Download AP Biology

Proteins
Multipurpose
molecules
AP Biology
2006-2007
Proteins
AP Biology
*^@%
I look
good!
Proteins!
AP Biology
PROTEINS
Elements
•Carbon
•Hydrogen
•Oxygen
•Nitrogen
•sometimes Sulfur
Monomer
 Amino Acid
NH2
 There are 20 different
Other variable
groups determine
properties.
AP Biology
COOH
amino acids found in
nature. Some of which we
cannot synthesize and must
be eaten, Essential Amino
Acids.
PROTEINS
 Muscles
 Cell receptors
 Most hormones
 Enzymes
 Antibodies
AP Biology
PROTEINS
• structure
• cell
communication
• control chemical
reaction rates
• fight diseases
AP Biology
Proteins
 Most structurally & functionally diverse

group of biomolecules
Function:

involved in almost everything







AP Biology
enzymes (pepsin, polymerase, etc.)
structure (keratin, collagen)
carriers & transport (membrane channels)
receptors & binding (defense: antibodies)
contraction (actin & myosin)
signaling (hormones: insulin)
storage (bean seed proteins)
Proteins
 Structure:

monomer = amino acids
 20 different amino acids

polymer = polypeptide
 protein can be one or more polypeptide
chains folded & bonded together
 large & complex molecules
 complex 3-D shape
hemoglobin
AP Biology
Rubisco
growth
hormones
Amino acids
 Structure:
central carbon
 amino group
 carboxyl group (acid)
 R group (side chain)

 variable group
 confers unique
chemical properties
of the amino acid
AP Biology
H O
H
| ||
—C— C—OH
—N—
|
H
R
Nonpolar amino acids
 nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?
AP Biology
Polar amino acids
 polar or charged & hydrophilic
AP Biology
Why are these polar & hydrophillic?
Ionizing in cellular waters
AP Biology
H+ donors
Ionizing in cellular waters
AP Biology
H+ acceptors
Sulfur containing amino acids
 Form disulfide bridges

cross links betweens sulfurs in amino acids
H-S – S-H
You wondered
why perms
smelled like
rotten eggs?
AP Biology
Building proteins
 Peptide bonds
linking NH2 of one amino acid to
COOH of another
 C–N bond

dehydration synthesis
AP Biology
peptide
bond
Building proteins
 Polypeptide chains
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
 twisted, folded, coiled into unique shape
pepsin
hemoglobin
AP Biology
collagen
Primary (1°) structure
 Order of amino acids in chain
amino acid sequence
determined by gene (DNA)
 slight change in amino acid
sequence can affect protein’s
structure & it’s 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
AP Biology
Secondary (2°) structure
 “Local folding”

folding along short
sections of
polypeptide
 interaction between
adjacent amino
acids
 H bonds between
R groups
 -helix
 -pleated sheet
AP Biology
Tertiary (3°) structure
 “Whole molecule
folding”

determined by
interactions
between R groups
 hydrophobic
interactions
 effect of water
in cell
 anchored by
disulfide bridges
(H & ionic bonds)
AP Biology
Tertiary structure results from interactions
of side chains on amino acids.
AP Biology
Quaternary (4°) structure
 More than one polypeptide chain
joined together

only then is it a functional protein
 hydrophobic interactions
collagen =
skin & tendons
AP Biology
hemoglobin
Protein structure (review)
R groups
hydrophobic
interactions,
disulfide bridges, van
der Waals, hydrogen
bonds
3°
multiple
polypeptides
hydrophobic
interactions
1°
aa sequence
peptide bonds
determined
by DNA
AP Biology
2°
R groups
H bonds
4°
Form Fits Function
H
A
R
E
Protein Structure
Give and example of
each
Globular
AP Biology
Fibrous
Fibrous Protein: keratin
AP Biology
Alpha helix held by hbonds allows for
stretching by breaking
bonds (example wool)
Beta sheets held by hbonds, resist pulling
(example silk)
Prions
Killer: viruses, bacteria, fungi,
protists….Proteins can cause a disease?
AP Biology
2006-2007
 What can cause rapidly progressive dementia, leading to
memory loss, personality changes and hallucinations
accompanied by physical problems such as speech
impairment, jerky movements, balance and coordination
dysfunction, changes in gait, rigid posture, and seizures?
Creutzfeld-Jacob
Syndrome in humans
and Bovine
Spongiform
Encephalitis in cows.
Mad Cow disease
 Bovine Spongiform
Encephalopathy is a fatal,
neurodegenerative disease in cattle,
that causes a spongy degeneration in
the brain and spinal cord. BSE has a
long incubation period, about 4 years,
usually affecting adult cattle at a peak
age onset of four to five years, all
breeds being equally susceptible
 Caused by feeding cattle remains of
other cattle in the form of meat and
bone meal.
 Spread to humans by consumption of
contaminated meat. YUCK!
Prion: It’s all about shape!
 The infectious agent in BSE is believed
to be a specific type of misfolded
protein called a prion.
 carry an allele which causes previously
normal protein molecules to contort by
themselves from an alpha helical
arrangement to a beta pleated sheet
 This results in protein aggregates,
which then form dense plaque fibers,
leading to the microscopic appearance
of "holes" in the brain, degeneration of
physical and mental abilities, and
ultimately death.
Mad Human disease??
 Cannibalism has also been implicated as a transmission
mechanism for abnormal prions, causing the disease known
as kuru, found primarily among women and children of the
Fore tribe in Papua New Guinea. The women and children
ceremonially ate the brains of the deceased and contracted
Creutzfeldt-Jakob Syndrome from infected brain tissue.
AP Biology
Denature a protein
 Unfolding a protein

