BIOLOGYNOTES

CHAPTER TWO

Matter – Anything that takes up space and has mass

- Living organisms are composed of matter

Element – Substance that cannot be broken down to other substances by chemical reactions

Compound – Substance consisting of two or more elements in a fixed ratio

- Type of bond does not matter in a compound

- A compound has characteristics DIFFERENT from characterics of the elements in said compound

DIFFERENCE BETWEEN ELEMENT, ESSENTIAL ELEMENT, AND TRACE ELEMENTS

ELEMENT – Substance that cannot be broken down to other substances by chemical reactions

ESSENTIAL ELEMENT- Elements that are essential and vital to the life of organisms

TRACE ELEMENT - Elements required by an organism only in minute quantities

SUBATOMIC PARTICLES

- Atoms are composed of three types of “LARGE” subatomic particles

PROTONS – Positive charge

Neutrons AND protons form the atomic nucleus of an atom

NEUTRONS – NO electrical charge

ELECTRONS - Negative charge

- Electrons occupy a space around the nucleus referred to as an ELECTRON CLOUD

ATOMIC NUMBER VS ATOMIC MASS

ATOMIC NUMBER – An element’s atomic number is THE SAME NUMBER OF PROTONS in its nucleus

- ALL ATOMS OF AN ELEMENT HAVE THE SAME NUMBER OF PROTONS

ATOMIC MASS - An element’s atomic mass is the SUM OF PROTONS PLUS NEUTRONS in the nucleus

ISOTOPES VS IONS

ISOTOPES – Atoms with the SAME number of protons, but DIFFERENT number of neutrons

Stable isotopes – DO NOT LOOSE PARTICLES / DO NOT GIVE OFF PARTICLES

Unstable isotopes – NUCLEUS DELAYS SPONTANEOUSLY GIIVNG OFF PARTICLES AND ENERGY

HOW ARE ISOTOPES UTILIZED IN BIOLOGY?

- Isotopes are utilized in Biology by being used as tracers within a living organism to trace what is going on inside the organism at an atomic level

- Labeling macromolecules in experimental cell and molecular biology research

- Radiation from decaying radioisotopes can damage or kill cells

ELECTON SHELL

- An electron shell is an electron’s state of potential energy

- Electrons of an atom have potential energy because of HOW they are arranged in relation to the nucleus

- NEGATIVELY charged electrons of an atom are attracted to the POSITIVELY charged nucleus

- For elements whose atoms have NO MORE THAN THREE ELECTRON SHELLS, the maximum number of electrons that can occupy each shell are as follows:

1st shell – max of two electrons

2nd shell – max of eight electrons

3rd shell – max of eight electrons

ENERGY LEVELS OF ELECTRONS

- The more distant an electron is FROM the nucleus of atom, the GREATER its potential energy

- Energy is required to move an electron FARTHER away from a nucleus

- Energy is released when an electron moves to a LOWER energy shell (shell closer to the nucleus)

VALANCE ELECTRONS

Valance electrons – Those in the OUTER electron shell, which is referred to as the VALENCE SHELL

- The chemical behavior of an atom is determined primarily by its valance electrons

- Elements with a full valance shell are chemically inert (nonreactive)

The maximum number of valance electrons in the first three electron shells for atoms with no more than three shells are:

1st shell – max of two electrons

2nd shell – max of eight electrons

3rd shell – max of eight electrons

CHEMICAL BONDS

- Covalent bonds – Strong bonds resulting from the SHARING OF VALENCE ELECTRONS by atoms:

- Nonpolar – Valence electrons shared equally by bonded atoms (H2)

- Polar – Valance electrons not shared equally by bonded atoms (H2O)

- Ionic – Bonds resulting from loss and gain of electrons by bonded atoms (NaCI), strong, BUTweaker than covalent bonds

- Hydrogen – Weak bond formed between a hydrogen atom in a polar compound and an electronegative atom in another polar compound

CHAPTER THREE

Water is a POLAR molecule!

