BIO105b test one

Matter

- occupies space and has mass
- composed of chemical elements

Element

- a substance that cannot be broken down into any other substance
- 92 natural, 25 essential to life

Compound

- substances containing 2 or more elements in a fixed ratio
- most contain carbon, nitrogen, hydrogen and oxygen

Atom

- smallest unit of matter that retains the properties of an element
- each element consists of one kind of these
- nucleus \= central core

Proton

- single positive electric charge

Neutron

- no electric charge

Electron

- single negative electric charge

Atomic Number

- number of protons in each atom of a particular element

Mass Number

- sum of the number of protons and neutrons in an atoms nucleus

isotope

- variant form of an atom
- same number of protons but different number of neutrons
- different forms of the same element behave identically in chemical reactions

radioactive isotope

- nucleus decays spontaneously, giving off particles and energy

electron shell

- energy level representing the distance of an electron from the nucleus of an atom
- valence shell \= outermost electron shell (determine the chemical properties of an atom)
- atoms with an incomplete valence shell interact with other atoms (attraction between atoms results in a chemical bond)

chemical bond

- attraction between to atoms resulting from a sharing of outer shell electrons or the presence of opposite charges on the atoms which hold them close together
- two atoms with incomplete valence shells react to complete their outer shell
- differ in types and strengths

covalent bond

- two atoms share one or more pairs of outer shell electrons
- strongest of the bonds
- valence \= the number of additional electrons needed to fill outer shell
- symbolized by a single line between atoms
- double bond: when two atoms share two pairs of electrons (symbolized by a pair of lines between the atoms)

electronegativity

- affinity of an atom for electrons in a covalent bond
- differences in this can cause unequal sharing of electron pairs in covalent bonds
- causes a more strong pull of shared electrons towards its nucleus (polarity in molecules)

non-polar covalent bond

- attraction between atoms that share one or more pairs of electrons equally because the atoms have similar electronegativity

polar covalent bond

- attractions between atoms that share electrons unequally because the atoms differ in electronegativity
- shared electrons are pulled closer to the more electronegative atom, making it partially negative and the other atom partially positive
- results in one atom partially negative and the other partially positive

polar molecule

- molecule containing polar covalent bonds
- has an unequal distribution of charge within the molecule
- water is an example of this due to the electronegativity difference between oxygen and hydrogen

ion

- atom or molecule that has gained or lost one or more electrons, thus acquiring an electrical charge
- cation: electron loss results in positive charge
- anion: electron gain results in negative charge

ionic bond

- electrical attraction of opposite charges holds ions together

ionic compound

- compound formed by ionic bonds
- often exists as crystals in nature
- bond strengths differ

hydrogen bonds

- nucleus is covalently bonded to one electronegative atom and forms a weaker bond with another electronegative atom

chemical reaction

- process leading to chemical changes in matter
- rearrangement of atoms in molecules to make new molecules
- do not create or destroy matter; only rearrange matter
- conversion of reactants to products
- accompanied by net release or absorption of energy

adhesion

- attraction between different kinds of molecules

cohesion

- attraction between molecules of the same kind
- plants depend on cohesion to help transport water and nutrients from roots to leaves

water

- at any instant, most \_________ molecules hydrogen bonded to other \__________ molecules
- cohesion much stronger for this than most other liquids

surface tension

- measure of how difficult it is to stretch or break the surface of a liquid
- related to cohesion

heat

- released when hydrogen bonds form

temperature

- measure of intensity of heat, reflecting the average kinetic energy or speed of molecules

thermal energy

- amount of energy associated with the movement of the atoms and molecules in a body of matter
- energy in its most random form

evaporative cooling

- property of a liquid whereby the surface becomes cooler during evaporation, owing to a loss of highly kinetic molecules to the gaseous surface
- the molecules with the greatest energy leave the surface

solution

- liquid consisting or a homogenous mixture or two or more substances

solvent

- dissolving agen

solute

- substance that is dissolved

aqueous solution

- solvent \= water

pH

- potential of hydrogen
- measure of the concentration of H+ (hydrogen ions) in a solution

