AP Bio Unit 1 Chemistry Of Life

Organic

Needs to have hydrogen and carbon

biological organization (smallest to largest)

Atoms, molecules, organelles, cells, tissues, organ, organ systems, organism

ecology levels (Smallest to biggest)

organisms, populations, communities, ecosystems, biosphere

Organ

2 or more tissues working together

Abiotic

Non-living

6 characteristics of life

1. All organisms reproduce

2. All have DNA

3. All require energy

4. All respond and adapt to their environment

5. All are made up of cells

Sexual Reproduction

-two cells from different parents unite to form the first cell of the new organism

Asexual Reproduction

-involves one parent

-offspring is genetically identical to parent

-most common method is binary fission

-unicellular organism divides in half to form two new organisms

Autotroph

self feeder

Heterotroph

organism that obtains energy from the foods it consumes; also called a consumer

3 domains

Bacteria, Archaea, Eukarya

Discovery of cells

Robert Hooke

-observed sliver of cork

-coined term cell

Cell Theory

-All living things are made of ells

-Smallest unit of structure and function of all organisms is the cell

-All cells come from pre-existing cells

Electronegativity

"thirst for electrons", for covalent bonds

non polar covalent bond

a covalent bond in which the bonding electrons are shared equally by the bonded atoms, resulting in a balanced distribution of electrical charge

Polar covalent bond

A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

Ionic bond

Formed when one or more electrons are transferred from one atom to another

Essential Elements of Life

CHON (Carbon, Hydrogen, Oxygen, Nitrogen)

Trace elements

required by an organism in only minute quantities

Mass, Atomic, and Neutron #

Mass # (top) = # of protons + neutrons

Atomic # (bottom) = # of protons, # of electrons in neutral atom

# of Neutrons = mass # - atomic #

Isotope

Atoms of the same element that have different numbers of neutrons

Radioactive Isotope

An isotope whose nucleus decays spontaneously, giving off particles and energy.

Electron Shells

An energy level representing the distance of an electron from the nucleus of an atom.

Valence Electrons

Electrons on the outermost energy level of an atom

-chemical behavior depends on this

Valence Shell

outermost electron shell

ions

extra positively or negatively charged atoms because they have gained or lost an electron

cation

positively charged ion

anion

negatively charged ion

ionic compounds/ salts

a compound resulting from the formation of an ionic bond

hydrogen bonds

-when hydrogen atom is covalently bonded to an electronegative atom it has a partial positive charge, attracting electronegative atoms

-van der waals interactions

-basis of property of water

Water Molecules

-covalent bonds

-partially negative O, partially positive H

-hydrogen bonds (weak)

-water properties

Properties of water

-cohesion

-adhesion

-high specific heat

-high heat of vaporization

-Ice is less dense than water

-universal solvent

Cohesion (Strong & High surface tension)

-attraction between other water molecules (Water & water)

-surface tension: how difficult it is to stretch or break the surface of a liquid

-bonded by hydrogen bonds

-transport of water and dissolved nutrients against gravity in plants

adhesion

-clinging of one substance to another such as water

-connected by hydrogen bonds

-water molecules stick to other surfaces

-ex. capillary action

high specific heat

-water resists changes in temperature (requires a lot of energy to cool or heat)

-Specific Heat: amount of het that must be absorbed or lost for 1g of that substance to change its temp by 1 degree C

-waters specific heat is 1cal/g*c

-helps regulate climate and body temp

high heat of vaporization

-Hydrogen Bonds have to be broken before evaporation can occur

-heat of vaporation: quantity of heat a liquid must absorb for 1g of it to be converted from liquid to gas

Floating of Ice/Ice is less dense than liquid Water

-ice floats on liquid water

-when in ice form the hydrogen bonds spread out

- >4*c, water expands as it warms

-at 0*c water freezes, each molecule bonded to 4 partners making ice less than 10% more dense than a liquid

-waters greatest density is at 4*c

Universal Solvent

- water can dissolve many polar or charged substances bc water is polar

Aqueous Solution

a solution in which water is the solvent

hydrophillic molecules

Attracted to water

Hydropobic molecules

substances that repel water because they are non-ionic or non polar (can't form hydrogen bonds)

Ex. Oil

Formulas H, H3O conversion

HCl= H+ + Cl-

NH3 + H+ = NH4+

NaOH= Na+ + OH-

H2CO3 = HCO3- + H+

[H+][OH-]= 10 ^-14

pH= -log[H+]

-log 10^-7 = -(-7) = 7

Van der Waals interactions

Weak attractions between molecules or parts of molecules that result from transient local partial charges.

Acids

-excess of H+ ions and a pH below 7.0 [H+] > [OH-]

bases

- excess of OH- ions, pH above 7.0 [H+] < [OH-]

buffers

substances that minimize changes in pH, accept H+ when depleted

carbonic acid (H2CO3)

important buffer of living systems it moderates pH changes in blood plasma and the ocean

Carbon

-usually completes valence shell by sharing 4 electrons with other atoms so 8 electrons are present

-tetrahedron shape

-carbon bonds to other molecules forming carbon skeletons

-forms up to 4 covalent bonds

carbon skeletons

the chain of carbon atoms in an organic molecule

hydrocarbons

Compounds composed of only carbon and hydrogen

Isomers are

compounds with the same molecular formula but different structures and properties

functional group

A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions.

