Proteins, Enzymes, Vitamins, and Hormones: Study Guide for Exam #1 (CHEM 123)

Proteins and Amino Acids

Drawing Peptides and Amino Acids

Understanding the structure of amino acids and peptides is fundamental in biochemistry. Peptides are short chains of amino acids linked by peptide bonds.

• Amino Acid Structure: Each amino acid contains an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a unique side chain (R group) attached to a central carbon (the alpha carbon).

• Peptide Bond: Formed between the carboxyl group of one amino acid and the amino group of another, releasing water (a condensation reaction).

• Drawing Peptides: To draw a peptide, connect the amino acids in the correct sequence, showing the peptide bonds and the side chains.

• Example: For a dipeptide Gly-Ala, draw glycine and alanine linked by a peptide bond.

Ionization States at Different pH

The ionization state of amino acids and peptides depends on the pH of the environment relative to their pKa values.

• pKa: The pH at which a functional group is 50% ionized.

• pI (Isoelectric Point): The pH at which the amino acid has no net charge.

• At low pH: Amino and carboxyl groups are protonated (NH3+, COOH).

• At high pH: Groups are deprotonated (NH2, COO-).

• Example: At pH 1, both groups are protonated; at pH 12, both are deprotonated.

Protein Structure

Levels of Protein Structure

Proteins have four levels of structure, each stabilized by specific interactions.

• Primary Structure: The linear sequence of amino acids in a polypeptide chain, held together by covalent peptide bonds (backbone atoms).

• Secondary Structure: Local folding into alpha-helices and beta-sheets, stabilized by hydrogen bonds between backbone atoms.

• Tertiary Structure: The overall 3D shape of a single polypeptide, stabilized by hydrogen bonds, salt bridges (ionic interactions), hydrophobic interactions, and disulfide bonds (side chain atoms).

• Quaternary Structure: The arrangement of multiple polypeptide subunits, stabilized by the same forces as tertiary structure.

Protein Hydrolysis and Denaturation

Proteins can be broken down or lose their structure through hydrolysis and denaturation.

• Hydrolysis: The cleavage of peptide bonds by water, producing smaller peptides or amino acids.

• Denaturation: The loss of secondary, tertiary, or quaternary structure without breaking peptide bonds. Caused by heat, pH changes, detergents, or chemicals (e.g., urea, heavy metals).

• Regions Affected: Denaturation affects non-covalent interactions (hydrogen bonds, salt bridges, hydrophobic interactions), but not the primary structure.

• Example: Cooking an egg denatures egg white proteins.

Enzymes

Enzyme Inhibition

Enzyme activity can be regulated by inhibitors, which decrease the rate of catalysis.

• Competitive Inhibition: Inhibitor resembles the substrate and binds to the active site, blocking substrate binding. Can be overcome by increasing substrate concentration.

• Uncompetitive Inhibition: Inhibitor binds only to the enzyme-substrate complex, preventing the reaction from proceeding.

• Enzyme Kinetics: Competitive inhibition increases apparent Km (Michaelis constant), Vmax unchanged; uncompetitive inhibition decreases both Km and Vmax.

• Graphical Representation: Lineweaver-Burk plots show different patterns for each inhibition type.

$\text{Competitive Inhibition:} \\ \frac{1}{V_0} = \frac{K_m}{V_{max}} \cdot \frac{1}{[S]} \left(1 + \frac{[I]}{K_i}\right) + \frac{1}{V_{max}}$

$\text{Uncompetitive Inhibition:} \\ \frac{1}{V_0} = \frac{K_m}{V_{max}} \cdot \frac{1}{[S]} + \frac{1 + \frac{[I]}{K_i'}}{V_{max}}$

Enzyme Classification

Enzymes are classified into six major categories based on the reactions they catalyze.

Class	Type of Reaction	Example
Oxidoreductases	Oxidation-reduction	Dehydrogenase
Transferases	Transfer of functional groups	Kinase
Hydrolases	Hydrolysis reactions	Protease
Lyases	Addition/removal of groups to form double bonds	Decarboxylase
Isomerases	Isomerization	Racemase
Ligases	Bond formation with ATP hydrolysis	Synthetase

Enzyme Regulation

Enzyme activity is regulated by several mechanisms to maintain metabolic balance.

• Feedback Control: The end product of a pathway inhibits an earlier enzyme in the pathway.

• Proenzyme (Zymogen) Synthesis: Enzymes are synthesized in inactive forms and activated when needed.

• Allosteric Control: Effectors bind to sites other than the active site, modulating activity (positive or negative modulation).

• Protein Modification: Covalent modification (e.g., phosphorylation) alters enzyme activity.

• Genetic Control: Regulation of enzyme synthesis at the gene expression level.

Vitamins

Classification and Functions

Vitamins are essential organic compounds classified by their solubility.

Vitamin	Solubility	Role	Sources	Deficiency Effect	Excess Effect
Vitamin C	Water	Antioxidant, collagen synthesis	Citrus fruits	Scurvy	Gastrointestinal upset
Vitamin B12	Water	Red blood cell formation	Meat, dairy	Pernicious anemia	Rare
Vitamin A	Fat	Vision, immune function	Liver, carrots	Night blindness	Liver toxicity
Vitamin D	Fat	Calcium absorption	Sunlight, dairy	Rickets	Hypercalcemia

Additional info: Other water-soluble vitamins include B-complex vitamins; other fat-soluble vitamins include E and K.

Hormones

Types of Hormones

Hormones are classified by their chemical structure and mode of action.

Type	Structure	Mode of Action	Function
Amino Acid Derivative	Derived from amino acids (e.g., tyrosine)	Bind to cell surface receptors	Regulate metabolism (e.g., epinephrine)
Polypeptide	Short or long chains of amino acids	Bind to cell surface receptors	Regulate growth, metabolism (e.g., insulin)
Steroid	Derived from cholesterol	Bind to intracellular receptors	Regulate gene expression (e.g., cortisol)

Mode of Action: Epinephrine

Epinephrine (adrenaline) is a hormone that triggers the "fight or flight" response.

1. Epinephrine binds to beta-adrenergic receptors on the cell membrane.

2. Activates G-protein, which stimulates adenylate cyclase.

3. Adenylate cyclase converts ATP to cyclic AMP (cAMP).

4. cAMP activates protein kinase A, leading to phosphorylation of target proteins.

5. Results in increased glucose release and energy mobilization.

Mode of Action: Acetylcholine

Acetylcholine is a neurotransmitter and cholinergic messenger.

1. Acetylcholine is released from nerve endings into the synaptic cleft.

2. Binds to receptors on the postsynaptic membrane.

3. Triggers opening of ion channels, leading to depolarization and nerve impulse transmission.

4. Acetylcholine is rapidly broken down by acetylcholinesterase, terminating the signal.

Additional info: For more detailed mechanisms, refer to textbook figures and diagrams as indicated in the exam guidelines.