A&P Chapter 2: Chemical levels of Organization

elements

chemically identical atoms

Atoms

• smallest units of matter that retain the properties and characteristics of an element

• identified using a name for the element

• composed of subatomic particles

  • proton

  • neutron

  • electron

Identifying elements

atomic number: # of protons in atom nucleus (= # of electrons)

mass number: # of protons and # of neutrons in an atom

atomic weight/mass: weighted average of all naturally occurring isotopes

Isotopes

Same # of protons and electrons but a different # of neutrons → different mass number

• Stable and radioactive forms

• examples: carbon, oxygen, nitrogen, iodine, cobalt

• Radioisotopes tend to be unstable and decay to more stable isotope forms by releasing energy

Ion

atom that has lost or gained electrons to become stable

• electrically charged:

  • Cation = positively charged ion, formed when an atom loses electrons

  • anion = negatively charged ion, formed when an atom gains electrons

Free Radical

atom or group of atoms with an unpaired electron in outermost shell, can damage tissues

Molecule

2+ atoms sharing electrons can be same or different elements

Compound

a substance that can be broken down into 2 or more different elements

all compounds are molecules, but not all molecules are compounds

chemical bonds

occur when atoms are held together by forces of attraction

bonds form using electrons because they have energy and can move

• electrons found in electron shells (orbitals)

• each shell has a max # of electrons

• outermost shell = valence shell

• # of electrons in a valence shell determines the likelihood that an atom will form a chemical bond with another atom

• When outermost shell is full, the atom is stable

Ionic Bond

• attraction between ions (cation and anion)

• formed when electrons are TRANSFERRED from one atom to another atom

Covalent bond

• Formed when atoms SHARE electrons

• each pair of electrons shared creates a bond

• bonds are polar or nonpolar

Polar covalent bonds

molecule has negative and positive ends (poles)

electrons not shared equally between atoms

ex: water

Non polar covalent bonds

electrons shared equally

electrically neutral

example: carbon dioxide

Hydrogen Bonds

• attraction of oppositely charged polar molecules or parts of molecules

• very weak bonds (shown as ….)

• Formed when hydrogen atom (H+) attracted to negative atom like oxygen or nitrogen

• Produces surface tension in water

• Can also form within molecules

  • shape of proteins, DNA

Chemical reactions

• occur when chemical bonds are formed, rearranged, or broken

  • reactants: starting substances

  • products: ending substances

• Amounts of reactants and products are shown in balanced equations

Reversible reactions

products can revert to original reactants

synthesis reactions

smaller particles are bonded together to form larger, more complex molecules

decomposition reactions

bonds are broken in larger molecules, resulting in smaller, less complex molecules

exchange reactions

bonds are both made and broken

also called displacement reactions

Chemical bonds represent

stored chemical energy

energy used to released as bonds are formed or broken

activation energy

energy needed for reaction to occur

catalysts

speed up reaction rate by decreasing amount of activation energy required → enzymes

biochemistry

study of chemical composition and reactions of living matter

inorganic compounds

water, salts, many acids and bases

typically do not contain carbon (except CO2, CO)

organic compounds

carbohydrates, lipids, proteins, nucleic acids

contain carbon, usually large, and have covalent bonds

Water

• polar molecule

• excellent solvent

  • in a solution, solvent dissolves the solute

  • water-soluble = hydrophilic

  • water-insoluble = hydrophobic

• ideal medium

dehydration synthesis

water is removed to form bonds

hydrolysis

water is added to break bonds

Characteristics of Water

• high heat capacity

• high heat of vaporization

• major component of body fluids

• lubricant (helps reduce friction as membranes and organs slide over one another)

electrolytes

release ions in water and conduct electricity

acids

electrolytes that dissociate to release hydrogen ions (H+) in water

bases

electrolytes that dissociate to release ions that can combine with hydrogen ions

salts

electrolytes that dissociate in water, neither or which result in H+ or OH-

pH scale

concentration of H+ in solution

neutral = pH 7

acidic = pH < 7

basic/alkaline = pH > 7

Buffers

maintenance of body fluid homeostasis is critical

buffer systems help maintain homeostasis by converting STRONG acids/bases into WEAK acids/bases to regulate pH

