Bio 107 Ch.2: The Molecules of Cells

Matter

anything that takes up space and has mass

3 states include solid, liquid, and gas

Elements

92 substances that can’t be broken down into simpler substances

Trace Elements

essential but only needed in small quantities and sometimes needed to prevent diseases

ex. iron and iodine

Atoms

made up of subatomic particles; protons, neutrons and electrons

Protons

positively charged, found in the nucleus

Neutrons

uncharged, found in nucleus

Electrons

negatively charged, move around nucleus

Atomic Mass

number of protons plus number of neutrons

Atomic Number

number of protons equal to the number of electrons

Isotopes

number of neutrons is different from number of protons

• mass number is different

Radioactive Isotopes

emits various types of energy as they decay

ex. used for medical imaging (PET) or radiation therapy

Orbitals

electrons move around nucleus

1st orbital = 2 electrons

What determines chemical properties?

the number of electrons in a valence shell

Chemical Bonds

attractions held by atoms staying close together by sharing, donating, or receiving electrons to complete valence shell

95% of the body has what elements?

oxygen, carbon, nitrogen, and hydrogen

The farther you are from the nucleus…

the more energy you have.

Covalent Bond

2 atoms sharing a pair of electrons, partially positive

• single/double covalent bond

• nonpolar/polar covalent bond

Molecules

2 or more atoms held together by covalent bonds

• form when same elements bond

• ex. O2

Compounds

form when different elements bond

ex. H2O

Single Covalent Bond

sharing one pair of electrons

Double Covalent Bond

sharing two pairs of electrons

Nonpolar Covalent Bond

the sharing of electrons is equal

ex. oxygen gas

Polar Covalent Bond

the sharing of electrons is unequal, different electronegativities

ex. water

Electronegativity

attraction of an atom for electrons in a covalent bond

• a polar bond has this

Ions

a atom that gains an electric charge because it gained or lost electrons

Ionic Bond

held together by an attraction between oppositely charged ions

• an electron transfer = charge imbalance

• strongest molecular interaction in an aqueous environment

When happens to the charge when you gain or lose electrons?

• gain 1 positive charge for every electron you lose

• gain 1 negative charge for every electron you gain

Hydrogen Bond

attractions between a partially negative oxygen and a partially positive hydrogen

• caused by a water molecule’s polarity

• weak individually but strong collectively

3 Types of Bonds

Covalent Bond

Ionic Bond

Hydrogen Bond

What bond does NOT share or exchange electrons?

Hydrogen bond

Properties of Water

Hight heat capacity

High heat of vaporization

Solvent

Cohesive

Adhesive

Transport System

High Surface Tension

Ice Density

Disassociation

Calorie (Water)

amount of heat energy needed to raise temperature by 1g

Vaporization (Water)

converting 1g of the hottest water to gas requires 540 calories

Solvent (Water)

facilities chemical reactions and dissolves chemical substances

Cohesive (Water)

water molecules cling together due to hydrogen bonding

Adhesive (Water)

water’s psoitive and negative poles allow it adhere to polar surfaces

Density (Water)

frozen water is less dense than liquid

Crystal Lattice (Water Density)

water expands as it freezes because it forms with hydrogen bonds further apart

Self-Disassociation (Water)

when water ionizes, it releases an equal number of hydrogen ions and hydroxide ions (only these change pH)

Acids

substances that release H+ when dissociated in water

• high H+ concentration

Bases

substances that release OH- or take up H+ when dissociated in water

• low H+ concentration

pH Scale

0-14 scale indicating the acidity or alkalinity of a solution

• below 7 = acidic, ex. lemon juice

• above 7 = alkaline, ex. baking soda

• 7 = neutral, ex. pure water

Buffer

a chemical or combination of chemicals keeping pH within normal limits

Objects exchange energy until they are what?

Equal

Organic Molecules

compounds that contain carbon-hydrogen bonds

Functional Groups

a specific combination of bonded atoms that dictates chemical behavior and characteristics

• Hydroxyl

• Carbonyl

• Carboxyl

• Amino

• Sulfhydryl

• Phosphate

Carboxyl and Amino (Functional Groups)

always found in amino acids

Macromolecules

contain several molecules joined together

• Monomers

• Polymers

Monomer

simple organic molecules that exist individually

Polymer

large organic molecules formed by combining monomers

• cells use common reactions (Dehydration or Hydrolysis) to build or degrade polymers

Dehydration Reaction (Polymers)

an -OH or -H are removed when monomers join to build polymers

Hydrolysis Reaction (Polymers)

water components added when polymers are broken down

What is most likely to form covalent bonds?

