BIO 101- Proteins and Nucleic acid
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Title: Biomolecules: Proteins and Nucleic Acids
Author: Oluwatosin B. Adu
Course: BIO 101
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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.
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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.
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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.
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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.
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Classification of Amino Acids
Based on R-Group Nature:
Nonpolar, aliphatic (e.g., Gly, Ala, Val)
Aromatic (e.g., Phe, Tyr, Trp)
Polar, uncharged (e.g., Ser, Thr, Cys)
Positive charged (acidic) (e.g., Lys, His, Arg)
Negative charged (basic) (e.g., Asp, Glu)
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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.
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Assignment
List all 20 amino acids along with their three-letter and one-letter notations.
Classify based on the three criteria discussed previously.
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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.
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Conjugated Proteins
Simple Proteins: Only amino acid residues (e.g., chymotrypsin).
Conjugated Proteins: Include additional chemical components (prosthetic groups).
Classification Examples:
Glycoproteins = Protein + Sugar.
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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.
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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).
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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).
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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).
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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.
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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.
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Nucleotide Structure
Features: Composed of purine and pyrimidine bases.
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Major Bases in Nucleic Acids
Purines: Adenine (A), Guanine (G).
Pyrimidines: Cytosine (C), Thymine (T in DNA), Uracil (U in RNA).
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Pentoses
DNA contains 2'-deoxy-D-ribose; RNA contains D-ribose.
Both exist in β-furanose form.
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Nucleic Acid Linkages
Nucleotide chains linked by phosphodiester bonds.
Structure: Alternating phosphate and pentose residues with nitrogenous bases.
Definitions: Oligonucleotides (≤50 nucleotides), polynucleotides (>50).
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Covalent Backbone Structure in Nucleic Acids
Illustration of phosphodiester linkages in DNA and RNA.
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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.
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DNA Structure
Secondary Structure: Double helix; visualized as a twisted ladder.
Components:
Sides: Sugar-phosphate backbones.
Rungs: Nitrogenous bases linked by hydrogen bonds.
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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.
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Functions of DNA and RNA
DNA: Information storage, determines organism characteristics.
RNA: Involved in decoding DNA for protein synthesis and structuring cellular components.
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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.