BIOCHEM PROTEINS AND ENZYMES REVIEWER

1. Amino Acids, Proteins, and Enzymes

2. Function of proteins
Fibrinogen helps blood clotting

3. Function of proteins

4. - Unlike lipids and carbohydrates, proteins are not stored, so they
must be consumed daily.
- Current recommended daily intake for adults is 0.8 grams of
protein per kg of body weight (more is needed for children).
- Dietary protein comes from eating meat and milk.
Proteins
- Proteins account for 50% of the dry weight of the human body.

5. Proteins
100,000 different proteins in human body
Fibrous proteins:
Insoluble in water – used for structural purposes (Keratin & Collagen).
Globular proteins:
More or less soluble in water – used for nonstructural purposes.

6. • Are the building blocks of proteins.
• Contain carboxylic acid and amino groups.
• Are ionized in solution (soluble in water).
• They are ionic compounds (solids-high melting points).
• Contain a different side group (R) for each.
side chain
H2N— C —COOH H3N— C —COO−
Amino acids
+
Zwitterion
α-carbon
H H
Ionized form (Salt)
R R
This form never exist in nature.

7. Amino acids
H
│
H3N—C —COO−
│
H glycine
CH3
│
H3N—C —COO−
│
H alanine
+
+
Only difference: containing a different side chain (R) for each.

8. Amino acids are classified as:
• Nonpolar (Neutral) amino acids
(hydrophobic) with hydrocarbon (alkyl
or aromatic) sides chains.
• Polar (Neutral) amino acids
(hydrophilic) with polar or ionic side
chains.
• Acidic amino acids (hydrophilic) with
acidic side chains (-COOH).
• Basic amino acids (hydrophilic) with –
NH2 side chains.
Amino acids

9. There are only 20 different amino acids in the proteins in humans.
There are many amino acids.
Amino acids
They are called α (alpha) amino acids.
- Humans cannot synthesize 10 of these 20 amino acids.
(Essential Amino Acids)
- They must be obtained from the diet (almost daily basis).

10. Nonpolar (Neutral) amino acids
NH3
+
COO-
NH3
+
COO-
NH3
+
COO-
NH3
+
COO-
NH3
+
COO-
S
NH3
+
COO-
N
H H
COO-
NH3
+
COO-
N
H
COO-
NH3
+
Alanine
(Ala, A)
Glycine
(Gly, G)
Isoleucine
(Ile, I)
Leucine
(Leu, L)
Methionine
(Met, M)
Phenylalanine
(Phe, F)
Proline
(Pro, P)
Tryptophan
(Trp, W)
Valine
(Val, V)

11. NH3
+
COO-
HS
NH3
+
COO-
HO
Cysteine
(Cys, C)
Tyrosine
(Tyr, Y)
NH3
+
COO-
H2 N
O
NH3
+
COO-
H2 N
O
NH3
+
COO-
HO
NH3
+
COO-
OH
Asparagine
(Asn, N)
Glutamine
(Gln, Q)
Serine
(Ser, S)
Threonine
(Thr, T)
Polar (Neutral) amino acids

12. NH3
+
COO-
-
O
O
NH3
+
COO-
-
O
O NH3
+
COO-
N
H
H2 N
NH2
+
NH3
+
COO-
N
N
H
NH3
+
COO-
H3 N
Glutamic acid
(Glu, E)
Aspartic acid
(Asp, D)
Histidine
(His, H)
Lysine
(Lys, K)
Arginine
(Arg, R)
+
Acidic and basic amino acids

13. Fischer projections
All of the α-amino acids are chiral (except glycine)
Four different groups are attached to central carbon (α-carbon).
H NH3
+
COO-
CH3
+
H3N H
COO-
CH3
D-Alanine L-Alanine
(Fischer projections)
H NH3
+
COO-
CH3
+
H3N H
COO-
CH3
D-Alanine L-Alanine
(Fischer projections)
CH2SH CH2SH
D-cysteine L-cysteine
L isomers is found in the body proteins and in nature.

