1. Multipurpose molecules
Proteins
Multipurpose molecules
clockwise:
Rubisco — most important protein on the planet?
Hemoglobin — a red blooded protein :-)
Collagen — strings you together
Growth Hormones — working hard in you right now!

2. Proteins

3. I look good!
Proteins!

4. PROTEINS Elements Monomer COOH NH2
•Carbon
•Hydrogen
•Oxygen
•Nitrogen
•sometimes Sulfur
Monomer
Amino Acid
There are 20 different amino acids found in nature. Some of which we cannot synthesize and must be eaten, Essential Amino Acids.
COOH
NH2
Other variable groups determine properties.

5. PROTEINS
Muscles
Cell receptors
Most hormones
Enzymes
Antibodies

6. PROTEINS • structure • cell communication • control chemical
reaction rates
• fight diseases

7. Proteins
Most structurally & functionally diverse group of biomolecules
Function:
involved in almost everything
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)
Storage: beans (seed proteins)
Movement: muscle fibers
Cell surface proteins: labels that ID cell as self vs. foreign
Antibodies: recognize the labels
ENZYMES!!!!

8. Proteins Structure: monomer = amino acids polymer = polypeptide
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
Rubisco
growth hormones

9. Amino acids H O | H || —C— C—OH —N— R Structure: central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
confers unique chemical properties of the amino acid |
—C— H
C—OH || O
—N— H R

10. Why are these nonpolar & hydrophobic?
Nonpolar amino acids
nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?

11. Why are these polar & hydrophillic?
Polar amino acids
polar or charged & hydrophilic
Why are these polar & hydrophillic?

12. Ionizing in cellular waters
H+ donors

13. Ionizing in cellular waters
H+ acceptors
Ionizing in cellular waters

14. 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?

15. dehydration synthesis
Building proteins
Peptide bonds
linking NH2 of one amino acid to COOH of another
C–N bond
dehydration synthesis
free COOH group on one end is ready to form another peptide bond so they “grow” in one direction from N-terminal to C-terminal
peptide bond

16. 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

17. Protein structure & function
Function depends on structure
3-D structure
twisted, folded, coiled into unique shape
Hemoglobin
Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood.
Pepsin
Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.
Collagen– Your Most Plentiful Protein
About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.
pepsin
hemoglobin
collagen

18. 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!
Sickle cell anemia: 1 DNA letter changes 1 amino acid = serious disease
Hemoglobin mutation: bends red blood cells out of shape & they clog your veins.
lysozyme: enzyme in tears & mucus that kills bacteria

19. Sickle cell anemia glutamic acid is acidic & polar
valine is non-polar = tries to “hide” from water of cell by sticking to another hemoglobin molecules.

20. Secondary (2°) structure
“Local folding”
folding along short sections of polypeptide
interaction between adjacent amino acids
H bonds between R groups
-helix
-pleated sheet
It’s a helix or B sheet within a single region. Can have both in one protein but a specific region is one or another

21. 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)
How the whole thing holds together

22. Tertiary structure results from interactions of side chains on amino acids.

23. Quaternary (4°) structure
More than one polypeptide chain joined together
only then is it a functional protein
hydrophobic interactions
Structure equals function wonderfully illustrated by proteins
Collagen is just like rope -- enables your skin to be strong and flexible.
collagen =
skin & tendons
hemoglobin

24. Protein structure (review)
R groups hydrophobic interactions,
disulfide bridges, van der Waals, hydrogen bonds 3°
multiple polypeptides
hydrophobic interactions
sequence determines structure and…
structure determines function.
Change the sequence & that changes the structure which changes the function. 1°
aa sequence
peptide bonds 2°
determined by DNA
R groups
H bonds 4°

25. Form Fits Function H A R E

26. Give and example of each
Protein Structure
Give and example of each
Globular
Fibrous

28. Fibrous Protein: keratin

29. Alpha helix held by h-bonds allows for stretching by breaking bonds (example wool)   
Beta sheets held by h-bonds, resist pulling (example silk)

30. Prions
Killer: viruses, bacteria, fungi, protists….Proteins can cause a disease?

31. 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?

32. Creutzfeld-Jacob Syndrome in humans and Bovine Spongiform Encephalitis in cows.

33. 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!

34. 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.

35. 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.

36. In Biology, size doesn’t matter,
Denature a protein
Unfolding a protein
disrupt 3° structure
pH  salt  temperature
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
In Biology, size doesn’t matter,
SHAPE matters!
Example:
Eggs:
Cooking an egg permanently denatures the proteins.

37. Chaperonin proteins Guide protein folding
provide shelter for folding polypeptides
keep the new protein segregated from cytoplasmic influences

38. Protein models Protein structure visualized by X-ray crystallography
extrapolating from amino acid sequence
computer modeling
lysozyme

39. 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!

40. Of course some people use extra collagen for cosmetic reasons!
But it can go wrong
Very wrong!
Better keep eating lots of limes!

41. CATALYST
A ______________ is a chemical that ____________ chemical reactions WITHOUT being __________ by that reaction.
CATALYST
SPEEDS UP
CHANGED

42. ENZYMES are protein catalysts
Enzymes decrease the activation energy
Enzymes are reused many times before the body gets rid of them.

