Bio 20 AP - Biochemistry Chapter 2-5

Pre-midterm biochem vocabulary based on note packages. Campbell Biology Chapters 2-5

Isotope

Changes in the number of neutrons

Radioactive Isotopes

Unstable isotopes whose nucleus gives off particles and energy. Used in cancer identification

Ion

1. Cation - positively charged ion

2. Anion - negatively charged ion

Elements of Life

25 elements that are essential for human life

4 main ones and trace elements

Molecule

Atoms that are covalently bonded together with a set molecular formula. Have a definite shape and number of atoms.

Ionic Compound

Formed from positively and negatively charged atoms attracting. Not involved in transfer of electrons if atoms are already ions. Technically not true molecules

Chemical Equilibrium

A form of dynamic equilibrium. Where a reaction and its reverse are equal (no net change)

Properties of Water

1. Cohesion/Adhesion

2. Moderation of temperature

3. Insulation of ice

4. Universal solvent

Properties of Water - Cohesion

Ability of water to hold itself through hydrogen-bonds. Increases surface tension

Surface Tension

Measure of how much liquids resist stress

Properties of Water - Adhesion

Water’s ability to attract other molecules through (induced) dipole forces

Properties of Water - Moderation of Temperature

Specific heat capacity of water allows it to absorb/release large amounts of heat with little change in temperature.

Heat

Total amount of kinetic energy in an object. Magnitude not ratio

Temperature

Average kinetic energy in an object

Calorie

Amount of heat needed to raise the temperature of 1g of water by 1°C = 4.184 J

Specific Heat Capacity

Amount of heat needed to change the temperature of 1g of a substance by 1°C

Heat of Vaporization

Heat to convert 1g of liquid into a gas. Water’s is very high because of its hydrogen bonds

Evaporative Cooling

Decrease in average Ek (temperature) as most energetic particles turn into gas. Important in maintaining stable temperatures in small bodies of water/cooling organisms through sweating/evaporation of sweat.

Properties of Water - Insulation of Ice

Ice is less dense than water which allows for liquid water to remain during periods of extreme cold. Causes seasonal turnover in lakes. Occurs because of hydrogen bonds pushing H2O molecules further apart.

Properties of Water - Universal Solvent

Water’s ability to dissolve a large variety of liquid. Creates hydration shells in aqueous solutions

Hydration Shells/Spheres

Sphere of water molecules forming around ions in an aqueous solution. Able to attract both positive/negative because of polarity.

Hydrophilic

Substances that attract water. Will typically dissolve in water

Hydrophobic

Substances that “repel” water. Typically insoluble in water and are useful in structures such as the cell membrane

Colloid

Stable suspension of fine particles in a liquid

Molarity

Number of moles of solute per liter of solution (n/L)

Properties of Water - Dissociation of Water

Water can dissociate into H+ and OH- ions. Bond to create acids and bases. Relates to pH: lower pH = more H+

Acid

Substances which increase H+ concentration in a solution. Have more H+ ions than OH-

Base

Substances that decrease H+ concentration in a solution. Can bond with H+ or dissociate into OH- ions in a solution

pH

Negative logarithm of hydrogen ion concentration

Buffer

A solution to minimize changes in H+ and OH- concentrations in a solution

Vitalism

Idea that “life force” existed outside the realm of physics/chemistry laws. Believed that only organisms could produce organic compounds

Friedrich Wohler

Chemist who created urea from NH4+ and CNO-. Results questioned because CNO- comes from blood so could contain life force

Hermann Kolbe

Chemist who created urea from acetic acid (inorganic compound). Disproved vitalism

Miller-Urey Experiment

Experiment designed to prove that organic compounds can be created by physical processes from inorganic compounds, discovered amino acids. Performed by Stanley Miller

Hydrocarbon

Combinations of C and H.

• Non-Polar

• Insoluble in water + hydrophobic

• Source of energy because of stability

Isomer

Molecules with same molecular formula but different shapes. Each with different chemical properties and biological functions.

1. Structural Isomer

2. Geometric Isomer

3. Enantiomer

Structural Isomer

Molecules with differences in covalent arrangement of the atoms

Geometric isomer

Difference in the spatial arrangement of the bonds between atoms

Enantiomer

Molecules that are the mirror image of another

Functional Groups

Parts of organic molecules that are involved in chemical reactions. Give molecules distinct properties and affects reactivity

1. Hydroxyl

2. Carbonyl

3. Carboxyl

4. Amino

5. Sulfhydryl

6. Phosphate

Functional Groups - Hydroxyl

OH with no charge. Turns compounds into alcohols. Changes name to —ol

Functional Groups - Carbonyl

C=O. Create ketones and aldehydes

Functional Groups - Carboxyl

COOH (O=C-OH). Creates organic acids

Functional Groups - Amino

NH2. Creates base (ammonia picks up H+ from solution). Compounds with NH2 = amines to make amino acids

Functional Groups - Sulfhydryl

SH. Compounds with SH = thiols. Stabilize structure of proteins

Functional Groups - Phosphate

PO4. Increase negative charge of a compound (highly reactive). Transfer energy between organic molecules

Macromolecules

Small organic molecules joining to form larger ones.