14. Ionization and pH
pH: 6 to 7 Isoelectric point (pI)
Positive charges = Negative charges
No net charge (Neutral) - Zwitterion
pH: 3 or less -COO- acts as a base and accepts an H+
+
R
H3N-CH-C-O
-
O
+ H3 O+ +
R
H3N-CH-C-OH
O
+ H2 O
pH: 10 or higher -NH3
+ acts as an acid and loses an H+
+
R
H3 N-CH-C-O
-
O
+ OH-
R
H2 N-CH-C-O-
O
+ H2 O
+
R
H3 N-CH-C-O
-
O
+ OH-
R
H2 N-CH-C-O-
O
+ H2 O
-

15. Ionization and pH
The net charge on an amino acid depends on the
pH of the solution in which it is dissolved.
pH 2.0 pH 5.0 - 6.0 pH 10.0
Net charge +1 Net charge 0 Net charge -1
+
R
H3 N-CH-C-O
-
O
+
R
H3 N-CH-C-OH
O
R
H2 N-CH-C-O-
O
OH-
H3 O+
OH-
H3 O+

16. 6.01
5.41
5.65
5.97
6.02
6.02
5.74
5.48
6.48
5.68
5.87
5.89
5.97
pI
valine
tryptophan
threonine
serine
proline
phenylalanine
methionine
leucine
isoleucine
glycine
glutamine
asparagine
alanine
Nonpolar &
polar side chains
10.76
2.77
5.07
3.22
7.59
9.74
5.66
pI
tyrosine
lysine
histidine
glutamic acid
cysteine
aspartic acid
arginine
Acidic
Side Chains
Basic
Side Chains pI
Ionization and pH
Each amino acid has a fixed and constant pI.

18. A dipeptide forms:
• When an amide links two amino acids (Peptide bond).
• Between the COO− of one amino acid and
the NH3
+ of the next amino acid.
Peptide
O
O-
H3N
CH3
H3N
O-
CH2 OH
O
H3N
N
CH3
O CH2 OH
O
O-
H
H2 O
+
Alanine (Ala) Serine (Ser)
+
+
+
peptide
bond
Alanylserine
(Ala-Ser)
+
(amide bond)

19. •Dipeptide: A molecule containing two amino acids
joined by a peptide bond.
•Tripeptide: A molecule containing three amino
acids joined by peptide bonds.
•Polypeptide: A macromolecule containing many
amino acids joined by peptide bonds.
•Protein: A biological macromolecule containing at
least 40 amino acids joined by peptide bonds.
Peptide

20. Naming of peptides
C-terminal amino acid: the amino acid at the end of the chain
having the free -COO- group (always written at the left).
N-terminal amino acid: the amino acid at the end of the chain
having the free -NH3
+ group (always written at the right).
H3N
OH
N
H O
H
N
COO-
O-
O
C6 H5
O
+
C-terminal
amino acid
N-terminal
amino acid
Ser-Phe-Asp

21. Naming of peptides
- Begin from the N terminal.
- Drop “-ine” or “-ic acid” and it is replaced by “-yl”.
- Give the full name of amino acid at the C terminal.
H3N-CH-C-NH-CH2-C-NH-CH-C-O
CH3 CH2OH
O O O
From alanine
alanyl
From glycine
glycyl
From serine
serine
Alanylglycylserine
(Ala-Gly-Ser)
+ -

22. Biologically Active Peptides
- Enkephalins, pentapeptides made in the brain, act as pain killers
and sedatives by binding to pain receptors.
- Addictive drugs morphine and heroin bind to these same pain
receptors, thus producing a similar physiological response, though
longer lasting.
- Enkephalins belong to the family of polypeptides called endorphins
(16-31 amino acids), which are known for their pain reducing and mood
enhancing effects.

23. Biologically Active Peptides
Enkephalins:
Met-enkephalin:
It contains a C-terminal methionine.
Leu-enkephalin:
It contains a C-terminal leucine.

24. Biologically Active Peptides
Oxytocin and vasopressin are cyclic nonapeptide hormones, which
have identical sequences except for two amino acids.

25. Oxytocin stimulates the contraction of uterine muscles, and signals for
milk production; it is often used to induce labor.
Vasopressin, antidiuretic hormone (ADH) targets the kidneys and helps
to limit urine production to keep body fluids up during dehydration.
Biologically Active Peptides

26. ASSIGNMENT
(LONG BOND PAPER)
• Draw the polypeptide sequence of the ff:
1. LIVE
2. HEAD
3. RATFINK
• EXPLAIN THE BIOCHEMICAL CAUSE
OF AGEING.

