CAPE Biology Unit One - Comprehensive Notes
Aspects of Biochemistry
Water's Structure and Properties
Water makes up over 70% of a cell's mass.
Water molecules are attracted to each other due to their molecular structure.
Water consists of two hydrogen atoms covalently bonded to one oxygen atom, creating a dipole.
The oxygen atom has a negative charge (δ-), while the hydrogen atoms have a positive charge (δ+).
This uneven charge distribution allows for weak electrical attractions between water molecules, resulting in cohesion and mass flow.
Hydrogen bonds are essential for many biological molecules.
Properties of Water & Enabling Factors
Temperature regulation: High specific heat capacity and ability to evaporate easily.
'Universal' solvent: Tiny charges attract other molecules or ions to form bonds.
Allows mass flow: H-bonds produce cohesion and surface tension.
Suitable for excretion
Assists buffers: Neutral pH allows H+ or OH- ions to be absorbed by proteins.
Reactivity: Used in hydrolysis reactions during digestion and in photosynthesis.
Carbohydrates: Glucose and Sucrose
Carbohydrates Defined: Organic molecules composed of carbon, hydrogen, and oxygen in a specific ratio.
Carbohydrate Types
Monosaccharides: One sugar unit. Examples include glucose, fructose, ribose, galactose, glyceraldehyde.
Cannot be further hydrolyzed.
General formula: .
A hexose sugar (e.g., glucose) has n=6, so glucose is .
A pentose sugar (e.g., ribose) has n=5, so ribose is .
Deoxyribose has one less oxygen atom: .
Disaccharides: Two sugar units. Examples include maltose, sucrose, lactose.
Formed when two monosaccharide molecules are bonded via a glycosidic bond which is a very strong bond.
Polysaccharides: More than two sugar units. Examples include starch, glycogen, cellulose, chitin.
Glucose
A hexose with a six-membered ring (five carbons, one oxygen).
Exists in straight-chain and ring structures and alternates between these forms.
Two forms: alpha and beta (H and OH are swapped on C-1 in beta-glucose).
Sucrose
A disaccharide formed from alpha-glucose and beta-fructose, bonded via a 1-2 glycosidic bond.
A condensation reaction removes a water molecule.
Sucrose yields two glucose molecules upon enzyme breakdown (one reformed from fructose).
Reducing vs. Non-Reducing Sugars
Benedict's solution tests for reducing sugars.
Non-reducing sugars (like sucrose) require hydrochloric acid (HCl) and sodium hydroxide (NaOH) to react with Benedict's reagent.
HCl breaks the glycosidic bond, and NaOH neutralizes the HCl.
Sucrose is used for transport because it is more complex, energy-efficient, and less reactive than glucose.
Polysaccharides: Starch, Glycogen, and Cellulose
General characteristics: Polysaccharides are large, complex molecules containing thousands of sugar units, making them insoluble.
Starch
Function: Energy reserve in plants after photosynthesis.
Composed of two polymers: amylose (spiral) and amylopectin.
Stored in plastids, which form grains.
Never found in animal cells.
Digested by amylase.
Amylose forms a spiral from many α-glucose molecules. It is held together by H-bonds that form between –OH groups attached to C-1 of each unit.
Glycogen
Function: Energy reserve in animals.
Easier to break down into glucose.
Usually found in the liver and muscles.
Made of many α-glucose molecules and are linked through α 1-4 glycosidic bonds with α 1-6 branches.
Cellulose
Function: Structural support in cell walls.
Always has a straight structure.
Very strong due to thousands of hydrogen bonds.
Large bundles of them are called fibers.
Difficult for animals to digest.
Made up of thousands of β- glucose molecules.
Their bonds are extremely strong due to the multitude of hydrogen linkages.
The type of bonds in cellulose are β 1-4 glycosidic bonds between the glucose molecules.
Each alternating glucose molecule is inverted.
Summary Table:
Feature, Amylose, Glycogen, Cellulose
Sugar unit: α-glucose, α-glucose, β-glucose
Overall shape: Linear and spiral, Linear, spiral, branches, Only linear
Solubility in water: Insoluble or very low, Insoluble or very low, Insoluble
Glycosidic bond type: α 1-4, α 1-4 and α 1-6, β 1-4
H-bonds: Within, Within, Within and between
Location: Starch grains, plastids, Animal liver cells, Cell walls
Breaking and Forming Bonds
Hydrolysis reaction: Breaking a covalent bond using a water molecule during the breakdown of polymers into monomers.
