Biochemistry Essentials: Carbohydrates, Lipids, and Proteins

Carbohydrates: Structure and Classification

Classification

• Monosaccharides: Single sugar unit (e.g., glucose, fructose).
• Disaccharides: Two sugar units joined (e.g., sucrose = glucose + fructose).
• Polysaccharides: Many sugar units linked (e.g., starch, glycogen).

Aldose vs. Ketose

• Aldose: Contains an aldehyde (-CHO) group (e.g., glucose).
• Ketose: Contains a ketone (>C=O) group (e.g., fructose).
• Number of Carbons: Triose (3C), Tetrose (4C), Pentose (5C), Hexose (6C).

Structural vs. Stereoisomers

• Structural Isomers: Same molecular formula, different bonding patterns or structure.
• Stereoisomers: Same connectivity, different spatial arrangement of atoms.

Chiral Carbons

• Chiral Carbon: A carbon atom bonded to four different groups, creating an asymmetric center.
• Achiral Carbon: A carbon atom bonded to two or more identical groups.

Enantiomers

• Non-superimposable mirror images of each other (often designated as D vs. L forms).

Fischer Projections

• A 2D representation of a 3D molecule.
• Vertical lines represent bonds projecting away from the viewer.
• Horizontal lines represent bonds projecting toward the viewer.
• D or L Configuration: Determined by the position of the -OH group on the chiral carbon farthest from the carbonyl group (right = D, left = L).

D and L Sugars

• D-Sugars: Have the -OH group on the right side of the bottom-most chiral center in a Fischer projection.
• Most naturally occurring sugars are in the D configuration.

Open-Chain Forms

• Glucose and Galactose are common aldohexoses.
• Fructose is a common ketohexose.

Cyclic Forms

• Hexoses commonly form pyranose rings (6-membered rings).
• Fructose can form either a furanose (5-membered) or a pyranose ring.

Oxidation and Reduction

• Aldoses can be oxidized to carboxylic acids (e.g., glucose → gluconic acid).
• The carbonyl group can be reduced to an alcohol (e.g., glucose → sorbitol).

Reducing Sugars

• Sugars that can act as reducing agents because they possess a free aldehyde group or a hemiacetal group in equilibrium with an open-chain aldehyde form.
• Sucrose is a non-reducing sugar because it lacks a free carbonyl or hemiacetal group.

Disaccharide Linkages

• Formed by a glycosidic bond between the hydroxyl (-OH) groups of two monosaccharides.
• Named α or β depending on the configuration of the anomeric carbon involved in the bond.

Common Disaccharides

• Maltose: Glucose + Glucose (α-1,4 linkage).
• Lactose: Glucose + Galactose (β-1,4 linkage).
• Sucrose: Glucose + Fructose (α-1,β-2 linkage) – non-reducing.

Common Polysaccharides

• Amylose: Unbranched chain of glucose units (α-1,4 linkages); component of starch.
• Amylopectin: Branched chain of glucose units (α-1,4 linkages with α-1,6 branches); component of starch.
• Glycogen: Highly branched glucose polymer; energy storage in animals.
• Cellulose: Unbranched chain of glucose units (β-1,4 linkages); structural component in plants.

Alpha vs. Beta Glycosidic Bonds

• α-1,4 Linkages (e.g., in starch): Generally digestible by humans.
• β-1,4 Linkages (e.g., in cellulose): Generally not digestible by humans.

Digestibility

• Humans can digest starch (containing α-linkages) using enzymes like amylase.
• Humans cannot digest cellulose (containing β-linkages) because they lack the necessary enzyme (cellulase).

Lipids: Types, Structure, and Reactions

Lipid Classes

• Fatty Acids: Long hydrocarbon chains with a carboxyl group. Can be saturated (no C=C double bonds) or unsaturated (one or more C=C double bonds, usually cis).
• Triacylglycerols (Triglycerides): Esters formed from one glycerol molecule and three fatty acid molecules; main form of energy storage.
• Phospholipids: Composed of glycerol, two fatty acids, a phosphate group, and often an alcohol component; major components of cell membranes.
• Steroids: Characterized by a core structure of four fused carbon rings (the steroid nucleus). Examples include cholesterol, testosterone, estrogen.
• Waxes: Esters formed from a long-chain fatty acid and a long-chain alcohol; provide protective coatings.

Saturated vs. Unsaturated Fats

• Saturated Fats: Contain primarily saturated fatty acids, tend to be solid at room temperature (e.g., animal fats like butter, lard).
• Unsaturated Fats: Contain primarily unsaturated fatty acids, tend to be liquid at room temperature (e.g., plant oils like olive oil, canola oil).

Wax, Fat, and Oil Structure

• Ester Linkages: Formed between the carboxyl group of fatty acids and the hydroxyl group of glycerol (in fats/oils) or a long-chain alcohol (in waxes).
• Waxes: Fatty Acid + Long-Chain Alcohol.
• Triglycerides (Fats/Oils): 3 Fatty Acids + Glycerol.

