1 functions of proteins proteins perform many different functions in the body
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Functions of Proteins
Proteins perform many different functions in the body.
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Amino Acids
Amino acids • are the building blocks of proteins.• contain a carboxylic acid group and an amino group on
the alpha () carbon.• are ionized in solution.• each contain a different side group (R).
R side chain R │ + │H2N—C —COOH H3N—C —COO−
│ │ H H Zwitterion (ionized form)
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Examples of Amino Acids
H + │H3N—C—COO−
│ H Glycine
CH3
+ │H3N—C—COO−
│ H Alanine
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• must be obtained from the diet.
• are 10 amino acids not synthesized by the body.
• are in meat and dairy products.
• are missing (one or more) in grains and vegetables.
Essential Amino Acids
Essential amino acids
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Types of Amino Acids
Amino acids are classified as
• nonpolar (hydrophobic) with hydrocarbon side chains.
• polar (hydrophilic) with polar or ionic side chains.
• acidic (hydrophilic) with acidic side chains.
• basic (hydrophilic) with –NH2 side chains.
Nonpolar Polar
AcidicBasic
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Nonpolar Amino Acids
An amino acid is nonpolar when the R group is H, alkyl, or aromatic.
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Polar Amino Acids
An amino acid is polar when the R group is an alcohol, thiol, or amide.
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Acidic and Basic Amino Acids
An amino acid is • acidic when the R group is a carboxylic acid.• basic when the R group is an amine.
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Solution
Identify each as (1) polar or (2) nonpolar.
+
A. H3N–CH2–COO− Glycine (2) nonpolar
CH3
| CH–OH + │
B. H3N–CH–COO − Threonine (1) polar
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A zwitterion
• has charged −NH3+ and COO– groups.
• forms when both the –NH2 and the –COOH groups in an amino acid ionize in water.
• has equal + and – charges at the isoelectric point (pI).
O O ║ + ║
NH2—CH2—C—OH H3N—CH2—C—O–
Glycine Zwitterion of glycine
Zwitterions
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In solutions more basic than the pI,
• the —NH3+ in the amino acid donates a proton.
+ OH–
H3N—CH2—COO– H2N—CH2—COO– Zwitterion Negative ion at pI pH > pI
Charge: 0 Charge: 1-
Amino Acids as Acids
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In solution more acidic than the pI,• the COO– in the amino acid accepts a proton.
+ H+ +
H3N—CH2—COO– H3N—CH2—COOH Zwitterion Positive ionat pI pH< pI
Charge: 0 Charge: 1+
Amino Acids as Bases
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pH and ionization
H+ OH–
+ +
H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–
Positive ion Zwitterion Negative ion
low pH pI high pH
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The Peptide Bond
A peptide bond• is an amide bond. • forms between the carboxyl group of one amino acid and
the amino group of the next amino acid.
O CH3 O
+ || + | ||H3N—CH2—C—O– + H3N—CH—C—O–
O H CH3 O + || | | ||
H3N—CH2—C—N—CH—C—O– peptide bond
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Formation of a Dipeptide
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Solution
Write the dipeptide Ser-Thr. OH CH3
| | CH2 O HCOH O + | ║ + | ║
H3N─CH─C─O– + H3N─CH─C─O– Ser Thr
OH CH3
| | CH2 O H HCOH O + | ║ | | ║
NH3─CH─C─N ─CH─ C─O– + H2O
Ser-Thr
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Naming Dipeptides
A dipeptide • is named from the free amine (NH3
+) using a -yl ending for the name.
• names the last amino acid with the free carboxyl group (COO–) by its amino acid name.
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Write the names and three-letter abbreviations of the tripeptides that could form from two glycine and one alanine.
Glycylglycylalanine Gly-Gly-Ala
Glycylalanylglycine Gly-Ala-Gly
Alanylglycylglycine Ala-Gly-Gly
Solution
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Solution
Tripeptides possible from one each of leucine, glycine, and alanine:
Leu-Gly-Ala
Leu-Ala-Gly
Ala-Leu-Gly
Ala-Gly-Leu
Gly-Ala-Leu
Gly-Leu-Ala
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Learning Check
Write the three-letter abbreviation and name for the
following tetrapeptide.