43. 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

44. Most enzyme names end in –ase!
There are
OODLES
of Enzymes!!
Each
ENZYME is
specific
to its
SUBSTRATE.
Most enzyme names end in –ase!

45. 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!!

46. Enzyme lock and key What determines active site?
The folding of the polypeptide chains

47. Enzyme Activity
Called the enzyme-substrate complex

48. Enzyme Action… again

49. Induced fit model: Active site is not rigid
More accurate model of enzyme action
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

50. Compounds which help enzymes
Activators
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
many vitamins
NAD (niacin; B3)
FAD (riboflavin; B2)
Coenzyme A
Fe in hemoglobin
Hemoglobin is aided by Fe
Chlorophyll is aided by Mg
Mg in chlorophyll

51. 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 3 O2 to bind

52. 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!

53. 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?

54. Factors affecting Enzymes: 3.CONCENTRATION
1. If there are 10 pizzas to deliver and ONE delivery guy…how fast do you get your pizza (assuming you are last on the list)?
4. Okay….now there are 20 pizzas and 10 delivery people? Can the delivery people work any faster?
2. What if there are 10 pizzas to be delivered (you are last again) and there are 5 delivery people working?
3. What if there are 10 pizzas to be delivered and 10 delivery people?
How does this scenario relate to enzyme and substrate concentration?

55. Factors affecting enzyme function
Enzyme concentration
as  enzyme =  reaction rate
more enzymes = more frequently collide with substrate
reaction rate levels off
substrate becomes limiting factor
not all enzyme molecules can find substrate
Why is it a good adaptation to organize the cell in organelles?
Sequester enzymes with their substrates!
enzyme concentration
reaction rate

56. 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!

57. Compounds which regulate enzymes
Inhibitors
molecules that reduce enzyme activity
competitive inhibition
noncompetitive inhibition
irreversible inhibition
feedback inhibition

58. 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
saturate solution with substrate so it out-competes inhibitor for active site on enzyme
Ethanol is metabolized in the body by oxidation to acetaldehyde, which is in turn further oxidized to acetic acid by aldehyde oxidase enzymes. Normally, the second reaction is rapid so that acetaldehyde does not accumulate in the body.
A drug, disulfiram (Antabuse) inhibits the aldehyde oxidase which causes the accumulation of acetaldehyde with subsequent unpleasant side-effects of nausea and vomiting. This drug is sometimes used to help people overcome the drinking habit.
Methanol (wood alcohol) poisoning occurs because methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness. Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol. Ethanol is oxidized in preference to methanol and consequently, the oxidation of methanol is slowed down so that the toxic by-products do not have a chance to accumulate.

59. 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
Basis of most chemotherapytreatments is enzyme inhibition. Many health disorders can be controlled, in principle, by inhibiting selected enzymes. Two examples include methotrexate and FdUMP, common anticancer drugs which inhibit enzymes involved in the synthesis of thymidine and hence DNA.
Since many enzymes contain sulfhydral (-SH), alcohol, or acid groups as part of their active sites, any chemical which can react with them acts as a noncompetitive inhibitor. Heavy metals such as silver (Ag+), mercury (Hg2+), lead ( Pb2+) have strong affinities for -SH groups.
Cyanide combines with the copper prosthetic groups of the enzyme cytochrome C oxidase, thus inhibiting respiration which causes an organism to run out of ATP (energy)
Oxalic and citric acid inhibit blood clotting by forming complexes with calcium ions necessary for the enzyme metal ion activator.

60. Allosteric Control: Second binding site causes change in enzyme’s active site, so no longer binds to intended substrate.

61. 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
doesn’t breakdown the neurotransmitter, acetylcholine
Another example of irreversible inhibition is provided by the nerve gas diisopropylfluorophosphate (DFP) designed for use in warfare. It combines with the amino acid serine (contains the –SH group) at the active site of the enzyme acetylcholinesterase. The enzyme deactivates the neurotransmitter acetylcholine.
Neurotransmitters are needed to continue the passage of nerve impulses from one neurone to another across the synapse. Once the impulse has been transmitted, acetylcholinesterase functions to deactivate the acetycholine almost immediately by breaking it down. If the enzyme is inhibited, acetylcholine accumulates and nerve impulses cannot be stopped, causing prolonged muscle contration. Paralysis occurs and death may result since the respiratory muscles are affected.
Some insecticides currently in use, including those known as organophosphates (e.g. parathion), have a similar effect on insects, and can also cause harm to nervous and muscular system of humans who are overexposed to them.

63. Metabolic pathways A  B  C  D  E  F  G A  B  C  D  E  F  G
enzyme 1 
enzyme 3 
enzyme 2 
enzyme 
enzyme 4 
enzyme 5 
enzyme 6 
Chemical reactions of life are organized in pathways
divide chemical reaction into many small steps
artifact of evolution
 efficiency
intermediate branching points
 control = regulation

64. allosteric inhibitor of enzyme 1
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
enzyme 1 
enzyme 2 
enzyme 3 
enzyme 4 
enzyme 5 
enzyme 6  X
allosteric inhibitor of enzyme 1

65. Whoa! All that going on in those little mitochondria!
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!

66. “Life is organized along a hierarchy of structure.”
Packaging Enzymes (for convenience) is an Emergent Property, which one?
“Life is organized along a hierarchy of structure.”