• will bind H+ if pH drops or release H+ if pH rises

Organic compounds

always contain carbon (carbon can combine in a variety of shapes, does not dissolve easily in water, and compounds are a good energy source)

also contain hydrogen and oxygen

larger than inorganic molecules

Carbohydrates

• include sugars and starches

• contain C, H, and O (CH2O)n: general formula

• Hydrogen and oxygen are in 2:1 ratio 

Functions of carbohydrates

• quickest source of energy

• stores in liver and muscles as glycogen

• converted to fats and stored in adipose tissue

• used to manufacture cell structures

Major classes of carbohydrates

monosaccharides

disaccharides

polysaccharides

Lipids

• contain C, H, O, but no 2:1 ratio for hydrogen:oxygen

• sometimes contains P and other elements

• insoluble in water (hydrophobic)

Triglycerides

• called fats when solid and oils when liquid

• composed of 3 fatty acids bonded to a glycerol molecule (sugar alcohol)

• main functions: energy storage, insulation, protection

Saturated fatty acids

• all carbons are linked via single covalent bonds → has maximum number of H atoms it can hold (saturated with H)

• create linear molecules which pack closely together forming a solid at room temperature

Unsaturated fatty acids

• one or more carbons are linked via double bonds, resulting in reduced H atoms (unsaturated)

  • causes a kink/bend in the fatty acid → cannot pack together closely, so they are liquid at room temperature

Trans fats

modified unsaturated fatty oils that resemble structure of saturated fats and considered healthy

omega 3 fatty acids

heart healthy

phospholipids

• modified triglycerides: glycerol and 2 fatty acids plus a phosphorus-containing group

• head is polar and hydrophilic

• tails are nonpolar and hydrophobic

• important in cell membrane structure

steroids

• consist of four interlocking ring structures

• most important steroid is cholesterol

  • made by liver and also found in animal products

  • starting material for synthesis of vitamin D, steroid hormones, and bile salts

  • important in cell plasma membrane structure

proteins

• 20-30% of cell mass

• many different functions

• contain C,H,O,N and sometimes S and P

• polymers of amino acid monomers held together by peptide bonds

• shape and function due to four structural levels

all proteins are made from….

20 types of amino acids

amino acids

• contain both an amine group and acid group

• can act as either an acid or base

• differ by which of 20 different “R groups” is present

Amino acids are joined together by….

covalent bonds called peptide bonds that connect amine group of one amino acid to the carboxyl group of another amino acid

dipeptide

2 amino acids

polypeptide

many amino acids

protein (polypeptide)

1 or more polypeptides

Enzymes

globular proteins that act as biological catalysts

• highly specific

• very efficient

• regulated by cellular controls

names usually end in -ase and are often named for the reaction they catalyze

Enzymes act on

a very specific substrate

• active site has a very specific and intricate shape with distinct chemical properties to match its substrate

• can only interact with substrates that match the characteristics of the active site - lock and key

• may interact with a single substrate, a group of similar substrates, or a particular type of bond

denaturation

proteins unfold and lose their functional 3-D shape

• active sites become deactivated on enzymes

Can be caused by changes in pH, heat, radiation, electricity, chemicals

Usually reversible if normal conditions restored

irreversible if changes are extreme or prolonged

Nucleic Acids

composed of C,H,O,P, and P

largest molecules in the body

composed of nucleotides

shape held together by hydrogen bonds - can be denatured just like proteins

DNA

genetic blueprint for snythesis of all proteins 

double stranded helical molecule located in cell nucleus

RNA

single stranded

3 types: 

• messenger RNA

• Transfer RNA

• Ribosomal RNA

ATP

chemical energy released when glucose is broken down is captured in ATP

directly powers chemical reactions in cells

Structure of ATP

andenin-containing RNA nucleotide with two extra phosphate groups 

How does ATP give energy

energy from the bond joining the terminal phosphate group to ATP can be transferred to other compounds to do work 

loss of end phosphate group converts ATP to ADP

loss of second group converts ADP to AMP