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acid

Polymer

Large molecules built by linking repeating molecules. Linked through dehydration synthesis

Monomer

Small molecules that form repeating units in a polymer. Held together with covalent bonds

Digestion/Hydrolysis

Using water to break down polymers. Reverse of dehydration synthesis. Requires enzymes and releases energy (exothermic)

Macromolecules - Carbohydrates

Molecules composed of C, H, O used for energy storage, structure, and raw materials. Polymers held together with glycosidic linkages

1. Monosaccharides

2. Disaccharides

3. Polysaccharides

Carbohydrates - Monosaccharides

Monomer of carbohydrates. Eg. glucose

Carbohydrates - Disaccharides

2 monosaccharides linked together using glycosidic linkages. Eg sucrose

Disaccharides - Maltose

Glucose + Glucose

Disaccharides - Sucrose (table sugar)

Glucose + Fructose

Disaccharides - Lactose

Glucose + Galactose

Carbohydrates - Polysaccharides

Large polymers made from many monosaccharides. Easy to build molecules that can easily release energy, branching molecules (eg. glycogen) for faster energy release. Eg starch, cellulose, chitin

Polysaccharide Diversity

Isomers of glucose to change function of the molecules, changes ability of organisms to digest polymers

Amylase

Starch found in plants formed of a long, singular chain of monosaccharides.

Amylopectin

Starch found in plants, formed of branching monosaccharides

Cellulose

Most abundant organic compound, used structurally in plants. Not digestible by most organisms

Coprophages

Organisms that eat their excrement in order to absorb leftover nutrients in it. Eg. Rabbits

Chitin

Second most common polysaccharide found in nature. Found in exoskeletons of arthropods and cell walls of fungi.

Macromolecules - Lipids

Long term energy storage molecules. Do not form a polymer. 3 family groups

1. Fats

2. Phospholipids

3. Steroids

Lipids - Family Groups

1. Fats

2. Phospholipids

3. Steroids

Lipids - Fatty Acid

CH chain with carboxyl group

Lipids - Fats

Glycerol and fatty acids. Formed with ester linkages (OH + COOH). Used for concentrated store energy, insulating body, cushioning organs

Fats - Saturated

Fats where all C are single bonded for maximum H atoms. Long, straight chain that’s solid at room temperature. Contributes to cardiovascular disease. Eg. Animal fats

Fats - Unsaturated

Fats with a double bonded C, prevented from packing tightly together. Liquid at room temperature. Eg. vegetable oil

Fats - Transfatty Acids

Unsaturated fats that are chemically converted to saturated fats

Fats - Phospholipids

Glycerol, 2 fatty acids, and a phosphate attached together. Have hydrophilic phosphate heads and hydrophobic fatty acid tails. Forms phospholipid bilayer when it self assembles into bubbles called micelles

Cell Membrane

Composed of phospholipid bilayer to define the inside and outside of the cell. Creates a barrier to water

Fats - Steroids

Modified cholesterol that is composed of 4 fused carbon rings and various functional groups. Eg. Sex hormones

Cholesterol

Important cell component that makes up animal cell membrane, allows membrane to be fluid and flexible. Excess may lead to cardiovascular disease

Macromolecules - Proteins

Most structurally and functionally diverse group. Used in enzymes, structure, transport, communication, defense, movement, and storage. Made of amino acids attached by peptide bonds

Amino Acid

Monomer of proteins. 20 different kinds. Made of central C, H, amino group, carboxyl, and R-group

Sulfur Containing Amino Acids

Form disulfide bridges - covalent bond to “lock” protein shape in place

Polypeptide

Polymer of proteins. Large and complex molecules formed by chains folding and bonding together with peptide bonds

Peptide Bond

Covalent bonds between amino group (NH2) of 1 amino acid and the carboxyl group (COOH) of another amino acid

N-terminus

NH2 end of a polypeptide chain

C-terminus

COOH end of a polypeptide chain

Primary Protein Structure

Order of amino acids in a chain, determined by gene

Lysosome

Enzymes in tears and mucus that kill bacteria

Secondary Protein Structure

“Local folding” - interactions along adjacent amino acids through H-bonds (folding short sections of the polypeptide). Forms sections of 3D structure as α-helix or β-pleated

Tertiary Protein Structure

“Whole molecule folding” - Interactions between distant amino acids (hydrophobic interactions, H-bonds + ionic bonds, disulfide bridges). Anchors shape of molecule

Quaternary Protein Structure

Multiple polypeptide chains bonding together to create functional protein

Protein Denaturation

“Unfolding a protein” - conditions disrupt H-bonds/disulfide bridges (eg. temperature, pH, salinity). Alter 2/3/4 structure to alter 3D shape and destroy functionality

Macromolecules - Nucleic Acids

Hold genetic material/information storage. Used to store information on how to make proteins/genes and transfer information during cell division. Made of nucleotides linked together with phosphodiester bonds. Eg. RNA, DNA

Central Dogma

Discovered by Crick who hypothesized information flow in a cell went DNA → RNA → protein

Nucleotides

Monomer of nucleic acids. Formed with nitrogen base (C-N ring), sugar, and phosphate.

1. Purines

2. Pyrimidines

Purines

Double ring N-base, A/G bases. Attach to T/C/U bases

Pyrimidines

Single ring N-base, C/T/U. Attach to A/G bases

Nucleic Polymer

Sugar phosphate backbone made of phosphodiester bonds with N-bases hanging off

Pairing Nucleotides

Nucleotides between strands of DNA temporarily bond with H-bonds

Copying DNA

A complementary strand can be built if 1 strand is intact (DNA replication). Occurs during cell reproduction and gamete production

ATP

Modified nucleotide used as energy in cells