27. ASSIGNMENT
• WORK IN GROUPS OF THREE
MEMBERS AND RESEARCH ON
DISEASES ASSOCIATED WITH
PROTEINS. USE THE FF FORMAT IN
DOING IT.
NAME OF THE
DISEASE
BIOCHEMICAL/
GENETIC
CAUSE
SYMPTOMS MEDICAL
DIAGNOSIS
MEDICAL
TREATMENTS

28. Structure of proteins
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure

29. Primary Structure of proteins
- The order of amino acids held together by peptide bonds.
- Each protein in our body has a unique sequence of amino acids.
- The backbone of a protein.
- All bond angles are 120o, giving the protein a zigzag arrangement.
Ala─Leu─Cys─Met
+
CH3
S
CH2
CH2
SH
CH2
CH3
CH3
CH
CH O
O-
C
CH
H
N
O
C
CH
H
N
O
C
CH
H
N
O
C
CH3
CH
H3N
+

30. Cysteine
The -SH (sulfhydryl) group of cysteine is easily oxidized
to an -S-S- (disulfide).
+
CH2
H3 N-CH-COO
-
SH
oxidation
reduction
+
CH2
H3 N-CH-COO
-
S
+
H3 N-CH-COO
-
CH2
S
Cysteine
Cystine
2
a disulfide
bond

31. Primary Structure of proteins
Chain A
C
O
O-
NH3
+
NH3
+
C
O
O-
Chain B
The primary structure of insulin:
- Is a hormone that regulates the glucose level
in the blood.
- Was the first amino acid order determined.
- Contains of two polypeptide chains linked by
disulfide bonds (formed by side chains (R)).
- Chain A has 21 amino acids and
chain B has 30 amino acids.
- Genetic engineers can produce it for
treatment of diabetes.

32. Secondary Structure of proteins
Describes the way the amino acids next to or near to each other
along the polypeptide are arranged in space.
1. Alpha helix (α helix)
2. Beta-pleated sheet (-pleated sheet)
3. Triple helix (found in Collagen)
4. Some regions are random arrangements.

33. Secondary Structure - α-helix
• A section of polypeptide chain coils into a rigid
spiral.
• Held by H bonds between the H of N-H group
and the O of C=O of the fourth amino acid
down the chain (next turn).
• looks like a coiled “telephone cord.”
• All R- groups point outward from the helix.
• Myosin in muscle and α-Keratin in hair
have this arrangement.
H-bond

34. Secondary Structure - -pleated sheet
O H
• Consists of polypeptide chains (strands) arranged side by side.
• Has hydrogen bonds between the peptide chains.
• Has R groups above and below the sheet (vertical).
• Is typical of fibrous proteins such as silk.

35. Secondary Structure – Triple helix (Superhelix)
- Collagen is the most abundant protein.
- Three polypeptide chains (three α-helix) woven together.
- It is found in connective tissues: bone, teeth, blood
vessels, tendons, and cartilage.
- Consists of glycine (33%), proline (22%), alanine (12%),
and smaller amount of hydroxyproline and hydroxylysine.
- High % of glycine allows the chains to lie close to each
other.
- We need vitamin C to form H-bonding (a special enzyme).

36. Tertiary Structure
The tertiary structure is determined by attractions and repulsions
between the side chains (R) of the amino acids in a polypeptide chain.
Interactions between side
chains of the amino acids
fold a protein into a specific
three-dimensional shape.
-S-S-

37. Tertiary Structure
(1) Disulfide (-S-S-)
(2) salt bridge (acid-base)
(3) Hydrophilic (polar)
(4) hydrophobic (nonpolar)
(5) Hydrogen bond

38. Shorthand symbols on a protein Ribbon diagram:
Tertiary Structure
Lysozyme (an enzyme)

39. Globular proteins
- Have compact, spherical shape.
- Almost soluble in water.
- Carry out the work of the cells:
Synthesis, transport, and metabolism
Myoglobin
Stores oxygen in muscles.
153 amino acids in a single polypeptide chain (mostly α-helix).