CH3
│ CH3 S │ │ CH–CH3 SH CH2
│ │ │ CH3 O H CH O H CH2 O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║H3N–CH–C–N–CH–C–N–CH–C–N–CH–C–O–
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Solution
Ala-Leu-Cys-Met Alanylleucylcysteinylmethionine
CH3
│ CH3 S │ │ CH–CH3 SH CH2
│ │ │ CH3 O H CH O H CH2 O H CH2 O
+ │ ║ │ │ ║ │ │ ║ │ │ ║H3N–CH–C–N–CH–C–N–CH–C–N–CH–C–O–
Ala Leu Cys Met
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Primary Structure of Proteins
The primary structure of a protein is• the particular sequence of amino acids.• the backbone of a peptide chain or
protein.
Ala─Leu─Cys─Met
CH3
SH
CH2
CH3
S
CH2
CH2CH O
O-CCH
H
N
O
CCH
H
N
O
CCH
H
N
O
CCHH3N
CH3
CH3CH
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Primary Structures
• The nonapeptides oxytocin and vasopressin have similar primary structures.
• Only the amino acids at positions 3 and 8 differ.
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Primary Structure of Insulin
Insulin• was the first protein to have its
primary structure determined.• has a primary structure of two
polypeptide chains linked by disulfide bonds.
• has a chain A with 21 amino acids and a chain B with 30 amino acids.
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Secondary Structure–Alpha Helix
The secondary structure of analpha helix is• a three-dimensional spatial
arrangement of amino acids in a polypeptide chain.
• 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.
• a corkscrew shape that looks like a coiled “telephone cord.”
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Secondary Structure–Beta-Pleated Sheet
The secondary structure of a beta-pleated sheet• consists of polypeptide chains arranged side by side.• has hydrogen bonds between chains.• has R groups above and below the sheet.• is typical of fibrous proteins, such as silk.
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Tertiary Structure
The tertiary structureof a protein • is an overall 3-
dimensional shape.• is determined by
attractions and repulsions between the side chains of the amino acids in a peptide chain.
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Crosslinks in Tertiary Structures
Crosslinks in tertiary structures involve attractions and repulsions between the side chains of the amino acids in the polypeptide chain.
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Select the type of tertiary interaction.
1) disulfide 2) ionic
3) H bonds 4) hydrophobic
A. leucine and valine
B. two cysteines
C. aspartic acid and lysine
D. serine and threonine
Learning check
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Select the type of tertiary interaction.
1) disulfide 2) ionic
3) H bonds 4) hydrophobic
A. 4 leucine and valine
B. 1 two cysteines
C. 2 aspartic acid and lysine
D. 3 serine and threonine
Solution
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Globular Proteins
Globular proteins • have compact, spherical
shapes.• carry out synthesis,
transport, and metabolism in the cells.
• such as myoglobin store and transport oxygen in muscle.
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Quaternary Structure
The quaternary structure • is the combination of two
or more protein units.• of hemoglobin consists
of four polypeptide chains as subunits.
• is stabilized by the same interactions found in tertiary structures.
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Fibrous Proteins
Fibrous proteins• consist of long, fiber-like shapes.• such as alpha keratins make up hair, wool, skin, and
nails.• such as feathers contain beta keratins with large
amounts of beta-pleated sheet structures.
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Summary of Protein Structure
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Summary of Protein Structure
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Identify the level of protein structure.
1) primary 2) secondary
3) tertiary 4) quaternary
A. beta-pleated sheet
B. order of amino acids in a protein
C. a protein with two or more peptide chains
D. the shape of a globular protein
E. disulfide bonds between R groups
Learning Check
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Identify the level of protein structure.1) primary 2) secondary3) tertiary 4) quaternary
A. 2 beta-pleated sheetB. 1 order of amino acids in a proteinC. 4 a protein with two or more peptide chainsD. 3 the shape of a globular proteinE. 3 disulfide bonds between R groups
Solution
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Denaturation involves • the disruption of bonds in the secondary, tertiary,
and quaternary protein structures.• heat and organic compounds that break apart H
bonds and disrupt hydrophobic interactions.• acids and bases that break H bonds between polar
R groups and disrupt ionic bonds.• heavy metal ions that react with S-S bonds to form
solids.• agitation such as whipping that stretches peptide
chains until bonds break.