acid

- release of H+ and lowers pH

base (alkali)

removes H+ ions and raises pH

buffer

- resists pH changes
- accepts H+ when it is depleted
- donates H+ when it is depleted
- contributes to pH stability in blood and other biological fluids

pH scale

- measure of the relative acidity of a solution
- ranges in value from 0-14

inorganic compounds

- lack carbon or lack hydrogen atoms

organic compounds

- molecules with a carbon backbone bonded to hydrogen atoms
- carbon based molecules: carbon bonded to other carbons and atoms of other elements

properties of carbon

- can bond with up to 4 other atoms
- can branch in up to 4 directions (variety of organic molecules possible)

carbon skeleton

- chain of carbon atoms
- may vary in length
- may be branched or unbranched
- may have double bonds
- may be arranged in a ring

functional groups

- commonly occurring combinations of atoms attached to a carbon backbone
- less stable that backbone and more likely to participate in chemical reactions (mainly responsible for properties and chemical reactivity fro organic molecules)
- 5 groups are polar and hydrophilic

hydroxyl group

- hydrogen bonded to an oxygen
- polar (hydrophilic)

carbonyl group

- carbon double bonded to an oxygen
- polar and acidic

carboxyl group

- carbon double bonded to an oxygen and bonded to a hydroxyl group
- polar and acidic

amino group

- nitrogen bonded to two hydrogens and the carbon skeleton
- can have 3 bonds
- polar and basic

phosphate group

- phosphorous bonded to four oxygens
- polar and acidic
- forms high energy bonds

methyl group

- carbon bonded to 3 hydrogens
- non polar

macromolecules

- large organic molecules
- usually polymers
- cells make thousands of different macromolecules from few monomers
- polymer synthesis and breakdown
- dehydration reactions and hydrolysis requires enzymes to make/break bonds

dehydration reaction

- addition of a monomer to a polymer

hydrolysis

- removal of a monomer from a polymer

carbohydrates

- sugars and polymers of sugars
- rang from a small monosaccharide to large polysaccharide

disaccharide

- two monosaccharides bonded in a dehydration reaction
- maltose \= 2 glucose monomers
- sucrose \= glucose and fructose

polysaccharide

- chains of monosaccharides
- functions: energy storage, structural support, transport of energy, cell surface interactions, component of nucleic acids

amino acids

- the monomers that make up proteins
- 20 different kinds, all with a common general structure

peptide bond

- amino acids are joined together by dehydration reaction to give this kind of bond

primary protein structure

- linear order of amino acids in the polymer; aa sequence

secondary protein structure

- regions of regular receptive structure; a-helix, β-strand, or β-pleated sheet, stabilized by H bonds between regions of the backbone

tertiary protein structure

- folding of the whole chain die to R group interactions; overall 3D shape

quaternary protein structure

- association of 2 or more polypeptide chains

conformation (shape)

- influences protein function
- results (at least partially) from primary structure
- depends (partly) on weak interactions (hydrogen bonds)

denaturation

- causes a polypeptide chain to change shape
- changes in pH, temperature, and salt can denature a protein

nucleic acids

- amino acid sequence of a polypeptide is programmed by a gene
- genes are a discrete unit of inheritance
- genes consist of DNA, a type of nucleic acid
- 2 types: DNA and RNA

DNA

- pairing up of bases (A&T, C&G)
- double helix: two polynucleotides wrapped around each other, held together by hydrogen bonds between paired bases

RNA

- usually a singly polynucleotide strand (U replaces T in nitrogenous bases)