Carbon (building blocks)

• share 4 electron pairs to complete valence shell

Type of Monomers

Carbohydrates

Monosaccharides

Disaccharides

Carbohydrates (Monomer)

primary source of energy for the body and also plays a structural role

• consists of both small molecules AND macromolecular polymers

• all composed of C, H and the functional group -OH

Monosaccharides (Monomer)

simple sugars that are building blocks of all carbohydrates that can NOT be broken down

Disaccharides (Monomer)

simple sugars containing 2 monosaccharides joined by a dehydration reaction

ex. maltose, glucose, and lactose

Types of Polymers

Polysaccharides

Lipids

Proteins

Peptides

• all synthesized from subunits by dehydration reactions

Polysaccharides (Polymer)

large polymers containing many glucose subunits

• ex. starch and glycogen (Energy Storage Poly.)

• ex. cellulose and chitin (Structural Poly.)

Energy Storage Polysaccharides

Starch: storage in form of glucose in plants

Glycogen: storage in form of glucose in animals’ liver

• has SOME branching

Structural Polysaccharides

Cellulose: found in plants’ cell wall and has different chemical linkage

Chitin: found in crabs’ exoskeleton

• HIGHLY branched

Lipids (Polymer)

organic compounds that contain more energy per gam and is hydrophobic (insoluble in water)

Types of Lipids

Fats

Oils

Fatty Acids

Phospholipids

Steroids

Fats/Triglyceride (Lipid)

store energy, insulate heat, protective cushion, of animal origin, and solid at room temperature

Oils (Lipid)

liquid at room temperature and of plant origin

Emulsification (Fats and Oils)

fats and oils can disperse in water with emulsifiers which contain molecules with a polar and nonpolar end

Fatty Acids (Lipid)

hydrocarbon chain ending with a carboxyl group

• Saturated Fatty Acids

• Unsaturated Fatty Acids

• Trans-Fats

Saturated Fatty Acids

no double bonds between carbon and solid at room temperature

Unsaturated Fatty Acids

1 or more double bonds between carbon

Trans-Fats

oils hydrogenated to make them solid, aka processed food

Phospholipids (Lipid)

composed of 2 fatty acids and a phosphate group

• phosphate group is polar and has a hydrophilic head

• fatty acids are nonpolar and has 2 hydrophobic tails

Phospholipids assemble into what?

A bilayer with water

Steroids (Lipid)

the backbone of 4 fused carbon rings

ex. cholesterol, testosterone, estrogen, etc

Proteins (Polymer)

polymers composed of amino acid monomers linked by dehydration synthesis and functions include:

• structural proteins give support

• enzymes speed up chemical reactions

• hormones as chemical messengers

• actin and myosin move cells and muscles

• antibodies protect cells

• transport molecules in blood

Amino Acids

either in an amino group, acidic group, or an R group varies

• 20 amino acids but 4 basic ones include alanine, valine, cysteine, and phenylaline

What makes amino acids different from each other?

different R groups attached to an alpha carbon

Peptides (Polymer)

Polypeptide: a single chain of amino acids

Peptide Bond: joins 2 amino acids and a protein’s primary structure

Levels of Protein Organisation

Primary Structure

Secondary Structure

Tertiary Structure

Quaternary Structure

Primary Structure of Proteins

the linear sequence of amino acids with peptide bonds

Secondary Structure of Proteins

when the protein takes on a certain orientation in space

• 2 types include Alpha Helix and Beta Sheet

Tertiary Structure of Proteins

the final 3D shape maintained by various bonds between R groups

• include covalent, ionic, and hydrogen bonding

Quaternary Structure of Proteins

found in proteins with multiple polypeptide chains and occurs when a protein is denatured (loses its function and structure)

When does a protein denature?

occurs when proteins are exposed to high heat or pH

Nucleic Acids

DNA and RNA

• polymers of nucleotides (contain a nitrogenous base, phosphate group, and a pentose sugar)

DNA

stores genetic information and replicates with cell division or reproduction

• Adenine, Thymine, Cytosine, and Guanine

• double helix strands held by hydrogen bonds

RNA

single stranded and involved in carrying genetic information from DNA to make proteins

• Uracil, Adenine, Cytosine, and Guanine

ATP (Adenosine Triphosphate)

a high energy molecule that undergoes hydrolysis so energy is released

What do hydrolizations from?

ADP (Adenosine Diphosphate)

• ATP can be rebuilt by adding P to ADP to create ATP