disrupt 3° structure
 pH

salt

temperature
In Biology,
size doesn’t matter,
SHAPE matters!
unravels or denatures protein
 disrupts H bonds, ionic bonds &
disulfide bridges


destroys functionality
 Some proteins can
return to their
functional shape
after denaturation,
many cannot
AP Biology
Chaperonin proteins
 Guide protein folding


AP Biology
provide shelter for folding polypeptides
keep the new protein segregated from
cytoplasmic influences
Protein models
 Protein structure visualized by
X-ray crystallography
 extrapolating from amino acid sequence
 computer modeling

lysozyme
AP Biology
Can 2 polypeptides have same amino acid
sequence but different conformations? How?
 Various pH or temps would change H-bond
 Presence or absence of cofactors/coenzymes

Collagen is in fibrous tissue of bone and blood vessels
 Vitamin C is coenzyme for proper folding
 Lack of vitamin C blocks modification of R-group causing
scurvy!
AP Biology
Of course some people use extra collagen for
cosmetic reasons!
 But it can go wrong
 Very wrong!
Better keep eating
lots of limes!
AP Biology
CATALYST
CATALYST
A ______________
is a chemical that
____________
SPEEDS UP chemical reactions WITHOUT
being __________
CHANGED by that reaction.
AP Biology
ENZYMES are protein catalysts
Enzymes
decrease the
activation
energy
AP Biology
-Enzymes
are reused many times before the body gets rid of them.
How does it work?
 Variety of mechanisms to lower
activation energy & speed up reaction

synthesis
 active site orients substrates in correct
position for reaction
 enzyme brings substrate closer together

digestion
 active site binds substrate & puts stress on
bonds that must be broken, making it easier
to separate molecules
AP Biology
There are
Most
enzyme
names end
in –ase!
OODLES
of Enzymes!!
Each
ENZYME
is
specific
to its
SUBSTRATE.
AP Biology
Enzyme Vocab
Enzyme: a protein catalyst that speeds up
chemical reactions without being changed by that
reaction.
Active Site: groove/depression where binds
Substrate: the molecule the enzyme is working
on.
Product: the molecule created by the enzyme.
NOTE* enzymes can JOIN molecules or SPLIT
them!!
AP Biology
Enzyme lock and key
What determines active site?
The folding of the
polypeptide chains
AP Biology
Enzyme Activity
Called the
enzymesubstrate
complex
AP Biology
Enzyme Action…
again
AP Biology
Induced fit model:
Active site is not rigid
 More accurate model of enzyme action


AP Biology
3-D structure of enzyme fits substrate
substrate binding cause enzyme to change
shape leading to a tighter fit
 “conformational change”
 bring chemical groups in position to catalyze
reaction
Compounds which help enzymes
Fe in
 Activators
hemoglobin

cofactors
 non-protein, small inorganic
compounds & ions
 Mg, K, Ca, Zn, Fe, Cu
 bound within enzyme molecule

coenzymes
 non-protein, organic molecules
 bind temporarily or permanently to
enzyme near active site
AP Biology
 many vitamins
 NAD (niacin; B3)
 FAD (riboflavin; B2)
 Coenzyme A
Mg in
chlorophyll
Cooperativity
 Substrate acts as an activator



