
tubulin in microtubules)
 storage (bean seed proteins, milkcasein, eggs-albumin)

AP Biology
Proteins
 Structure – they contain C, H, O, N
H2O
and sometimes P &/or S

monomer = amino acids
 20 different amino acids

polymer = polypeptide
 protein can be one or more polypeptide
chains
 large & complex molecules (Ex. Hemoglobin
is C3032H4811O872N780S8Fe4 )
 complex 3-D shape
hemoglobin
AP Biology
growth
hormones
Amino acids
 Structure
central carbon
 amino group (base)
 carboxyl group (acid)
 R group (side chain)

H O
H
| ||
—C— C—OH
—N—
|
H
R
 variable group
 different for each amino acid
 confers unique chemical
properties to each amino acid
AP Biology
Oh, I get it!
amino = NH2
acid = COOH
Kinds of R groups
Nonpolar
 nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?
AP Biology
Polar
 polar or charged & hydrophilic
AP Biology
Why are these polar & hydrophillic?
Review of R groups
 Non-polar



ex. R is -CH3 or –(CH2)nCH3
Polar (uncharged)
ex. R is –OH, -SH
Polar, + charge
ex. R is –NH2 which becomes –NH3+
Polar, - charge
ex. R is –COOH which becomes –COO-
AP Biology
R- groups or side chains
Determine the properties of the amino acids
 -NH2 accepts H+ and is therefore
BASIC
 -COOH donates H+ and is therefore
ACIDIC
 Non-polar groups are hydrophobic
Where in a protein would they be found?
On the inside (away from the water)
AP Biology
Building proteins
 Peptide bonds
covalent bond between NH2 (amine) of
one amino acid & COOH (carboxyl) of
another
 C–N bond

H2O
dehydration synthesis
AP Biology
peptide
bond
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
AP Biology
Protein structure & function
 Function depends on structure

3-D structure (fibrous, globular)
 twisted, folded, coiled into unique shape
pepsin
hemoglobin
AP Biology
collagen
Levels of structure
 Primary
 Secondary
 Tertiary
 Quartenary – not all proteins
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Primary (1°) structure
 Order of amino acids in chain
determined by gene (DNA)
 slight change in amino acid
sequence (caused by DNA
mutation) can affect protein’s
structure & its function

 even just one amino acid change
can make all the difference!
AP Biology
lysozyme: enzyme
in tears & mucus
that kills bacteria
Sickle cell anemia
I’m
hydrophilic!
AP Biology
Just 1
out of 146
amino acids!
But I’m
hydrophobic!
Primary structure
 Is held together by peptide bonds
(which are covalent)
 Primary structure can only be broken
by hydrolysis (digestion)
 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?
20100
 DNA determines the correct sequence
AP Biology
Secondary (2°) structure
 “Local folding”
interactions between
nearby amino acids
 Held by H bonds
 weak bonds
between H (from NH2 and
O (from COOH)
Two kinds of secondary structure
 Alpha helix
 -pleated sheet
AP Biology
AP Biology
Alpha Helix
Wool has
alpha helices
AP Biology
Beta pleated sheet
Silk has beta
pleated sheets
AP Biology
Tertiary (3°) structure
 “Whole molecule bending and folding”
interactions between R groups of distant
amino acids
 Gives protein its 3D
shape
 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 -NH3+)
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
 More than one polypeptide chain bonded
together
only then does polypeptide become
functional protein
 Not all proteins have this

AP Biology = skin & tendons
collagen
hemoglobin
Fibrous or Globular
AP Biology
 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)
R groups
hydrophobic interactions
disulfide bridges
(H & ionic bonds)
3°
1°
multiple
polypeptides
amino acid
sequence
peptide bonds
determined
by DNA
AP Biology
4°
2°
H bonds
Shape
Protein shape allows the protein to function
 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
 Guide protein folding


AP Biology
provide shelter for folding polypeptides
keep the new protein segregated from
cytoplasmic influences
2005-2006
Protein models
 Protein structure visualized by
X-ray crystallography
 extrapolating from amino acid sequence
 computer modelling

lysozyme
AP Biology
2005-2006
Protein denaturation
 Unfolding a protein

conditions that disrupt H bonds, ionic
bonds, disulfide bridges





temperature
pH
Salinity
Heavy metals
alter 2° & 3° structure
(3-D shape)

AP Biology
In Biology,
size doesn’t matter,
SHAPE matters!
destroys functionality
Change in Temperature
 Heat disrupts the H + bonds and other
weak links
AP Biology
 Why do we cook meat?
 To denature the proteins to make it
easier to chew.
AP Biology
Change in pH
 Adding acids increases the amount of
H+ in the solution
 The H+ are attracted to negative parts
of protein and disrupt the original
attractions
Ex. sour milk
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Heavy metals
 Arsenic, lead, mercury, etc. are
poisonous because
 They disrupt the salt bridges by
attaching to the –COO This changes the shape of proteins and
Arsenic poisoning
they don’t work!
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Stirring – mechanical
 Weak bonds (attractions) can be
changed by stirring or whipping
Whipped cream from heavy cream
Meringue from egg white
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Alcohol denatures bacterial
proteins
It interferes with the H bonds
AP Biology
Oxidation-reduction
 Perms cause oxidation and reduction of
disulfide bonds
AP Biology
 What would happen if you moved a
protein from water and put it in an
organic (non-polar) solvent?
 The non-polar amino acids would move
to the outside of the protein, changing
its shape
AP Biology