40. Fibrous proteins
α-keratin: skin, nail, hair, and bone
- Have long, thin shape and insoluble in water.
- Involve in the structure of cells and tissues.
-keratin: feathers of birds
Large amount of -pleated sheet
Superhelix:
Collagen

41. - They are made of two mainly a-helix chains coiled
around each other in a superhelix (supercoil).
- These coils wind around other coils making
larger and stronger structures (like hair).
Fibrous proteins
α-keratin: hair, wool, skin, and nails
- α-helix chains bond together by disulfide bond (-S-S-)
- More disulfide bonds, more rigid materials
(horns & nails).
Collagen

42. Quaternary Structure
• Occurs when two or more protein units
(polypeptide subunits) combine.
• Is stabilized by the same interactions
found in tertiary structures (between side
chains).
• Hemoglobin consists of four polypeptide
chains as subunits.
• Is a globular protein and transports
oxygen in blood (four molecules of O2).
• CO is poisonous because it binds 200
times more strongly to the Fe2+ than does
O2 (Cells can die from lack of O2).
 chain
 chain
α chain
α chain
Hemoglobin

43. Conjugated Proteins
They are composed of a protein unit and a nonprotein molecule.
Myoglobin & Hemoglobin
Heme: a complex organic compound containing the Fe2+.

44. Sickle Cell Hemoglobin
Sickle cell anemia is a disease where a single amino acid of both β
subunits is changed from glutamic acid to valine.
- Red blood cells containing these mutated hemoglobin units become
elongated and crescent (sickle) shaped (more fragile).
- These red blood cells will rupture capillaries,
causing pain and inflammation, leading
to organ damage, and eventually
a painful death.
- A genetic mutation in the DNA sequence that is responsible for synthesis
of hemoglobin.

45. Summary of protein Structure

46. Summary of protein Structure

47. Denaturation
Active protein
Denatured protein
- Is a process of destroying a protein
by chemical and physical means.
- We can destroy secondary, tertiary,
or quaternary structure but the primary
structure is not affected.
- Denaturing agents: heat, acids and bases,
organic compounds, heavy metal ions, and
mechanical agitation.
- Some denaturations are reversible,
while others permanently damage the protein.
Ovalbumin

48. Denaturation
•Heat: H bonds, Hydrophobic interactions
•Detergents: H bonds
•Acids and bases: Salt bridges, H bonds.
•Reducing agents: Disulfide bonds
•Heavy metal ions (transition metal ions Pb2+, Hg2+): Disulfide bonds
•Alcohols: H bonds, Hydrophilic interactions
•Agitation: H bonds, Hydrophobic interactions

49. Enzymes

50. Enzyme
Eact
Eact
- Like a catalyst, they increase the rate of biological reactions (106 to 1012 times faster).
- Lower the activation energy for the reaction.
 2HI
H2 + I2 
H…H
I … I
…
…
- Less energy is required to convert reactants to products.
- But, they are not changed at the end of the reaction.
- They are made of proteins.

51. Enzyme
- Most of enzymes are globular proteins (water soluble).
- Proteins are not the only biological catalysts.
- Most of enzymes are specific.
(Trypsin: cleaves the peptide bonds of proteins)
- Some enzymes are localized according to need.
(digestive enzymes: stomach)

52. Names of Enzymes
- By replacing the end of the name of reaction or reacting compound
with the suffix « -ase ».
Oxidoreductases: oxidation-reduction reactions (oxidase-reductase).
Transferases: transfer a group between two compounds.
Hydrolases: hydrolysis reactions.
Lyases: add or remove groups involving a double bond without hydrolysis.
Isomerases: rearrange atoms in a molecule to form a isomer.
Ligases: form bonds between molecules.

53. Enzyme
- Substrate: the compound or compounds whose reaction an enzyme
catalyzes.
- Active site: the specific portion of the enzyme to which a substrate binds
during reaction.

54. Enzyme catalyzed reaction
An enzyme catalyzes a reaction by,
• Attaching to a substrate at the active site
(by side chain (R) attractions).
• Forming an Enzyme-Substrate
Complex (ES).
• Forming and releasing products.
• E + S ES E + P
Enzyme: globular protein

55. 1. Lock-and-Key model
- Enzyme has a rigid, nonflexible shape.
- An enzyme binds only substrates that
exactly fit the active site.
-The enzyme is analogous to a lock.
- The substrate is the key that fits into the lock

56. 2. Induced-Fit model
- Enzyme structure is flexible, not rigid.
- Enzyme and substrate adjust the shape
of the active site to bind substrate.
- The range of substrate specificity
increases.
- A different substrate could not induce
these structural changes and no
catalysis would occur.