- In a water molecule, the electrons of its polar covalent bonds spend more time near the oxygen atom than the hydrogen atoms

- This property makes water a POLAR MOLECULE regarding distribution of its overall charge:

-Oxygen – partial negative charge

-Hydrogens – partial positive charges

PROPERTIES OF WATER

Cohesive and adhesive properties

- Cohesion – Chemical attraction between particles of the SAME substance

- Adhesion – Chemical attraction between DIFFERENT particles

Ability to moderate temperature

- Water has HIGH specific heat – It can absorb or release a large amount of heat with only slight change in its own temperature

- Water’s high specific heat can be traced to hydrogen bonding

- Water absorbs heat when hydrogen bonds are broken (in warmer air)

- Water releases heat when hydrogen bonds are formed (in cooler air)

Expands upon freezing

Versatility as a solvent for other polar and ionic compounds

- Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily

- When an ionic compound (NaCI) is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell

- Example of a solution: SALT WATER

- Solvent – Water

- Solute – Sodium Chloride (NaCI)

- Solution – Salt water

HYDROPHILIC AND HYDROPHOBIC SUBSTANCES

- Hydrophilic substance – One that has an affinity for water

- Hydrophobic substance – One that does not have an affinity for water

ACIDS, BASES, AND BUFFERS

Acids – Any substance that increases the H+ concentration of a solution

Bases – Any substance that decreases the H+ concentration of a solution

Buffers - Substances that minimizes changes in concentrations of H+ and OH- in a solution

pH scale

- The pH scale (0-14) is a measure the concentration of H+ ions in an aqueous solution:

- pH of 7 is neutral (H+ = OH-)

- pH of

- pH >7 is basic (H+ < OH-)

- As the concentration of H+ increases, pH decreases

- Most biological fluids have pH in the range of 6 to 8

OCEAN ACIDIFICATION

- A reduction in the pH of the ocean over an extended period, caused primarily by uptake of carbon dioxide (CO2) from the atmosphereAE

CHAPTER FOUR

ORGANIC MOLECULES

- Carbohydrates

- Lipids

- Proteins

- Nucleic Acids

HYDROCARBONS

- Hydrocarbons are organic molecules consisting of only carbon and hydrogen

- Many organic molecules, such as fats, have hydrocarbon components

- Hydrocarbons can undergo chemical reactions that release large amounts of energy

- Hydrocarbons are the major components of fossil fuels, which formed from the fossilized remains of dead plants, algae, and animals by exposure to heat and pressure in the earth’s crust over hundreds of years

- Hydrocarbons are nonpolar because of the close and small difference between the electronegatives of carbon and hydrogen

ISOMERS

- Isomers are compounds that have the same molecular formula but different structures

Structural isomers – Have different covalent arrangements of their atoms

Cis-trans isomers – Have the same covalent bonds but differ in spatial arrangements

cis isomer: The two Xs trans isomer: The two Xs are

are on the same side.

on opposite sides.

Enantiomers – Isomers that are mirror images of each other

FUNCTIONAL GROUPS

- Hydroxyl group – polar due to electronegative oxygen. Forms hydrogen bonds with water (POLAR) (-OH)

- Carbonyl group – sugars with ketone groups are called ketoses; those with acetone are called aldoses (POLAR) (C = O)

- Carboxyl group – acts as an acid (POLAR) (-COOH)

- Animo group – acts as a base (POLAR) (-NH2)

- Sulfhydryl group – SH groups can react, forming a “cross-link” that helps stabilize protein structure (POLAR) (-SH)

- Phosphate group – contributes negative charge. When attached, confers on a molecule the ability to react with water, releasing energy (POLAR) (-OPO32-)

- Methyl group – affects the expression of genes. Affects the shape and function of sex hormones (NON-POLAR) (CH3)

CHAPTER FIVE

POLYMERS VS MONOMERS

Polymers – Long molecule consisting of monomers

Monomers – A molecule that can be bonded to other identical molecules to form a polymer

Dehydration Reactions – Covalent bonding of two molecules to each other through loss of a water molecule

Hydrolysis Reactions – The reverse of the dehydration reaction

CARBOHYDRATES

Monomer of carbohydrate – Monosaccharide with the basic formula of a carbon, two hydrogens, and an oxygen molecule

