Biochemistry: Molecules and Macromolecules

• Biochemistry test notes cover these topics:
  • Properties of polar molecules
  • Functional groups in molecules
  • Macromolecules
  • Lipids
  • Proteins
  • Nucleic acids,
  • Function of the four macromolecules
  • Biochemical reactions
  • Enzymes
  • Cell membrane
  • Passive vs active transport

Properties of a Polar Molecule

• Polar molecules have partial positive and negative charges due to unequal electron sharing.
• This polarity enables hydrogen bonds with other polar molecules/ions and water (H2O) is a polar molecule.
• Molecular shape determines polarity; tetrahedral, trigonal planar, and linear shapes are non-polar.
• Dipole symmetry changes impact polarity.

Functional Groups in a Molecule

• Functional groups are specific atom groups that give molecules unique chemical properties.
• Hydroxyl (-OH): polar, found in carbohydrates, nucleic acids, proteins, and lipids.
• Carbonyl (C=O): polar, found in carbohydrates and nucleic acids.
• Carboxyl (-COOH): polar-acidic (donates a proton), found in proteins and lipids.
• Amino (-NH2): polar-basic (accepts a proton), found in proteins and nucleic acids.
• Sulfhydryl (-SH): slightly polar, found in proteins.
• Phosphate (PO4): polar negatively charged, found in nucleic acids.
• Amide (R-CO-NR'R"): polar, found in proteins, amino acids, DNA, and hormones.
• Ether (R-O-R'): slightly polar, found in carbohydrates and lipids like essential oils.
• Ester (R-COOR'): polar, found in lipids and triglycerides.

Macromolecules

• Monomers are small, basic building block units.
• Polymers are large molecules from monomers linking via condensation (dehydration) reactions

Carbohydrates

• Carbohydrates consist of C, H, and O in a 1:2:1 ratio (ex: CH2O) and are hydrophilic.
• Have carbonyl and hydroxyl functional groups.
• Monosaccharides: glucose, fructose, galactose.
• Disaccharides: sucrose (glucose + fructose), lactose (glucose + galactose).
• Polysaccharides:
  • Starch is an energy storage in plants.
  • Glycogen is an animal energy storage, converted from glucose and stored in the liver.
  • Cellulose provides structural support in plants and is indigestible for humans.

Lipids

• Consist of C, H, and O, store twice the energy of carbohydrates, are hydrophobic.
• Triglycerides = glycerol + 3 fatty acids, formed through condensation/dehydration, have 3 ester groups.
• Phospholipids = glycerol + two fatty acids + phosphate group.
  • Feature a polar, hydrophilic head and non-polar, hydrophobic tails.
  • Form the lipid bilayer in cell membranes.
  • Have phosphate and ester functional groups.
• Steroids are composed of 4 rings and are seen in hormones.
• Cholesterol component in cell membranes restricts blood flow, builds plaque, and is converted into vitamin D and bile salts.
• Waxes are long-chain fatty acids + alcohols/carbon rings and act as hydrophobic coatings.

Proteins

• Consist of C,H,O,N
• Amino acids are the monomer which include a hydrogen atom, an amino acid group, a carboxyl group, a variable R group, and are somewhat polar.
• They are linked by condensation/dehydration into polypeptide polymers:
  • Carboxyl
  • Amino
  • R group
  • Sulfhydryl
  • Amide are their functional gropus
• Primary (1°) structure: The polypeptide chain, formed by covalent peptide bonds, begins at the N-terminal of amino acid 1.
• Secondary (2°) structure: Folding and interactions of the polypeptide chain due to hydrogen bonding, forming alpha helices or beta-pleated sheets.
• Tertiary (3°) structure: Hydrophobic and hydrophilic interactions within the cell determine protein shape, folding alpha helices and beta sheets.
• Quaternary (4°) structure involves multiple polypeptide chains linked by covalent bonds.
• Different 3° structures interact to form a 4° structure, mediated by hydrogen bonds, dipole interactions, and hydrophobic/philic interactions.
• Proteins may denature, irreversibly disrupting shape.

Nucleic Acids

• Consist of C, H, O, N, P
• Nucleotides (DNA or RNA) are the monomer.
• Carbonyl, hydroxyl, amino, phosphate and amide are the functional groups
• DNA includes phosphate group + sugar + nitrogenous base + –H at the end of the sugar
• RNA includes phosphate group + sugar + nitrogenous base + –OH at the end of the sugar
• DNA: G (Guanine) + C (Cytosine), A (Adenine) + T (Thymine)
• RNA: Guanine, Adenine, Cytosine, and Uracil (G, A, C, U)

Bonds

• Peptide bonds are in proteins.
• Glycosidic bonds are in carbohydrates.
• Ester bonds are in lipids.
• Phosphodiester bonds are in nucleic acids (DNA/RNA).

