Ch 3 review

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Biomolecules and Isomerism

Isomers

Isomers are molecules that have the same molecular formula but different structural arrangements. This difference in structure can lead to distinct chemical and physical properties.

Definition: Isomers are compounds with the same chemical formula but different connectivity or spatial arrangement of atoms.
Types: Structural isomers (different connectivity), stereoisomers (same connectivity, different spatial arrangement).
Example: Glucose and fructose are structural isomers (both C6H12O6).

Geometric (cis/trans) Isomers

Geometric isomers are a type of stereoisomer where the arrangement of groups differs around a double bond or ring structure.

Definition: Geometric isomers have the same covalent arrangements but differ in spatial arrangements due to restricted rotation (e.g., double bonds).
Cis Isomer: Similar groups are on the same side of the double bond.
Trans Isomer: Similar groups are on opposite sides of the double bond.
Example: cis-2-butene vs. trans-2-butene.

Enantiomers (Optical Isomers)

Enantiomers are mirror-image isomers that cannot be superimposed on each other, often due to the presence of a chiral carbon.

Definition: Enantiomers are pairs of molecules that are non-superimposable mirror images.
Chirality: A carbon atom bonded to four different groups is called a chiral center.
Example: D- and L-glucose.

Functional Groups in Organic Molecules

Common Functional Groups

Functional groups are specific groups of atoms within molecules that are responsible for characteristic chemical reactions.

Hydroxyl Group (-OH): Found in alcohols; increases solubility in water.
Carbonyl Group (C=O): Found in aldehydes (at the end of a molecule) and ketones (within the molecule).
Carboxyl Group (-COOH): Acts as an acid; can be ionized (-COO-).
Amino Group (-NH2): Acts as a base; can be ionized (-NH3+).
Sulfhydryl Group (-SH): Found in thiols; can form disulfide bridges (S-S) in proteins.
Phosphate Group (-PO4): Important in energy transfer (ATP); can be ionized.

Recognizing Functional Groups

Hydroxyl Group: -OH attached to a carbon.
Carbonyl Group: C=O at the end (aldehyde) or within (ketone) a molecule.
Carboxyl Group: -COOH (unionized), -COO- (ionized).
Amino Group: -NH2 (unionized), -NH3+ (ionized).
Sulfhydryl Group: -SH; forms disulfide bridges (S-S).
Phosphate Group: -PO4; can be ionized or non-ionized.

Table: Functional Groups and Their Properties

Functional Group	Structure	Properties
Hydroxyl	-OH	Polar, forms hydrogen bonds
Carbonyl (Aldehyde)	CHO	Polar, reactive
Carbonyl (Ketone)	CO	Polar, reactive
Carboxyl	-COOH	Acidic, can ionize
Amino	-NH2	Basic, can ionize
Sulfhydryl	-SH	Forms disulfide bonds
Phosphate	-PO4	Acidic, energy transfer

Macromolecules: Carbohydrates, Proteins, and Lipids

Monomers, Subunits, and Residues

Macromolecules are large molecules made up of smaller units called monomers. In proteins, these are called residues.

Monomer: Single building block (e.g., amino acid, monosaccharide).
Subunit: A component of a larger structure.
Residue: A monomer within a polymer chain.

Condensation (Dehydration) and Hydrolysis Reactions

Macromolecules are formed and broken down by specific chemical reactions.

Condensation/Dehydration Reaction: Two monomers join, releasing water.
Hydrolysis Reaction: A polymer is split into monomers by adding water.
Equation:

(condensation)

(hydrolysis)

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen, typically with the formula (CH2O)n.

Definition: Carbohydrates are sugars and their polymers.
Monosaccharide: Simple sugar (e.g., glucose, fructose).
Disaccharide: Two monosaccharides joined (e.g., sucrose).
Polysaccharide: Many monosaccharides joined (e.g., starch, glycogen, cellulose).
Naming: Sugars often end in "-ose" (e.g., glucose, fructose); enzymes end in "-ase" (e.g., sucrase).
Types: Aldose (aldehyde group), ketose (ketone group), triose (3C), pentose (5C), hexose (6C).

