Gr. 12 - Unit 1 (Biochemistry) for Biology Exam

Biochemistry

The basis to life which is the chemical

reactions that take place in the cell.

Isotopes

Variants of a chemical element that have the same number of protons but different numbers of neutrons, resulting in different atomic masses.

Radioactive Isotope

An isotope that emits radiation due to the instability of its nucleus, leading to decay over time.

Hydrophobic

“Water fearing” substances that are insoluble in water (non-polar).

Hydrophillic

"Water loving" substances that are soluble in water (polar).

“Like-dissolves-like”

• polar-dissolves-polar

• nonpolar-dissolves-nonpolar

Non-polar Covalent Bond

Electrons are shared equally.

Polar Covalent Bond

Electrons are shared unequally.

Ionic Bond

Electrons are transferred.

Intramolecular Forces

Attractive forces that hold atoms together within a molecule, including ionic and covalent bonds.

• Very strong forces

Intermolecular Forces

Attractive forces that occur between molecules, including covalent bonds.

• Weaker than intermolecular forces

• Include: LDF, Dipole-dipole, Hydrogen bonds, and Ion-dipole

Ion-dipole

A type of intermolecular force that occurs between an ion and a polar molecule.

Ex. When NaCl or KCl dissolve in water, the ions separate and interact with the polar water molecules since this interactions is stronger than the ions interacting with each other.

Hydrogen Bond

Type of dipole-dipole interaction that occurs between the lone pair of an electronegative atom and the hydrogen that is bound to either an oxygen, nitrogen or fluorine atom.

Dipole-dipole

Attractive forces between polar molecules due to the positive end of one molecule interacting with the negative end of another.

London-Dispersion Force (LDF)

Forces that occur between any molecules and are the only force found in non-polar molecules.

When adjacent molecules have their electrons move to certain positions, that results in temporary dipoles.

Cohesion

Force of attraction between like molecules.

Ex. water to water

• responsible for surface tension

Surface Tension

The cohesive force at the surface of a liquid that causes it to resist external force (eg. gravity).

• allows for insects to walk on surface

Adhesion

Force of attraction between different molecules.

Ex. water to spider web

• water will stick to other substances/objects

Capillary Action

Upward motion against gravity due to both adhesion & cohesion.

Ex. water moving up a straw or glass tube

Water Density

Ice is less dense than liquid water, which is why it “floats”.

Ice acts as an insulator to prevent cooler air temperatures from mixing with water. This property is important for ponds, lakes & oceans; preventing them from freezing solid & allows aquatic life to continue to thrive under the icy surface.

Biochemical Reactions

1. Condensation

2. Hydrolysis

3. Neutralization

4. Oxidation-Reduction (REDOX reactions)

Macromolecules

Large complex molecules that are composed of repeating smaller subunits that are covalently linked.

Monomer

Small repeating subunits.

Polymer

Large repeating subunits.

Catabolism

Reactions that break macromolecules into individual monomer subunits.

• Hydrolysis Reaction

Anabolism

Reactions that produce large molecules from smaller subunits.

• Condensation Reaction

Condensation Reaction/Dehydration Synthesis Reaction

Water is removed in order to form a covalent bond between monomer subunits. This creates a longer polymer chain (anabolic reaction).

Types of Condensation Reactions

1. Glycosidic Linkage

2. Ester Linkage

3. Peptide Bond

Glycosidic Linkage

• Carbohydrates

• Monosaccharide subunits are joined through glycosidic bonds

Ester Linkage

• Lipids

Peptide Bonds

• Proteins

• An amide linkage that holds amino acids together in polypeptide chains

Hydrolysis Reaction

Catabolic reactions where water is added to break covalent bonds between monomer subunits.

• a large molecule is split into smaller

  subunits

Neutralization Reactions

When an acid is mixed with a base the solution is neutralized due to the water that is formed.

Acid + Base —> Salt + Water

Conjugate Acids

Acids that gain a proton during the reaction.

• Was a base but gained a H+

Conjugate Base

Bases that lose protons during the reaction.

• Was an acid but lost an H+

Buffer

A substance that maintains pH levels by donating or accepting H+ as needed.

Bicarbonate Buffer

Used by humans to control the pH levels in our blood.

CO2 + H2O —>/<— H2CO3- —>/<— H+ + HCO3-

Oxidation

• Loss of electrons

• Addition of oxygen, Loss of hydrogen

Reduction

• Gain of electrons

• Loss of oxygen, Addition of hydrogen

Carbohydrates

• Sugars

• Humans main source of energy

• Made up of carbon, hydrogen, and oxygen

• General formula: (CH2O)n

• Polar & water soluble

Types of Carbohydrates

• Monosaccharides

• Disaccharides

• Polysaccharides

Monosaccharides

Glucose, Fructose, Galactose

• Simple sugars (smallest unit of carbohydrates)

• C6H12O6

Stereoisomers for Monosaccharides

1. Alpha Linkage: hydroxyl group found on the bottom

2. Beta Linkage: hydroxyl group found on the top

Disaccharides

Maltose, Sucrose, Lactose

• 2 monosaccharides pair up

• Covalent bonds form glycosidic linkages

Maltose

Glucose + Glucose

Sucrose

Glucose + Fructose

Lactose

Galactose + Glucose

Polysaccharides

Cellulose (fibre), Starch (amylose), Glycogen

• Long chains of monosaccharides joined by glycosidic linkages

Lipids

• Non-polar molecules/hydrophobic/insoluble in water

• Form cell membrane

• Energy source

• Hormones

• Insulation

Fatty Acids

A single hydrocarbon chain that contains a carboxyl group (COOH).