- Carbohydrates include sugars and the polymers of sugars

- The simplest carbohydrates are monosaccharides, or simple sugars

- Polysaccharides are sugar polymers consisting of many sugars building blocks

LIPIDS

Structure AND components of TRIGLYCERIDES

- Triglycerides are constructed from two types of smaller molecules: glycerol and fatty acids

- Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon

- A fatty acid consists of a carboxyl group attached to a long hydrocarbon tail (e.g., palmitic acid)

- Saturated fatty acids – Have the maximum number of hydrogen atoms and no double bonds

- Unsaturated fatty acids – Have one of more double bonds

PHOSPHOLIPIDS

- A phospholipid consists of two fatty acids and a phosphate group attached to a glycerol backbone

- The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a polar (hydrophilic) head

-

STEROIDS

- Steroids are lipids characterized by a carbon skeleton consisting of four fused rings

- The steroid cholesterol is a component of animal cell membranes and a precursor from which other steroids are synthesized

- Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease

- Some steroids are hormones

- The sex hormone estradiol and testosterone produce the contrasting features of female and male animals

PROTEINS

- Proteins are large organic polymers made of amino acid monomers arranged in a linear chain and joined together by peptide bonds

Peptide – A molecule that contains TWO or MORE amino acids

Polypeptide – A substance that contains MANY amino acids

PROTEIN STRUCTURE AND FUNCTION

Protein Structure Levels

- The primary structure of a protein is its unique sequence of amino acids

- Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

- Tertiary structure is determined by interactions among various side chains (R groups)

- Quaternary structure results when a protein consists of 2 or more polypeptide chains

Denaturation – The breaking of many of the weak bonds

CHAPTER SIX

TYPES OF MICROSCOPES

- Light Microscope

- Bright Field Microscope

- Phase-Contrast Microscope

- Differential Interference Contrast Microscope

- Fluorescence Microscope

- Confocal Microscope

PROKARYOTES VS EUKARYOTIC CELLS

Prokaryotic

- No membrane-bound organelles

- DNA, typically double stranded and circular in structure, is contained in a non-membrane bound region called the nucleoid

- Cytoplasm is bound only by a plasma membrane

-

Eukaryotic

- Membrane – bound organelles

- DNA, double stranded and circular in structure, is contained in a membrane bound organelle called the nucleus

- Other membrane-bound organelles

- Cytoplasm in the region between the plasma membrane and nucleus

- Generally, much larger than prokayrotic cells

-

Plasma Membrane Structure

-

CHAPTER 7

Phospholipid Membrane

- The lipid bilayer is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around the cells.

- Phospholipids in a plasma membrane can move within the bilayer

- Most of the lipids, and some proteins, drift later within the membrane

- Phospholipids very rarely “flip-flop” transversely across a cell membrane

Membrane Fluidity

- As temperatures cool, membranes transition from a fluid state to a solid state

- The temperature at which a membrane solidifies depends on its lipid composition

- Cell membranes rich in phospholipids containing unsaturated fatty acids are more fluid than those rich in saturated fatty acids

- Membranes must be fluid to function properly – they are usually about as fluid as salad oil!

- Many proteins in the plasma membrane can drift within the phospholipid bilayer

- Proteins are much larger than lipids and move more slowly

WHAT TYPES OF MOLECULES MOVE DIRECTLY THROUGH PHOSPHOLIPID BILAYER

- Gases, hydrophobic molecules, and small polar uncharged molecules

TRANSPORT: ACTIVE VS PASSIVE

Active Transport – Requires energy for the movement of molecules

Passive Transport – Does not require energy for the movement of molecules

NAME OF WATER PORES

Aquaporins - Integral membrane proteins that serve as channels in the transfer of water, and in some cases, small solutes across the membrane

ENDOCYTOSIS

Three types of endocytosis

- Phagocytosis – A cell engulfs a particle, or even another cell, by forming a food vacuole

- Pinocytosis – Molecules dissolved in the extracellular environment of a cell are taken up when extracellular fluid is engulfed into tiny vesicles

- Receptor-mediated endocytosis – Binding of ligands to receptors triggers vesicle formation

- Ligand – Any molecule that binds specifically to a receptor site of another molecule

SODIUM/POTASSIUM PUMP

- Major electrogenic pump of animal cells