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

4 Macromolecules

carbohydrates, lipids, proteins, nucleic acids

number of unpaired electrons in an atom =?

amount of bonds it can form

cis-trans isomer

carbons have covalent bonds to the same atoms, but these atoms differ in their spatial arrangements due to the inflexibility of double bonds

enatiomer

One of two molecules that are mirror images of each other.

Hydroxyl Group

polymers

large compound formed from combinations of many monomers

-large carbohydrates, proteins, etc are polymers

monomer

small chemical unit that makes up a polymer

-form larger molecules by dehydration synthesis

-enzymes speed up process

dehydration synthesis/condensation

A chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule.

Hydrolysis reaction

A chemical reaction that breaks apart a larger molecule by adding a molecule of water

-reverse reaction

Carbohydrates

-include simple sugars (glucose, fructose, galactose, ribose, deoxyribose, etc)

-ratio of 1 carbon: 2 hydrogen: 1 oxygen or CH2O (1:2:1)

-consist of monosaccharides

monosaccharides

monomers of carbohydrates; simple sugars

disaccharides

Carbohydrates that are made up of two monosaccharides

-joined by covalent bond called glycosidic linkage

polysaccharides

Carbohydrates that are made up of more than two monosaccharides

-joined by dehydration synthesis (covalent glycosidic linkages)

glycosidic linkage

A covalent bond formed between two monosaccharides by a dehydration reaction.

Glycogen

Storage form of glucose, polymer

cellulose

Carbohydrate component of plant cell walls.

-polysaccharide

-glucose monomers joined by glycosidic linkages

microfibrils

strong fibres that hold together cellulose nolecules

Chitin

A structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods.

lipids

Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

- all HYDROPHOBIC

fats (triglycerides)

LIPIDS

composed of 3 fatty acids attached to a glycerol

fatty acids

chains of carbon atoms bonded to hydrogen atoms (hydrocarbons)

-non polar (hydrophobic)

saturated fatty acids

have the maximum number of hydrogen atoms possible and no double bonds

-pack solidly at room temp

unsaturated fatty acids

-A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail

-double carbon bonds

-Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton.

phospholipids

A molecule that is a constituent of the inner bilayer of biological membranes

-are polar,

-2 fatty acids

-have a glycerol backbone (hydrophilic head )a nonpolar

-hydrophobic tail.

-neither phobic or phillic which allows them to form bilayers in cell membranes

steroids

lipids characterized by a carbon skeleton consisting of four fused rings

-cholesterol is a steroid, so are estrogen and testosterone

Proteins

polymers made up of amino acid monomers

amino acids

contain a central carbon bonded to a carboxyl group, an amino group, a hydrogen atom, and a R group

R group

An R-group is any group in which the carbon or hydrogen is attached to the rest of the molecule.

used to represent one of 20 possible side chains found in amino acids of living systems

Peptide bonds

Covalent bonds linking amino acids in proteins

-formed by dehydration synthesis

-function depends on order and # of amino acids

- R group determines characteristics of each amino acid

Protein functions

1. Enzymatic

2. Storage

3. Hormonal

4. Contractile/Motor

5. Defensive

6. Transport

7. Receptor

8. Structural

4 Levels of Protein Structure

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Primary Structure

sequence of amino acids

-covalent bonds

Secondary Structure

The second level of protein structure; the regular local patterns of coils or folds of a polypeptide chain.

- Alpha Helix is a coiled shaped (DNA-like)

- Beta pleated sheet is an accordion shape

-hydrogen bonds between backbone atoms

Tertiary structure

-the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain

-complex globular shape

-van der Waals interactions

-hydrogen bonds, ionic, hydrophobic,

-disulfide bridges

-enzymes are held in place by R-group interactions

quarternary structure

The overall protein structure that results from the aggregation of two or more polypeptide subunits.

-same bonds as tertiary

protein shape determines

protein function

-misfolds cause function changes

-amino acid substitutions cause misfolds

chaperonins

protein molecules that assist the proper folding of other proteins

denaturation

loss of normal shape of a protein due to heat or other factor

DNA

-deoxyribonucleic acid

-double-stranded helix

-nucleotides include adenine, thymine, cytosine, and guanine

-A=T, C=G

(Think: apples in trees, cars in garages)

RNA

-ribonucleic acid

-single stranded

-protein synthesis

-Nucleotides are adenine, uracil, cytosine, and guanine

- A=U , C=G

(U replaces T)

Monomer of each macromolecule

Carbohydrates: Monosaccharide

Proteins: Amino acid

Nucleic Acids: Nucleotide

Lipids: (no repeating monomer units) Glycerol, fatty acids

Elements Associated with Carbohydrates

C- Always

H- Always

O- Always

N- Never

P-Never

S-Never

Remember: CHO

Elements Associated with Lipids

C- Always

H- Always

O- sometimes

N- Never

P-Sometimes

S-Never

Remember: CH and sometimes OP

Elements Associated with Proteins

C- Always

H- Always

O- Always

N- Always

P-Never

S-Sometimes

Remember: CHON, sometimes S

Elements Associated with Nucleic Acids

C- Always

H- Always

O- Always

N- Always

P-Always

S-Never

Remember: CHONP

Compounds that can be composed of CHO ALONE

Only carbohydrates and lipids

Which Functional Group is this?

Hydroxyl
-OH

Alcohol