ATP

- adenosine triphosphate stores energy in bonds between the phosphate groups and releases that energy when the bonds are broken

cAMP

- cyclic adenosine monophosphate acts as a messenger molecule in cells

NAD+ and FAD

electron carriers; transport energy in the form of high energy electrons

lipids

- consist mainly of carbon and hydrogen atoms linked by non polar covalent bonds
- hydrocarbon chains or rings (hydrophobic), often with a polar or charged functional group (hydrophilic) attached
- store energy, surface coatings, components of biological membranes, chemical signals

fats

- lipids containing only carbon, hydrogen and oxygen
- consists of three fatty acids attached to glycerol (triglyceride)

phospholipid

- similar to fat, but glycerol attached to two fatty acids and a phosphate group
- spontaneously assemble into bilayers in aqueous solutions

kinetic energy: matter in motion

- energy contained in a moving mass or in a moving particle
- whenever energy is transferred through a work process, kinetic energy is involved

chemical energy

- energy that is stored in molecular bonds
- bond energy: for any particular chemical bond, the amount of energy it takes to break that bond is exactly the same as the amount of energy released when the bond is formed

exergonic reactions

- release energy
- reactants contain more potential energy than the products

endergonic reactions

- require input of energy
- yield products with more potential energy than the reactants

cellular metabolism

- the sum of endergonic and exergonic reactions in a cell
- metabolic pathway: series of chemical reactions that build or break down complex molecules

energy coupling

- using energy released from exergonic reactions to drive essential endergonic reactions

adenosine triphosphate

- powers cellular work
- consists of: nitrogenous base, 5 carbon sugar, three phosphate groups
- hydrolysis is exergonic

phosphorylation

- transfer of phosphate groups from ATP to other molecule

enzymes

- highly specific for their substrates
- substrate: substance that the enzyme works on
- active site: part of enzyme that binds to substrate, changes shape when substrate is bound (induced fit)
- enzymes are regenerated during the reaction (do not get used up)

competitive inhibitor

- resembles enzymes normal substrate and competes with substrate for active site

non-competitive inhibitor

- does not enter the active site, but binds elsewhere

feedback inhibition

- product may act as an inhibitor of one of the enzymes in the pathway that produced it

membrane functions

- form boundary surrounding cells
- bound organelles -\> partition cells into compartments
- control traffic of essential substances into and out of cells and organelles
- allow communication among cells
- create attachments within and between cells
- regulate many biochemical reactions

the fluid mosaic model

- membrane building blocks: lipids (phospholipids), proteins, carbohydrates bonded to proteins and lipids
- membrane fluidity: components can diffuse laterally

concentration gradient

- difference in solute concentration across a membrane or between 2 different regions of a solution

selective permeability

- property of biological membranes that allows some substances to cross more easily than others, and blocks the passage of other substances completely

diffusion

- spontaneous overton of particles of any kind from where they are more concentrated to where they are less concentrated
- dispersion of atoms, molecules, or ions as a result of random thermal motions
- the higher the temperature and the greater the [ ] gradient, the faster the rate of diffusion
- diffusion continues unto equilibrium is reached

simple diffusion

- very small molecules with no net charge
- lipid soluble molecules, e.g. ethanol, steroid hormones
- increase [ ] gradient, increase temperature, increase lipid solubility, lower molecular size

facilitated diffusion

- down a gradient
- ions and large polar molecules, e.g. sugars, amino acids, ions
- no energy is needed
- transport protein is needed: carrier and channel proteins

osmosis

- diffusion of water across selective permeable membranes
- moves water down its concentration gradient
- solutes reduce the concentration of free molecules in a solution

isotonic solutions

- solution of equal solute concentration

hypertonic solution

- solution with higher solute concentration

hypotonic solution

- solution with lower solute concentration

osmoregulation

- homeostatic maintenance pf solute concentrations and balance of water gain and loss
- crucial to organisms survival

osmotic strength

- tendency to attract water across a membrane
- if 2 solutions are separated by a membrane that is selectively permeable to water: solution with higher [solute] is hypertonic and has higher strength, solution with lower [solute] is hypotonic and has lower strength

tonicity

- ability of a solution to cause a cell to gain or lose water: isotonic causes equal gain and loss, hypotonic causes water to enter cell, hypertonic causes water to exit the cell