Proteins, Enzymes, and Nucleic Acids: Structure and Function in General Biology

Proteins and Amino Acids

Structure of Amino Acids

Amino acids are the building blocks of proteins, each containing a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

• Central group: $\ce{C}$ atom with four different groups attached.

• Amino group: $\ce{-NH2}$ (basic, can accept hydrogen).

• Carboxyl group: $\ce{-COOH}$ (acidic, can donate hydrogen).

• Side chain (R group): Determines the properties and reactivity of the amino acid.

Nature of Side Chains

The side chains (R groups) of amino acids affect their chemical reactivity and solubility.

• Functional groups: Affect reactivity and participation in chemical reactions.

• Polarity: Side chains can be hydrophilic (water-loving) or hydrophobic (water-repelling).

• Types of amino acids:

  • Nonpolar

  • Polar

  • Basic

  • Acidic

Connecting Amino Acids

Amino acids are linked together by peptide bonds to form polypeptides and proteins.

• Monomer: Single amino acid.

• Polymer: Chain of amino acids (polypeptide).

• Condensation (dehydration) reaction: Forms peptide bonds by removing water. This process is endothermic (requires energy).

• Hydrolysis: Breaks peptide bonds by adding water.

Protein Structure

Peptide Backbone

The peptide backbone is formed by repeating units of amino acids linked by peptide bonds.

• Directionality: Proteins have an N-terminus (amino end) and a C-terminus (carboxyl end).

• Oligopeptide: < 50 amino acids.

• Polypeptide: > 50 amino acids.

Levels of Protein Structure

• Primary structure: Sequence of amino acids in a protein.

• Secondary structure: Formed by hydrogen bonding between backbone atoms (e.g., alpha helices, beta sheets).

• Tertiary structure: Overall 3D shape formed by interactions between side chains (R groups).

• Quaternary structure: Multiple polypeptide chains interacting to form a functional protein.

Interactions Involving Side Chains

• Hydrogen bonding

• Van der Waals interactions

• Covalent bonds (e.g., disulfide bridges)

• Ionic bonding

Protein Folding and Function

Protein Folding

Protein folding is directed by the amino acid sequence and is essential for proper function.

• Denatured proteins lose their structure and function.

• Chaperone proteins help facilitate proper folding and prevent aggregation.

Protein Function Regulation

Protein function can be regulated by changes in shape (conformation) and by external signals.

• Example: Calmodulin regulates blood vessel diameter.

Prions

Prions are infectious proteins that can cause neurodegenerative diseases by inducing abnormal folding in normal proteins.

• Examples: Bovine spongiform encephalopathy (mad cow disease), Creutzfeldt-Jakob disease, Scrapie.

Enzymes and Catalysis

Enzymes as Catalysts

Enzymes are biological catalysts that increase the rate of chemical reactions by lowering activation energy.

• Organic catalysts: Proteins (enzymes).

• Cofactors: Inorganic ions (e.g., Fe2+, Zn2+).

• Coenzymes: Organic molecules (e.g., vitamins, NAD+, FAD).

Effect of Enzymes on Reactions

• Enzymes lower the activation energy ($E_a$) required to start a chemical reaction.

Enzyme Physiology

• Substrate: Molecule that enzyme acts on.

• Active site: Region of enzyme where substrate binds; shape is complementary to substrate.

• Induced fit model: Enzyme changes shape to fit substrate upon binding.

Factors Affecting Enzyme Activity

• Temperature

• pH

• Substrate concentration

• Presence of inhibitors

Enzyme Categories

• Hydrolases: Break down molecules by adding water.

• Isomerases: Rearrange atoms within molecules.

Nucleic Acids

Structure and Components

Nucleic acids (DNA and RNA) are polymers made of nucleotide monomers.

• Phosphate group

• 5-carbon sugar: Ribose (RNA) or deoxyribose (DNA)

• Nitrogenous base: Purines (A, G), Pyrimidines (C, T, U)

Types of Nucleotides

• Ribonucleic acid (RNA): Single-stranded, bases A, U, G, C

• Deoxyribonucleic acid (DNA): Double-stranded, bases A, T, G, C

Nitrogenous Bases

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only)

Formation of Nucleic Acids

• Nucleotides are linked by phosphodiester bonds via condensation reactions.

• Directionality: 5' to 3' end.

DNA Structure and Replication

• Double helix structure discovered by Watson and Crick, with key data from Rosalind Franklin.

• Base pairing: A-T (2 hydrogen bonds), G-C (3 hydrogen bonds).

• DNA replication: Strands separate, each serves as a template for new strand synthesis.

RNA Structure

• Single-stranded

• Sugar is ribose

• Bases: A, U, G, C

HTML Table: Comparison of DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double-stranded	Single-stranded
Bases	A, T, G, C	A, U, G, C
Function	Genetic material	Protein synthesis, regulation

Key Equations

• Peptide bond formation: $\ce{Amino ext{-}acid_1} + \ce{Amino ext{-}acid_2} \rightarrow \ce{Dipeptide} + \ce{H2O}$

• Phosphodiester bond formation: $\ce{Nucleotide_1} + \ce{Nucleotide_2} \rightarrow \ce{Dinucleotide} + \ce{H2O}$

Additional info:

• Chaperone proteins are specialized proteins that assist in the proper folding of other proteins.

• Enzyme inhibitors can be competitive (bind to active site) or noncompetitive (bind elsewhere).