Denaturation
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Denaturation of protein occurs when• an egg is cooked. • the skin is wiped with
alcohol.• heat is used to cauterize
blood vessels.• instruments are
sterilized in autoclaves.
Applications of Denaturation
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Enzymes are Biological Catalysts
Enzymes are proteins that
• Catalyze nearly all the chemical reactions taking place in the cells of the body.
• Increase the rate of reaction by lowering the energy of activation.
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Lock-and-Key Model
In the lock-and-key model, the• active site has a rigid shape.• enzyme only binds substrates that exactly fit the
active site.• enzyme is analogous to a lock.• substrate is the key that fits that lock.
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Induced-Fit Model
In the 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.• shape changes improve catalysis during reaction.
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The name of an enzyme
• usually ends in –ase.
• identifies the reacting substance. For example, sucrase catalyzes the reaction of sucrose.
• describes the function of the enzyme. For example, oxidases catalyze oxidation.
• could be a common name, particularly for the digestion enzymes, such as pepsin and trypsin.
Names of Enzymes
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Enzymes are classified by the reaction they catalyze.
Class Type of Reactions CatalyzedOxidoreductases Oxidation-reductionTransferases Transfer groups of atomsHydrolases HydrolysisLyases Add atoms/remove atoms to or
from a double bondIsomerases Rearrange atomsLigases Use ATP to combine small molecules
Classification of Enzymes
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Match the type of reaction with an enzyme
1) aminase 2) dehydrogenase
3) isomerase 4) synthetase
A. 3 Converts a cis-fatty acid to a trans-fatty acid.
B. 2 Removes 2 H atoms to form double bond.
C. 4 Combines two molecules to make a new compound.
D. 1 Adds NH3.
Solution
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Enzymes• are most active at an
optimum temperature (usually 37 °C in humans).
• show little activity at low temperatures.
• lose activity at high temperatures as denaturation occurs.
Temperature and Enzyme Action
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Enzymes• are most active at
optimum pH.• contain R groups of
amino acids with proper charges at optimum pH.
• lose activity in low or high pH as tertiary structure is disrupted.
pH and Enzyme Action
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Optimum pH Values
Enzymes in• the body have an optimum pH of about 7.4.• certain organs operate at lower and higher optimum pH
values.
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Substrate Concentration
As substrate concentration increases, • the rate of reaction
increases (at constant enzyme concentration).
• the enzyme eventually becomes saturated, giving maximum activity.
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Sucrase has an optimum temperature of 37 °C and an optimum pH of 6.2. Determine the effect of the following on its rate of reaction.
1) no change 2) increase 3) decrease
A. 2 Increasing the concentration of sucrase
B. 3 Changing the pH to 4
C. 3 Running the reaction at 70 °C
Solution
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Inhibitors• are molecules that cause a loss of catalytic activity.• prevent substrates from fitting into the active sites.
E + S ES E + P
E + I EI no P
Enzyme Inhibition
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Competitive Inhibition
A competitive inhibitor• has a structure that is
similar to that of the substrate.
• competes with the substrate for the active site.
• has its effect reversed by increasing substrate concentration.
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A noncompetitive inhibitor• has a structure that is much
different than the substrate.• distorts the shape of the
enzyme, which alters the shape of the active site.
• prevents the binding of the substrate.
• cannot have its effect reversed by adding more substrate.
Noncompetitive Inhibition
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Identify each description as an inhibitor that is
1) competitive or 2) noncompetitive.
A. 1 Increasing substrate reverses inhibition.B. 2 Binds to enzyme surface, but not to the active site.C. 1 Structure is similar to substrate.D. 2 Inhibition is not reversed by adding more
substrate.
Solution