Page 1

Title: Biomolecules: Proteins and Nucleic Acids

Author: Oluwatosin B. Adu

Course: BIO 101

Page 2

Proteins

• Definition: Large organic molecules made of chains of amino acids.

• Etymology: "Protein" comes from Greek "proteios" meaning "holding first place."

• Functions:

  • Control metabolism, cell growth, and neurotransmission.

  • Provide structure and can act as energy sources.

  • Enzymatic Role: Crucial for enabling chemical reactions necessary for life.

• Structure:

  • Polymers of amino acids.

  • Amino acids are linked by peptide bonds.

• Common Amino Acids: Twenty different amino acids.

Page 3

Amino Acids

• All 20 common amino acids are α-amino acids.

• Structure:

  • Have a carboxyl group and an amino group attached to the same carbon atom (α carbon).

  • Different in their R groups (side chains), affecting structure, size, charge, and water solubility.

• Abbreviations: Each has a three-letter abbreviation and one-letter symbol used for shorthand notation.

Page 4

Amino Acid Structure

• Configuration (except glycine):

  • α-carbon bonded to four different groups: carboxyl, amino, R group, and hydrogen.

• Chiral Center: α-carbon is a chiral center, leading to two stereoisomers, D and L.

• Protein Composition: Only L stereoisomers are found in protein molecules.

• Rare occurrence of D-amino acids in small peptides like some bacterial cell walls.

Page 5

Zwitter ions

• At neutral pH, amino acids exist primarily as zwitterions.

• Structure:

  • Amino group: positive charge (NH3+).

  • Carboxyl group: negative charge (CO2−).

• Properties: Amphoteric; can act as both acid and base.

Page 6

Classification of Amino Acids

Based on R-Group Nature:

1. Nonpolar, aliphatic (e.g., Gly, Ala, Val)

2. Aromatic (e.g., Phe, Tyr, Trp)

3. Polar, uncharged (e.g., Ser, Thr, Cys)

4. Positive charged (acidic) (e.g., Lys, His, Arg)

5. Negative charged (basic) (e.g., Asp, Glu)

Page 7

Classification Based on Metabolic Fate:

• Glucogenic: Contribute to glucose generation (e.g., Phe, Tyr, Ile).

• Ketogenic: Convert to ketone bodies (e.g., Leu, Lys).

• Some, like Trp, Phe, and Tyr, are both glucogenic and ketogenic.

Nutritional Needs:

• Essential Amino Acids: Cannot be synthesized; obtained from diet (e.g., His, Ile).

• Nonessential Amino Acids: Can be synthesized (e.g., Pro, Ser).

• Essential amino acids for children: 10; for adults: 8.

Page 8

Assignment

• List all 20 amino acids along with their three-letter and one-letter notations.

• Classify based on the three criteria discussed previously.

Page 9

Proteins

• Peptide Formation:

  • Two amino acids linked via peptide bond = dipeptide.

  • Three amino acids: tripeptide (uses two peptide bonds).

  • Oligopeptides: few amino acids; polypeptides: many; proteins: thousands.

• Molecular weights: Polypeptides <10,000, proteins >10,000.

• N-Terminal and C-Terminal Residues: Defined by free amino and carboxyl groups at the ends respectively.

Page 10

Conjugated Proteins

• Simple Proteins: Only amino acid residues (e.g., chymotrypsin).

• Conjugated Proteins: Include additional chemical components (prosthetic groups).

• Classification Examples:

  • Glycoproteins = Protein + Sugar.

Page 11

Structural Organization of Proteins

• Conformation: Spatial arrangement essential for function.

• Levels of Structure:

  • Primary Structure: Linear sequence of amino acids.

  • Secondary Structure: Formed by twisting; stabilized by hydrogen bonds.

Page 12

Common Secondary Structures:

• α-helix: Left-handed spiral, common in globular proteins (e.g., hormones).

• β-pleated sheet: Crimped shape, found in structural proteins (e.g., silk).

Page 13

Tertiary and Quaternary Structure

• Tertiary Structure: 3D shape of a folded amino acid chain stabilized by various bonds.

• Quaternary Structure: Formed from multiple polypeptide associations (e.g., hemoglobin).

Page 14

Functions of Proteins

• Enzymes: Speed up chemical reactions.

• Structural Role: Part of plasma membranes and cytoskeletal proteins.

• Support Cells: Extracellular matrix proteins (e.g., collagen).

Page 15

• Transport: Regulate material movement in and out of cells.

• Cellular Identity: Glycoproteins mark cell types.

• Motility: Cytoskeletal proteins facilitate movement.

• Communication: Signaling receptors, e.g., insulin.

• Organization: Chaperone proteins assist in folding and positioning.

Page 16

Nucleic Acids

• Importance: Nucleotides drive biochemical reactions and are fundamental to RNA and DNA structure.

• Structure: Comprised of a nitrogenous base, pentose sugar, and phosphate groups.

• Nucleoside: Molecule without a phosphate.

Page 17

Nucleotide Structure

• Features: Composed of purine and pyrimidine bases.

Page 18

Major Bases in Nucleic Acids

• Purines: Adenine (A), Guanine (G).

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

Page 19

Pentoses

• DNA contains 2'-deoxy-D-ribose; RNA contains D-ribose.

• Both exist in β-furanose form.

Page 20

Nucleic Acid Linkages

• Nucleotide chains linked by phosphodiester bonds.

• Structure: Alternating phosphate and pentose residues with nitrogenous bases.

• Definitions: Oligonucleotides (≤50 nucleotides), polynucleotides (>50).

Page 21

Covalent Backbone Structure in Nucleic Acids

• Illustration of phosphodiester linkages in DNA and RNA.

Page 22

Primary Structure of Nucleic Acids

• Sequence of nucleotides determines the primary structure.

• Differences between DNA and RNA:

  • Thymine in DNA, Uracil in RNA.

  • Deoxyribose in DNA, Ribose in RNA.

• DNA: Double-stranded; RNA: Single-stranded.

Page 23

DNA Structure

• Secondary Structure: Double helix; visualized as a twisted ladder.

• Components:

  • Sides: Sugar-phosphate backbones.

  • Rungs: Nitrogenous bases linked by hydrogen bonds.

Page 24

Antiparallel Structure

• DNA chains are antiparallel, maintained by hydrogen bonds between bases.

• Base Pairing: A with T, C with G; complementary base rule: A=T and C=G.

Page 25

Functions of DNA and RNA

• DNA: Information storage, determines organism characteristics.

• RNA: Involved in decoding DNA for protein synthesis and structuring cellular components.

Page 26

Types of RNA

• Messenger RNA (mRNA): Carries DNA's protein code to ribosomes.

• Transfer RNA (tRNA): Matches amino acids to the mRNA code.

• Ribosomal RNA (rRNA): Forms part of the ribosome structure.