substrate causes conformational
change in enzyme
 induced fit
favors binding of substrate at 2nd site
makes enzyme more active & effective
 hemoglobin
Hemoglobin
 4 polypeptide chains
 can bind 4 O2;
 1st O2 binds
 now easier for other
O2 to bind
AP3Biology
Factors affecting Enzymes:
TEMPERATURE
&
pH
•too HIGH of a temperature or change in pH will
denature enzymes
• too LOW of a temperature will ONLY SLOW DOWN
their function…NOT denature them!
Denature:
Extreme conditions can cause enzymes to
denature, or change shape.
Normal
Denatured
Based on what you know about enzyme
function, how does this change of shape impact
how enzymes work?
Factors affecting Enzymes:
3.CONCENTRATION
1.
IfOkay….now
thereifare
10there
pizzas
to20
deliver
and
ONE
delivery
4.
2.
What
there
are
10
are
pizzas
pizzas
to
be
and
delivered
10
delivery
(you
3.How
What
if there
are 10 pizzas
to
be
delivered
and
does
this
scenario
relate
to
enzyme
and
guy…how
fastthe
do
you
get are
your
pizza
(assuming
you
people?
are
last
again)
Can
and
delivery
there
people
5
delivery
work
any
people
faster?
10
deliveryconcentration?
people?
substrate
are
last on the list)?
working?
Factors affecting enzyme function
 Enzyme concentration

as  enzyme =  reaction rate
 more enzymes = more frequently collide with
substrate

reaction rate levels off
reaction rate
 substrate becomes limiting factor
 not all enzyme molecules can find substrate
AP Biology
enzyme concentration
Factors affecting enzyme function
 Salt concentration

changes in salinity
 adds or removes cations (+) & anions (–)
 disrupts bonds, disrupts 3D shape
 disrupts attractions between charged amino acids
 affect 2° & 3° structure
 denatures protein

enzymes intolerant of extreme salinity
 Dead Sea is called dead for a reason!
AP Biology
Compounds which regulate enzymes
 Inhibitors
molecules that reduce enzyme activity
 competitive inhibition
 noncompetitive inhibition
 irreversible inhibition
 feedback inhibition

AP Biology
Competitive Inhibitor
 Inhibitor & substrate “compete” for active site


penicillin
blocks enzyme bacteria use to build cell walls
disulfiram (Antabuse)
treats chronic alcoholism
 blocks enzyme that
breaks down alcohol
 severe hangover & vomiting
5-10 minutes after drinking
 Overcome by increasing substrate
concentration

AP Biology
saturate solution with substrate
so it out-competes inhibitor
for active site on enzyme
Non-Competitive Inhibitor
 Inhibitor binds to site other than active site


allosteric inhibitor binds to allosteric site
causes enzyme to change shape
 conformational change
 active site is no longer functional binding site
 keeps enzyme inactive

some anti-cancer drugs
inhibit enzymes involved in DNA synthesis
 stop DNA production
 stop division of more cancer cells

cyanide poisoning
irreversible inhibitor of Cytochrome C,
an enzyme in cellular respiration
 stops production of ATP
AP Biology
Allosteric Control: Second binding site
causes change in enzyme’s active site, so no
longer binds to intended substrate.
AP Biology
Irreversible inhibition
 Inhibitor permanently binds to enzyme

competitor
 permanently binds to active site

allosteric
 permanently binds to allosteric site
 permanently changes shape of enzyme
 nerve gas, sarin, many insecticides
(malathion, parathion…)
 cholinesterase inhibitors

AP Biology
doesn’t breakdown the neurotransmitter,
acetylcholine
AP Biology
Metabolic pathways







ABCDEFG
5
6
enzyme enzyme enzyme
enzyme enzyme enzyme
enzyme
1
2
3
4
 Chemical reactions of life
are organized in pathways

AP Biology
divide chemical reaction
into many small steps
 artifact of evolution
  efficiency
 intermediate branching points
  control = regulation
Feedback Inhibition
 Regulation & coordination of production


product is used by next step in pathway
final product is inhibitor of earlier step
 allosteric inhibitor of earlier enzyme
 feedback inhibition

no unnecessary accumulation of product






ABCDEFG
1
2
3
4
5
6
X
enzyme enzyme enzyme enzyme enzyme enzyme
AP Biology
allosteric inhibitor of enzyme 1
Efficiency
 Organized groups of enzymes

enzymes are embedded in membrane
and arranged sequentially
 Link endergonic & exergonic reactions
Whoa!
All that going on
in those little
mitochondria!
AP Biology
Packaging Enzymes (for convenience)
is an Emergent Property, which one?
“Life is organized along a hierarchy of
structure.”