Lecture Exam #2

Atom

The smallest unit of an element that still has the properties of that element.

Molecule

Two or more atoms chemically joined together.

Isotopes

Atoms of the same element that have the same number of protons but different numbers of neutrons.

Protons

Positively charged particles found in the nucleus of an atom.

Neutrons

Particles with no electrical charge found in the nucleus.

Electrons

Negatively charged particles that move around the nucleus.

Atomic number

The number of protons in an atom.

Atomic weight

The average mass of an element's naturally occurring isotopes.

Electron shell

A region around the nucleus where electrons are found.

Energy levels

The different amounts of energy an electron can have depending on its location around the nucleus.

Valence

The ability of an atom to form chemical bonds based on its outermost electrons.

Chemical bond

An attractive force that holds atoms together.

Ionic bond

A bond formed when one atom transfers electrons to another atom.

Example: NaCl

Covalent bond

A bond formed when atoms share electrons.

Example: H₂O

Hydrogen bond

A weak attraction between a hydrogen atom and another electronegative atom, usually oxygen or nitrogen.

Important: Hydrogen bonds are weaker than ionic and covalent bonds.

Endergonic reaction

A reaction that requires an input of energy.

Think: Energy goes in.

Exergonic reaction

A reaction that releases energy.

Think: Energy comes out.

Synthesis reaction

A reaction where smaller molecules combine to form a larger molecule.

A + B → AB

Decomposition reaction

A reaction where a larger molecule breaks into smaller molecules.

AB → A + B

Reversible reaction

A reaction that can proceed forward or backward depending on conditions.

A ⇌ B

Exchange reaction

A reaction where atoms or groups are rearranged between molecules.

AB + CD → AC + BD

Inorganic compound

A compound that generally does not contain carbon bonded to hydrogen.

Examples:

• Water

• Oxygen

• Sodium chloride

Organic compound

A carbon-containing compound, usually with carbon-hydrogen bonds.

Examples:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Polar molecule

A molecule with an uneven distribution of electrical charge.

Example: Water

Water has a slightly positive side and slightly negative side.

Polar = has charged ends

Nonpolar molecule

A molecule with an even distribution of charge.

Nonpolar molecules generally do not mix well with water.

Nonpolar = no charged ends

Acid

A substance that releases H⁺ ions in solution.

pH < 7

Base

A substance that accepts H⁺ or releases OH⁻ in solution.

pH > 7

Buffer

A substance that helps resist changes in pH when small amounts of acid or base are added.

Biomolecules

The four major types are:

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

Carbohydrate

An organic molecule made mainly of carbon, hydrogen, and oxygen.

Main functions:

• Quick energy

• Energy storage

• Structural support

Examples:

• Glucose

• Starch

• Glycogen

• Cellulose

Basic unit:

Monosaccharide

Lipids

A group of mostly nonpolar molecules that do not dissolve well in water.

Functions:

• Long-term energy storage

• Cell membranes

• Insulation

• Some hormones

Examples:

• Fats

• Oils

• Phospholipids

• Steroids

Proteins

A large molecule made of amino acids joined together by peptide bonds.

Functions:

• Enzymes

• Transport

• Structure

• Movement

• Defense

Basic unit:

Amino acid

Nucleic acids

A molecule that stores and transmits genetic information.

Two major types:

• DNA

• RNA

Basic unit:

Nucleotide

DNA

Deoxyribonucleic acid

Stores the cell's genetic information.

Bases:

• Adenine (A)

• Thymine (T)

• Cytosine (C)

• Guanine (G)

RNA

Ribonucleic acid

Helps use genetic information to make proteins.

Bases:

• Adenine (A)

• Uracil (U)

• Cytosine (C)

• Guanine (G)

Differences between DNA and RNA

DNA

RNA

Usually double-stranded

Usually single-stranded

Has thymine

Has uracil

Stores genetic information

Helps use genetic information

Metabolism

All of the chemical reactions occurring inside a cell.

