chapter 22 & 23 proteins and enzymes chemistry b11
TRANSCRIPT
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Chapter 22 & 23
Proteins and Enzymes
Chemistry B11
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Function of proteins
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Function of proteins
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- 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 account for 50% of the dry weight of the human body.
Proteins
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Proteins
100,000 different proteins in human body.
Fibrous proteins:
Insoluble in water – used for structural purposes.
Globular proteins:
More or less soluble in water – used for nonstructural purposes.
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• 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.
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Amino acids
H │
H3N—C —COO−
│ H glycine
CH3 │
H3N—C —COO−
│ H alanine
+
+
Only difference: containing a different side group (R) for each.
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Amino acids are classified as:
• Nonpolar amino acids (hydrophobic) with hydrocarbon (alkyl or aromatic) sides chains.
• Polar 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
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There are only 20 different amino acids in the proteins in humans.
There are many amino acids.
Amino acids
They are called α amino acids.
- Humans cannot synthesize 10 of these 20 amino acids. (Essential Amino Acids)
- They must be obtained from the diet (almost daily basis).
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Nonpolar amino acids
NH3+
COO-
NH3+
COO-
NH3+
COO-
NH3+
COO-
NH3+
COO-S
NH3+
COO-
NH H
COO-
NH3+
COO-
NH
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)
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NH3+
COO-
HS
NH3+
COO-
HO
Cysteine (Cys, C)
Tyrosine (Tyr, Y)
NH3+
COO-H2N
O
NH3+
COO-
H2N
O
NH3+
COO-
HO
NH3+
COO-OH
Asparagine (Asn, N)
Glutamine (Gln, Q)
Serine (Ser, S)
Threonine (Thr, T)
Polar amino acids
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NH3+
COO--O
O
NH3+
COO--O
O NH3+
COO-
NH
H2N
NH2+
NH3+
COO-
N
NH
NH3+
COO-H3N
Glutamic acid (Glu, E)
Aspartic acid (Asp, D)
Histidine (His, H)
Lysine (Lys, K)
Arginine (Arg, R)
+
Acidic and basic amino acids
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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.
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Ionization and pH
pH: 6 to 7 Isoelectric point (pI)
Positive charges = Negative chargesNo net charge (Neutral) - Zwitterion
pH: 3 or less -COO- acts as a base and accepts an H+
+
RH3N-CH-C-O
-O
+ H3O+ +
RH3N-CH-C-OH
O+H2O
pH: 10 or higher -NH3+ acts as an acid and loses an H+
+
RH3N-CH-C-O
-O
+ OH-
RH2N-CH-C-O
-O
+H2O
+
RH3N-CH-C-O
-O
+ OH-
RH2N-CH-C-O
-O
+H2O
-
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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 10.0Net charge +1 Net charge 0 Net charge -1
+
RH3N-CH-C-O
-O+
RH3N-CH-C-OH
O
RH2N-CH-C-O
-OOH-
H3O+
OH-
H3O+
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6.015.41
5.655.976.026.025.745.486.485.685.87
5.895.97
pI
valinetryptophan
threonineserineprolinephenylalaninemethionineleucineisoleucineglycineglutamine
asparaginealanine
Nonpolar &polar side chains
10.76
2.77
5.073.22
7.599.74
5.66
pI
tyrosine
lysinehistidine
glutamic acidcysteine
aspartic acid
arginine
AcidicSide Chains
BasicSide Chains pI
Ionization and pH
Each amino acid has a fixed and constant pI.
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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
CH3H3N O-
CH2OH
O
H3NN
CH3
O CH2OH
O
O-
H
H2O+
Alanine (Ala) Serine (Ser)
++
+
peptide bond
Alanylserine (Ala-Ser)
+
(amide bond)
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•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 30 to 50 amino acids joined by peptide bonds.
Peptide
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Naming of peptides
C-terminal amino acid: the amino acid at the end of the chain
having the free -COO- group.
N-terminal amino acid: the amino acid at the end of the chain
having the free -NH3+ group.
H3N
OH
NH O
HN
COO-
O-
OC6H5O
+
C-terminalamino acid
N-terminalamino acid
Ser-Phe-Asp
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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 alaninealanyl
From glycineglycyl
From serineserine
Alanylglycylserine(Ala-Gly-Ser)
+ -
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Structure of proteins
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
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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
CH3CH
CH O
O-CCH
H
N
O
CCH
H
N
O
CCH
H
N
O
C
CH3
CHH3N
+
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Cysteine
The -SH (sulfhydryl) group of cysteine is easily oxidized
to an -S-S- (disulfide).
+
CH2
H3N-CH-COO-
SH
oxidation
reduction
+
CH2
H3N-CH-COO-
S
+H3N-CH-COO
-CH2
S
CysteineCystine
2
a disulfidebond
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Primary Structure of proteins
Chain A
CO
O-
NH3+ NH3
+
CO
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.
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Secondary Structure of proteins
Describes the way the amino acids next to or near to each otheralong 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.
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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
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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.
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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).
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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-
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Tertiary Structure
(1) Disulfide (-S-S-)
(2) salt bridge (acid-base)(3) Hydrophilic (polar)(4) hydrophobic (nonpolar)(5) Hydrogen bond
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Globular proteins
- Have compact, spherical shape.
- 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).
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Fibrous proteins
α-keratin: hair, wool, skin, nails, and bone
- Have long, thin shape.
- Involve in the structure of cells and tissues.
Three α-helix bond together by disulfide bond (-S-S-)
-keratin: feathers of birds
Large amount of -pleated sheet
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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).
chain
chain
α chain
α chain
Hemoglobin
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Summary of protein Structure
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Summary of protein Structure
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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.
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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
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Enzymes
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Enzyme
Eact
Eact
- Like a catalyst, they increase the rate of the reactions (biological reactions).
- Lower the activation energy for the reaction.
2HIH2 + 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.
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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.
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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
(ES) complex.
• Forming and releasing products.
• E + S ES E + P Enzyme: globular protein
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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
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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.
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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
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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: 35°C or body temperature.
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pH
- Optimum pH: is 7.4 in our body.
- Lower or higher pH can change the shape of enzyme. (active site changes 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.
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Substrate and enzyme concentration
Maximum activity
Enzyme concentration ↑ Rate of reaction ↑
Substrate concentration ↑ First: Rate of reaction ↑
End: Rate of reaction reachesto its maximum: all of the enzymesare combined with substrates.
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Enzyme inhibition
Inhibitors cause enzymes to lose catalytic activity.
Competitive inhibitor
Noncompetitive inhibitor
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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.
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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.
- 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
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Enzyme cofactors
protein
protein
protein
Metal ion
Organicmolecules
(coenzyme)
Simple enzyme
Enzyme + Cofactor
Enzyme + Cofactor
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.
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Enzyme cofactors
- Enzyme and cofactors work together.
- Catalyze reactions properly.
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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.