Protein Functions

• Enzymatic catalysis to speed up specific biological reactions.
• Structural support such as bones, tendons, skin, hair, nails, claws, and beaks.
• Transport small molecules like oxygen or transfer things in and out of the cell.
• Enabling movement: animals move by muscle contraction from actin and myosin.
• Signaling via hormones that carry signals between cells.
• Defence provide by antibodies to combat bacterial and viral infections

Carbohydrate Glucose Functions

• Primary energy source and is metabolized through glycolysis and oxidative phosphorylation to produce ATP.
• Blood sugar regulation and imbalances lead to conditions like hypoglycemia or hyperglycemia.
• Fructose is a monosaccharide found in fruits, vegetables, and is metabolized in the liver.
• Galactose is a monosaccharide forming lactose and is involved in brain development.
• Sucrose, a disaccharide, provides a quick energy source and is broken down by sucrase in the small intestine.
• Lactose is a disaccharide providing energy and is broken down by lactase; lactose intolerance occurs with insufficient lactase activity.
• Glycogen stores glucose in animals, mainly in the liver and muscles; glycogenolysis maintains blood sugar levels.
• Starch stores in plants, broken down by amylase, and some forms act as dietary fiber.
• Cellulose forms plant cell walls, assists in digestion, and provides structural support.

Lipid Functions

• Energy storage for long term energy , provide insulation, protect and cushion organs, water repellent
• Phospholipids in cell membrane structure, and steroids for signaling.

Nucleic Acids Functions

• DNA stores genetic information for growth, development, reproduction, and inheritance. DNA replicates itself during cell division.
• mRNA carries genetic instructions for protein synthesis
• tRNA brings amino acids to ribosomes, helping to assemble proteins based on mRNA sequences and rRNA forms ribosomes, which facilitates peptide bond formation.
• Regulatory RNAs control gene expression.

Saturated vs Unsaturated Fats

• Saturated fats have no double bonds and are "saturated" with hydrogen, which are found in animal products and are solid at room temperature. Also, they can raise LDL cholesterol.
• Unsaturated fats have one or more double bonds and are found in olive oil, nuts, fish, and vegetable oils and are liquid at room temperature.
• Monounsaturated (one bond) and polyunsaturated (multiple bonds

Cis vs. Trans Fats

• Cis fats (healthy) have hydrogen on the same side of the double bond, causing a bend/kink.
• Trans fats (unhealthy) have hydrogen on opposite sides, straightening the chain, are found in processed foods and raise heart disease risk.

Phospholipid Structure

• Phospholipids consist of a hydrophilic phosphate head and hydrophobic fatty acid tails, forming a bilayer in cell membranes that is selectively permeable.

Protein 3D Structure

• Primary structure is the amino acid sequence.
• Secondary structure is the folding of the polypeptide into a-helices or ẞ-pleated sheets stabilized by hydrogen bonds.
• Tertiary structure is the three-dimensional shape with interactions between R-groups.
• Quaternary structure is the arrangement of multiple polypeptide chains.

Biochemical Reactions

• Neutralization: acid + base = Salt + water.
• Redox reactions: oxidation and reduction. One gains, the other loses electrons.
• Condensation reactions: joins two reactants removing water.
• Hydrolysis reaction: adds water to break bonds.

Enzymes

• Activation energy: The energy needed to start a chem reaction.
• Enzymes are proteins, lower activation energy, and increase reaction rate.
• Inorganic enzymes: Cofactors
• Organic enzymes: Coenzymes
• pH affects enzyme by functioning best in acidic/basic and extreme pH can denature enzymes
• Temperature can denature enzymes and low temperatures reduce their activity.
• Substrate concentration: Higher concentrations increase reaction rates until the enzyme is saturated.
• Enzyme regulation by activating by cofactors/coenzymes or inhibiting with allosteric or competitive inhibitors.

Cell Membrane Structure and Function

• The cell membrane is composed of a phospholipid bilayer with proteins, cholesterol, and carbohydrates.
• The cell membrane regulates the entry and exit of substances, maintaining homeostasis and separates from extracellular environments, with fatty acid tails (hydrophobic) point inwards and polar heads (hydrophilic) face outwards.
• Selectively permeable to small, non-polar molecules (oxygen, carbon dioxide) that pass easily, while large polar molecules and ions require transport proteins.
• The phospholipid bilayer has hydrophobic tails face inward and hydrophilic heads face outward and maintains fluidity due to intermolecular forces.

Factors Affecting Membrane Permeability

• Increased temperature increases fluidity and double bonds increase fluidity due to kinks.
• Increased tail length decreases fluidity due to increased intermolecular forces.

Solutions

• Hypertonic: higher solute concentration than the cell, leading to water loss.
• Hypotonic: a lower solute concentration than the cell, leading to water uptake.
• Isotonic: the same solute concentration as the cell, resulting in no net water movement.

Carrier Proteins

• Carrier proteins bind to specific molecules, changing shape for transport and channel proteins having polar interiors.

Passive Transport

• Does not require energy (ATP) and relies on concentration gradients which leads to the diffusion from areas of higher to lower concentration (small molecules like oxygen or carbon dioxide).
• Osmosis moves water through a semipermeable membrane from low to high solute concentration and facilitated diffusion where molecules move across the membrane with transport proteins.

Active Transport

• Requires energy (ATP) to move against concentration gradient.
• Primary transport occurs through a pump protein using direct ATP which creates the Sodium-potassium (Na+/K+) pump.
• Secondary transport uses previously created gradients via co-transport or antiport systems like the sodium-glucose symporter.
• Bulk transport moves large quantities using vesicles (endocytosis/exocytosis).