Metabolism includes:

Anabolism + Catabolism

Anabolism

Builds larger molecules from smaller molecules.

Requires energy.

Think: BUILD

Catabolism

Breaks larger molecules into smaller molecules.

Often releases energy.

Think: BREAK

Metabolic pathway

A series of chemical reactions in which the product of one reaction becomes the reactant for the next reaction.

Collision theory

Chemical reactions occur when molecules collide with enough energy and the correct orientation.

Activation energy

The minimum amount of energy needed to start a chemical reaction.

Enzyme

A biological catalyst that speeds up a chemical reaction without being consumed.

Active site

The specific region of an enzyme where the substrate binds.

Substrate

The substance that an enzyme acts on.

Enzyme-substrate complex

The temporary combination formed when a substrate binds to an enzyme's active site.

Apoenzyme

The protein portion of an enzyme.

Apoenzyme = protein

Cofactor

A nonprotein helper required by some enzymes.

Often an inorganic ion.

Examples: Mg²⁺, Zn²⁺

Cofactor = helper

Coenzyme

An organic cofactor that helps an enzyme function.

Many coenzymes are derived from vitamins.

Holoenzyme

The complete, active enzyme consisting of an apoenzyme plus its required cofactor/coenzyme.

Holoenzyme = complete enzyme

NAD

Nicotinamide adenine dinucleotide

A coenzyme involved in electron transfer during cellular respiration.

NAD⁺

The oxidized form that accepts electrons.

NADH

The reduced form carrying high-energy electrons.

Factors Affecting Enzyme Activity

Temperature

Each enzyme has an optimal temperature.

Too much heat can denature the enzyme.

pH

Each enzyme works best within a certain pH range.

Extreme pH can change the enzyme's shape and reduce activity.

Substrate concentration

Increasing substrate concentration usually increases reaction rate until the enzymes become saturated.

Enzyme concentration

More enzyme can increase the reaction rate if enough substrate is available.

Competitive inhibitor

Competes with the substrate for the active site.

Think:

"Competes for the spot."

Noncompetitive inhibitor

Binds somewhere other than the active site and changes the enzyme's shape.

Think:

"Changes the shape."

Ribozyme

An RNA molecule that acts as an enzyme and catalyzes a chemical reaction.

ATP

Adenosine triphosphate

The main energy-carrying molecule used by cells.

Substrate-level phosphorylation

ATP is produced by directly transferring a phosphate group to ADP.

Oxidative phosphorylation

ATP is produced using energy from electrons passing through the electron transport system.

Oxidation-Reduction Reactions

Oxidation

A substance loses electrons.

OIL = Oxidation Is Loss

Reduction

A substance gains electrons.

RIG = Reduction Is Gain

Redox reaction

A reaction involving the transfer of electrons between substances.

Glycolysis

The pathway that breaks one glucose molecule into two pyruvic acid molecules.

Occurs in the cytoplasm.

It does not directly require oxygen.

Main purpose:

Produces:

• ATP

• NADH

• Pyruvate

Krebs cycle

A series of reactions that further breaks down carbon compounds and produces NADH, FADH₂, ATP/GTP, and CO₂.

In bacteria, it occurs in the cytoplasm.

In eukaryotic cells, it occurs in the mitochondrial matrix.

Electron Transport System (ETS)

A series of electron carriers that transfer electrons and help create a proton gradient used to make ATP.

Main purpose:

Produces large amounts of ATP through oxidative phosphorylation.

Alternative Pathways to Glycolysis:

1) Pentose-phosphate pathway

An alternative pathway for breaking down glucose that produces:

• NADPH

• Pentose sugars

It is important for biosynthesis and nucleotide production.

Alternative Pathways to Glycolysis

2) Entner-Doudoroff pathway

An alternative pathway for glucose breakdown used by some bacteria.