Common Lipid Reactions

• Hydrogenation: Addition of hydrogen (H₂) across double bonds in unsaturated fatty acids, converting them to saturated fatty acids (e.g., converting oils to margarine).
• Hydrolysis: Breaking of ester bonds by adding water, yielding fatty acids and glycerol (or alcohol for waxes). Can be acid or enzyme-catalyzed.
• Saponification: Base-catalyzed hydrolysis of triacylglycerols (usually with NaOH or KOH), producing glycerol and fatty acid salts (soap).

Steroid Nucleus

• Consists of three six-membered rings and one five-membered ring fused together.
• Cholesterol is a key steroid, serving as a precursor for other steroids (like testosterone, estrogen) and a component of cell membranes.

Lipoproteins

• Complexes that transport lipids (like cholesterol and triglycerides) through the bloodstream.
• VLDL (Very Low-Density Lipoprotein): Primarily transports triglycerides synthesized in the liver to tissues.
• LDL (Low-Density Lipoprotein): Transports cholesterol to tissues; often referred to as "bad" cholesterol when levels are high.
• HDL (High-Density Lipoprotein): Transports excess cholesterol from tissues back to the liver; often referred to as "good" cholesterol.

Lipid Bilayer

• The fundamental structure of cell membranes, composed primarily of phospholipids.
• Phospholipids arrange themselves with their hydrophilic (polar) heads facing the aqueous environment (inside and outside the cell) and their hydrophobic (nonpolar) tails facing inward.
• Forms a selectively permeable barrier; described by the fluid mosaic model, indicating it's dynamic and contains embedded proteins.

Amino Acids, Proteins, and Enzymes Fundamentals

Protein Functions

• Diverse roles including: Structural support (e.g., collagen, keratin), Transport (e.g., hemoglobin), Enzymatic catalysis, Hormonal signaling (e.g., insulin), Defense (e.g., antibodies), Movement (e.g., actin, myosin).

Amino Acid Structure

• Basic building blocks of proteins.
• Contain a central alpha (α) carbon bonded to: an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom (-H), and a variable side chain (R group).

Classification by R Group

• Amino acids are categorized based on the properties of their R group:
• Nonpolar: Hydrophobic R groups.
• Polar: Neutral, hydrophilic R groups.
• Acidic: R groups containing a carboxyl group (negatively charged at physiological pH).
• Basic: R groups containing an amino group (positively charged at physiological pH).

Zwitterions

• At physiological pH (around 7.4), amino acids exist as zwitterions: molecules with both a positive charge (on the amino group, -NH₃⁺) and a negative charge (on the carboxyl group, -COO⁻), but an overall neutral charge.

Peptides

• Chains of amino acids linked by peptide bonds.
• Dipeptide: Two amino acids linked.
• Polypeptide: Many amino acids linked. A protein consists of one or more polypeptide chains.

Peptide Bonds

• An amide bond formed between the carboxyl group (-COOH) of one amino acid and the amino group (-NH₂) of another, with the removal of a water molecule.

Protein Structure Levels

• Primary Structure: The unique linear sequence of amino acids in a polypeptide chain.
• Secondary Structure: Localized folding patterns formed by hydrogen bonding between backbone atoms, such as the α-helix and β-pleated sheet.
• Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, determined by interactions between R groups (hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges).
• Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) in a functional protein complex (e.g., hemoglobin has four subunits).

Denaturation

• The disruption of the secondary, tertiary, and/or quaternary structure of a protein, leading to loss of biological function. Primary structure usually remains intact.
• Caused by factors like extreme heat, changes in pH, organic solvents (e.g., alcohol), or heavy metal ions.

Enzymes

• Biological catalysts, typically proteins, that speed up biochemical reactions without being consumed.
• Enzyme names often end in the suffix "-ase" (e.g., sucrase, lipase, polymerase).

Enzyme Function

• Enzymes lower the activation energy required for a reaction to occur.
• The reactant molecule(s) an enzyme acts upon is called the substrate.
• The substrate binds to a specific region on the enzyme called the active site, forming an enzyme-substrate complex, where catalysis occurs, converting substrate(s) to product(s).

Factors Affecting Enzyme Activity

• Temperature: Activity generally increases with temperature up to an optimal point; excessively high temperatures cause denaturation and loss of activity.
• pH: Each enzyme has an optimal pH range; extreme pH values can alter enzyme structure (denaturation) and affect the charge states of the active site and substrate, reducing activity. Many human enzymes function optimally around pH 7.4.
• Substrate Concentration: Increasing substrate concentration generally increases reaction rate until the enzyme becomes saturated (all active sites are occupied).
• Inhibitors: Substances that decrease enzyme activity.
  • Competitive Inhibitors: Bind to the active site, competing with the substrate.
  • Noncompetitive Inhibitors: Bind to a site other than the active site, changing the enzyme's shape and reducing its efficiency.