57. Factors affecting enzyme activity
Activity of enzyme: how fast an enzyme catalyzes the reaction.
1. Temperature
2. pH
3. Substrate concentration
4. enzyme concentration
5. Enzyme inhibition

58. Temperature
- Enzymes are very sensitive to temperature.
- At low T, enzyme shows little activity (not an enough amount of energy for
the catalyzed reaction).
- At very high T, enzyme is destroyed (tertiary structure is denatured).
- Optimum temperature: 37°C or body temperature.

59. pH
- Optimum pH: is 7.4 in our body.
- Lower or higher pH can change the shape of enzyme.
(active site change and substrate cannot fit in it)
- But optimum pH in stomach is 2.
Stomach enzyme (Pepsin) needs an acidic pH to digest the food.
- Some damages of enzyme are reversible.

60. Substrate and enzyme concentration
Maximum activity
Enzyme concentration ↑ Rate of reaction ↑
Substrate concentration ↑ First: Rate of reaction ↑
End: Rate of reaction reaches
to its maximum: all of the enzymes
are combined with substrates.

61. Enzyme inhibition
Inhibitors cause enzymes to lose catalytic activity.
Competitive inhibitor
Noncompetitive inhibitor

62. Competitive Inhibitor
- Inhibitor has a structure that is so similar to the substrate.
- It competes for the active site on the enzyme.
- Solution: increasing the substrate concentration.

63. Noncompetitive Inhibitor
- Inhibitor is not similar to the substrate.
- It does not compete for the active site.
- When it is bonded to enzyme, change the shape
of enzyme (active site) and substrate cannot fit in
the active site (change tertiary structure).
- Like heavy metal ions (Pb2+, Ag+, or Hg2+) that
bond with –COO-, or –OH groups of amino acid
in an enzyme.
- Penicillin inhibits an enzyme needed for formation
of cell walls in bacteria: infection is stopped.
- Solution: some chemical reagent can remove the
inhibitors.
Inhibitor
Site

64. Competitive and Noncompetitive Inhibitor

65. Enzyme cofactors
protein
protein
protein
Metal ion
Organic
molecules
(coenzyme)
Simple enzyme (apoenzyme)
Enzyme + Cofactor
Enzyme + Cofactor (coenzyme)
Metal ions:
bond to side chains.
obtain from foods.
Fe2+ and Cu2+ are gain or loss electrons in redox reactions.
Zn2+ stabilize amino acid side chain during reactions.

66. Enzyme cofactors
- Enzyme and cofactors work together.
- Catalyze reactions properly.

67. Vitamins and Coenzymes
Water-soluble vitamins: have a polar group (-OH, -COOH, or …)
Vitamins are organic molecules that must be obtained from the diet.
(our body cannot make them)
Fat-soluble vitamins: have a nonpolar group (alkyl, aromatic, or …)
- They are not stored in the body (must be taken).
- They can be easily destroyed by heat, oxygen,
and ultraviolet light (need care).
- They are stored in the body (taking too much = toxic).
- A, D, E, and K are not coenzymes, but they are important:
vision, formation of bone, proper blood clotting.

68. Zymogens (Proenzymes)
Zymogen (Proenzyme): an inactive enzyme that becomes an active
enzyme after a chemical change (remove or change some polypeptides).
Trypsinogen (inactive enzyme)
Trypsin (active enzyme)
Digestive enzyme (hydrolyzes the peptide bonds of proteins)
Pancreas
Small intestine

69. Enzymes in medicine
- Most of enzymes are in cells.
- Small amounts of them are in body fluids (blood, urine,…).
Level of enzyme activity can be monitored.
Find some diseases

70. Certain enzymes are present in higher amounts in particular cells.
If these cells are damaged or die, the enzymes are released into the
bloodstream and can be detected.
Enzyme Condition
Creatine phosphokinase Heart attack
Alkaline phosphatase Liver or bone disease
Acid phosphatase Prostate cancer
Enzymes in medicine

71. Penicillin inhibits the enzyme that forms cell walls of bacteria, destroying
the bacterium.
ACE inhibitors are given to those with high blood pressure to prevent
ACE’s synthesis from it’s zymogen.
ACE (angiotensin-converting enzyme) causes blood vessels to narrow,
increasing blood pressure.
HIV protease inhibitors interfere with this copying, decreasing the virus
population in the patient.
HIV protease is an essential enzyme that allows the virus to make
copies of itself.
Enzymes in medicine
Inhibitors can be useful drugs.