Saturated Fatty Acids

• Bound to the maximum possible number of Hydrogens

• Carbons are linked with only single bonds

Unsaturated Fatty Acids

• Double bond is present in the hydrocarbon tail

• The double bond creates a “kink” (bend) in the hydrocarbon tail

Monounsaturated Fatty Acid

1 double bond in hydrocarbon tail.

Polyunsaturated Fatty Acid

More than 1 double bond in hydrocarbon tail.

Fats

Triglyceride: 1 glycerol & 3 fatty acids join together through an ester linkage.

Trans Fatty Acids

• 1 or more double bonds in hydrocarbon tail

• Straight configuration

Phospholipids

• Form cell membrane (phospholipid bilayer)

• 2 hydrophobic fatty acid tails

• 1 hydrophilic phosphate head

Amphipathic Molecule

Phospholipid: both hydrophobic & hydrophilic.

Steroids

• 4 fused carbon rings

• Cholesterol can be converted into Vitamin D

• Sex hormones control the growth and development of sexual traits and sex cells

Waxes

• Large lipid molecules made of long fatty acid chains linked to alcohols or carbon rings

• Extremely non-polar and hence hydrophobic

• Usually soft solids at room temperature

• These characteristics allow for waterproof barriers

Protein

A large molecule that consists of many amino acid subunits that are joined together by peptide bonds folded into a specific 3D shape.

Backbone of Amino Acid

• Amino group (NH2)

• Side chain (R)

• Carboxyl group (COOH)

Essential Amino Acids

Amino acids that we cannot synthesize ourselves. We must obtain them from our diet.

1. Histidine

2. Isoleucine

3. Leucine

4. Lysine

5. Methionine

6. Phenylalanine

7. Threonine

8. Tryptophan

9. Valine

Dipeptide

2 amino acid long peptide.

Oligopeptide

2-20 amino acid long peptide.

Polypeptide

>20 amino acid long peptide.

Primary Structure

A simple polypeptide chain.

Secondary Structure

Occur from hydrogen bonding (O, N, H) between its backbone.

• Alpha helix

• Beta-pleated sheet

Alpha Helix

• Coil structure that has H-bonds between every 4th amino acid

• Every turn of the helix is 3.6 amino acid residues

Beta-Pleated Sheet

• Side-by-side alignment of polypeptides that allows for

  H-bonding

• Can be in a parallel or antiparallel arrangement

Tertiary Structure

• R group interactions cause shape

• Intermolecular reactions:

  • Ionic bonds

  • Hydrogen bonds

  • Hydrophobic interactions

  • Disulfide bridges

Denaturation

Under extreme conditions, such as temperature and pH, a protein can unfold leading to a loss of structure and function.

Quaternary Structure

Interactions of many polypeptides/tertiary structures, forming subunits.

• Same forces that hold tertiary structures together

Prosthetic Groups

Non-peptide groups that join to proteins to assist them in performing certain functions.

• Usually metal ions

DNA Pentose Sugar

Deoxyribose

RNA Pentose Sugar

Ribose

DNA (Deoxyribonucleic Acid) Nucleotides

• Adenine

• Guanine

• Cytosine

• Thymine

RNA (Ribonucleic Acid) Nucleotides

• Adenine

• Guanine

• Cytosine

• Uracil

3 Parts of Nucleotide

• Phosphate group

• Pentose sugar group

• Nitrogenous base

2 Types of Nitrogenous Bases

1. Purines

2. Pyrimidines

Purines

Double Ring

• Adenine

• Guanine

Pyrimidines

Single Bond

• Cytosine

• Thymine (DNA)

• Uracil (RNA)

DNA & RNA Hydrogen Bonds

• Adenine + Thymine/Uracil

  • double hydrogen bond

• Guanine + Cytosine

  • triple hydrogen bond

Enzyme

A protein catalyst that increases the rate of a reaction, lowers the activation energy, and binds to a substrate to break it down.

Substrate

A substance that is recognized by and binds to an enzyme.

Active Site

A pocket or groove in an enzyme that binds its substrate.

3 Ways Enzymes Can Lower Activation Energy

1. The R-group of the protein interferes with the molecule bonds in the substrate

2. Transfer of electrons between the enzyme and substrate

3. Add or remove hydrogen ions to or from the substrate

Factors Affecting Enzyme Activity

• Temperature

• pH

• Enzyme concentration

• Substrate concentration

Saturation Point

All of the active sites are full. Adding more substrate will no longer have an effect on the rate of reaction because all of the enzymes are occupied.

Cofactor

A non-protein group that binds to an enzyme and is essential for catalytic activity.

• can activate enzyme

Coenzyme

An organic molecule that acts as a cofactor of an enzyme.

• can activate enzyme

Competitive Inhibition

A substance that binds to the active site of an enzyme to block enzyme activity.

• The greater the inhibitor concentration, the less likely it is that a reaction will occur

Non-Competitive Inhibition

A situation in which molecules bind to an enzyme at a site that is not the active site, changing the enzymes shape, thus blocking enzyme activity.

• By increasing the substrate concentration, the reaction rate does not change because the shape has changed and therefore will not bind

Allosteric Site

A binding site on an enzyme that binds regulatory molecules.

Allosteric Regulation

The regulation of one site of a protein by binding to another site on the same protein.

Allosteric Activation

When a substance binds to an enzyme on the site that is not the active site, changing the shape of the enzyme, thus allowing for the substrate to bind.

Feedback Inhibition

The product of one reaction becomes the substrate of another enzymatic reaction.

The product formed in the last step of the pathway can become an inhibitor for the first enzymatic reaction to stop the process.

• prevents overproduction of a certain substance

Endomembrane System

A group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins.

Glycolipid

Any membrane lipid that is bound to a carbohydrate.

Glycoprotein

A membrane component that contains a sugar, or carbohydrate, bound to an amino acid.