Ring Structures and Conformations

Monosaccharides can exist in different ring conformations, commonly alpha (α) and beta (β).

α and β Conformations: Differ in the position of the hydroxyl group on the anomeric carbon.
Example: α-glucose vs. β-glucose.

Polysaccharides: Starch, Glycogen, and Cellulose

Starch: Storage polysaccharide in plants; composed of α-glucose.
Glycogen: Storage polysaccharide in animals; highly branched.
Cellulose: Structural polysaccharide in plants; composed of β-glucose.
Similarities: Both starch and glycogen are energy storage molecules.
Differences: Glycogen is more branched than starch; cellulose has different glycosidic bonds.

Proteins and Amino Acids

Amino Acids

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

General Structure: Central (α) carbon, amino group (-NH2), carboxyl group (-COOH), hydrogen, and R group.
Chiral Carbon: All amino acids except glycine have a chiral (asymmetric) carbon.
Subunits: Amino acids are called residues when incorporated into proteins.
Polypeptide: Another name for a protein chain.

Protein Structure

Proteins have four levels of structure, each contributing to their function.

Primary Structure: Sequence of amino acids.
Secondary Structure: Local folding (α-helix, β-sheet) stabilized by hydrogen bonds.
Tertiary Structure: 3D folding due to interactions among R groups.
Quaternary Structure: Association of multiple polypeptide chains.

Table: Levels of Protein Structure

Level	Description	Stabilizing Forces
Primary	Amino acid sequence	Peptide bonds
Secondary	α-helix, β-sheet	Hydrogen bonds
Tertiary	3D folding	Hydrophobic interactions, disulfide bridges, ionic bonds
Quaternary	Multiple polypeptides	Same as tertiary, plus subunit interactions

Denaturation, Renaturation, and Degradation

Denaturation: Loss of protein structure due to environmental changes (heat, pH, chemicals).
Renaturation: Regaining native structure under favorable conditions.
Degradation: Breakdown of protein into amino acids.

Amino Acid Abbreviations

Three-letter codes: e.g., Ala (Alanine), Gly (Glycine).
One-letter codes: e.g., A (Alanine), G (Glycine).

Lipids

Types of Lipids

Lipids are hydrophobic molecules including fats, oils, phospholipids, and steroids.

Fatty Acid: Long hydrocarbon chain with a carboxyl group.
Triacylglycerol (Triglyceride): Three fatty acids linked to glycerol.
Phospholipid: Two fatty acids, glycerol, and a phosphate group.
Sterol: Lipid with a four-ring structure (e.g., cholesterol).

Saturated vs. Unsaturated Fats

Saturated Fat: No double bonds; solid at room temperature.
Unsaturated Fat: One or more double bonds; liquid at room temperature.

Phospholipids and Membranes

Phospholipids form bilayers in aqueous solutions, with hydrophilic heads facing water and hydrophobic tails facing inward.

Major Parts: Glycerol backbone, two fatty acids, phosphate group.
Bilayer Structure: Polar heads (hydrophilic) face outward; nonpolar tails (hydrophobic) face inward.

Table: Lipid Types and Structures

Lipid Type	Structure	Function
Fatty Acid	Hydrocarbon chain + carboxyl group	Energy storage
Triglyceride	Glycerol + 3 fatty acids	Energy storage
Phospholipid	Glycerol + 2 fatty acids + phosphate	Membrane structure
Sterol	Four fused rings	Membrane fluidity, hormones

Sterols

Examples: Cholesterol, testosterone, estrogen.
Differences: Side chains and functional groups attached to the ring structure.

Amino Acid Groupings

Grouped by: Polarity, charge, hydrophobicity.
Examples: Nonpolar (Leucine), polar (Serine), acidic (Aspartic acid), basic (Lysine).

Additional info: This guide covers foundational concepts in biomolecule structure and function, suitable for introductory college biology.