It produces:

• Pyruvate

• NADH

• NADPH

• ATP

Cellular respiration

A series of metabolic reactions that extract energy from nutrients to produce ATP.

Aerobic respiration

Uses oxygen as the final electron acceptor.

Produces a relatively large amount of ATP.

Anaerobic respiration

Uses a substance other than oxygen as the final electron acceptor.

Examples:

• Nitrate

• Sulfate

Fermentation

An anaerobic process that uses an organic molecule as the final electron acceptor.

It does not use an electron transport system.

Main purpose:

Regenerates NAD⁺ so glycolysis can continue.

Examples:

• Alcohol fermentation

• Lactic acid fermentation

Deep-freezing

Storing materials at very low temperatures to slow or stop microbial growth.

It usually does not kill all microorganisms.

Lyophilization

Also called freeze-drying.

Water is removed from a frozen material under a vacuum.

Used to preserve:

• Microbial cultures

• Foods

• Biological materials

Binary fission

The main method of bacterial reproduction.

One cell divides into two genetically similar cells.

Budding

A new cell develops as a small growth or bud from the parent cell.

Generation time

The time required for a population to double in number.

Bacterial Growth phase

There are four major phases:

1) Lag phase

2) Log phase

3) Stationary phase

4) Death phase

Lag phase

Cells are adjusting to their new environment.

Little or no increase in cell number.

Log phase

Cells are growing and dividing rapidly.

Also called the exponential phase.

Stationary phase

The number of new cells approximately equals the number of dying cells.

Nutrients become limited and waste accumulates.

Death phase

The number of dying cells exceeds new cells.

Direct measurement

Measures the actual number of cells or organisms.

Examples:

• Direct microscopic count

• Viable plate count

Indirect measurement

Estimates microbial growth by measuring something related to cell number.

Examples:

• Turbidity

• Metabolic activity

• Dry weight

MPN

Most Probable Number

A statistical method used to estimate the number of viable microorganisms in a sample.

It is especially useful when organisms cannot easily be counted using standard plate counts.

Sterilization

Destroys or removes all microbial life, including endospores.

Disinfection

Destroys or reduces microorganisms on nonliving surfaces.

Antisepsis

Reduces microorganisms on living tissue using chemical agents.

Biocide

A chemical or physical agent that kills microorganisms.

Bacteriostatic

An agent that stops or slows bacterial growth without necessarily killing the bacteria.

Bactericidal

An agent that kills bacteria.

Physical Methods of Microbial Control

Heat

Kills microorganisms by damaging proteins and other cellular components.

Moist heat

Uses water/steam to kill microorganisms.

Example: Autoclave.

Dry heat

Uses hot air or direct flame.

Example: Hot-air oven.

Filtration

Physically removes microorganisms from liquids or gases.

Radiation

Damages microbial DNA.

UV = nonionizing

X-rays/gamma rays = ionizing

Low temperature

Slows microbial growth.

Desiccation

Removes water and inhibits microbial growth.

Osmotic pressure

High salt or sugar concentrations remove water from cells and can cause plasmolysis.

Chemical Methods

Alcohols

Damage membranes and denature proteins.

Examples:

• Ethanol

• Isopropanol

Halogens

Damage cellular components.

Examples:

• Chlorine

• Iodine

Phenolics

Damage cell membranes and proteins.

Hydrogen peroxide

An oxidizing agent that damages cellular components.

Surfactants

Help remove microorganisms from surfaces.

Example: Soap.

Heavy metals

Interfere with proteins and enzymes.

Examples:

• Silver

• Copper

Aldehydes

Damage proteins and nucleic acids.

Examples:

• Formaldehyde

• Glutaraldehyde

What is a fermentation test used for?

It determines whether bacteria ferment a carbohydrate and produce acid and/or gas. A pH indicator changes color when acid is produced, and a bubble in the Durham tube shows gas production.