Condensation reaction: Formation of a bond releases a molecule. If water is released, it is a dehydration reaction.
Examples of dehydration reactions include the formation of sucrose (from glucose & fructose) and the formation of a dipeptide molecule from two amino acids.
Hydrogen bonds: Form between water molecules. Hydroxyl groups (-OH) form hydrogen bonds because hydrogen is slightly +ve and oxygen is slightly –ve. Dipole or polar molecules are hydrophilic while non-polar molecules are hydrophobic.
Lipids and Triglycerides
Lipid structure: Similar to carbohydrates but contain a much higher proportion of hydrogen, and are insoluble in water.
Main lipids: Fats and oils, used as energy reserves and insulation.
Triglycerides: Composed of three fatty acids attached to a glycerol molecule.
Insoluble in water and hydrophobic.
Fatty acids contain a carboxyl group (-COOH) that reacts with the -OH groups of glycerol, forming ester bonds.
Glycerol acts as the 'backbone' of the triglyceride structure.
In triglycerides, all the C atoms are bonded to H, which makes it a yield more energy upon breakdown than carbs.
Adipose Tissue and Obesity
*Triglycerides are an energy reserve and are stored in tissues in humans called ADIPOSE tissue. Accumulation of excess adipose tissue will eventually lead to OBESITY.
*Studies of fat are constantly yielding new information and show that fats act almost like endocrine organs, affecting hormonal secretion and metabolism. The cells shown are called ADIPOCYTES. „White fat‟ cells have a much higher concentration of triglycerides than „brown fat‟ cells. Brown fat cells tend to have a high concentration of mitochondria, which regularly „burn‟ off the energy reserves.
Saturated vs. Unsaturated Fats
Saturated fats: Have the last carbon atom bonded to three hydrogens, 'saturated' with hydrogen.
Considered "bad" fats, contributing to LDL (low-density lipoprotein) cholesterol build-up and coronary heart disease.
A SATURATED fat molecule has its last carbon atom bonded to three hydrogens. Thus, it has been „saturated‟ with hydrogen. This is usually referred to as the „bad‟ fat, as it forms a dense structure that can contribute to the build-up of LDL (low- density lipoprotein) cholesterol, leading to coronary heart disease.
Unsaturated fats: Have at least one carbon atom double-bonded to another, reducing hydrogen.
The bend in the structure prevents tight packing and arterial plaque build-up.
An UNSATURATED fat molecule has at least one carbon atom double-bonded to another, reducing the amount of hydrogen that is holds. Observe below to see that it causes a slight bend in the linear structure. Imagine that this bend prevents the fat from packing too tightly and contributing to arterial plaque build-up.
Trans fats: Artificially made semi-solid oils through hydrogenation (insertion of gases through oils to solidify them).
Affect bonding linkages.
Have been banned in certain foods (e.g., margarine, shortening, certain fast foods).
Phospholipids
Phospholipid structure: Similar to a triglyceride, but one fatty acid is replaced by a phosphate group.
Phosphate 'heads' are hydrophilic, while fatty acid 'tails' are hydrophobic.
In water, they form a bilayer structure, essential for cells to keep their organelles together.
Proteins and Amino Acids
Protein functions: Cellular growth, repair, enzymes, hormones.
Amino acid structure: A central carbon atom connected to four groups:
An amino group (-NH2)
A carboxyl group (-COOH)
A hydrogen (H) atom
Another group or chain of amino acids, represented as 'R'
Peptide bonds: Amino acids bond with each other during condensation reactions via strong covalent bonds called peptide bonds.
A water molecule is released (H atom joins with an –OH).
The reason the ‘head’ is attracted is because it has a negative charge. This is attracted to the positive charge of the H atoms on the water molecule. The ‘head’ is water-soluble.
Polypeptides
Polypeptide formation: Protein synthesis occurs in ribosomes. Condensation reactions occur when amino acids are bonded, producing water molecules.
Chains of amino acids: Many amino acids linked by peptide bonds form a polypeptide chain.
Polypeptides can be non-linear. Example: hemoglobin has four polypeptides connected in a coiled structure.
Polypeptide breakdown: Water is consumed during a hydrolysis reaction.
Example: pepsin digests proteins in the stomach.
Amino Acid Examples:
*Serine – Used in the synthesis of components in the brain cell membranes and neurones.Leucine – Involved in increasing lean muscle mass.
Valine – High levels are associated with insulin resistance and diabetes.
Tryptophan – Converts to serotonin, which affects mood and sleep
Aspartic acid – Contributes to the formation of urea.