BIOL 1P91 Midterm
L1: what is Matter?
- anything that has mass and takes up space
- all life forms are composed of matter
- can exist as a: solid, liquid, gas
L1: what are Atoms?
smallest functional units of matter
- form all chemical substances
- each specific type of atom is a chemical element
L1: what are Molecules?
- one or two atoms bonded together
L1: subatomic particle: PROTONS
- positive charge (+)
- found in atomic nucleus
L1: subatomic particle: Neutrons
- neutral
- found in atomic nucleus
- help stabilize the nucleus
L1: subatomic particle: Electrons
- negative charge (-)
- found in orbitals
L1: True or false, protons and electrons are present in equal amounts and it is only the number of neutrons that changes
true
L1: true or false, scientists initially viewed atoms as a miniture solar system
true
L1: true or false, a better model of an atom is a central nucleus surrounded by cloudlike orbitals
true
L1: what are noble gases and where are they located on the periodic table?
- elements that have their shells completely full
- VERY unreactive, quite stable
- 8th column on periodic table
L1: what is the octet rule?
- tendency of atoms to prefer to have 8 electrons in the valence shell
- with less than 8 electrons, will tend to form compounds
exception is hydrogen which fills its outer shell with just 2 electrons
L1: how many electrons max in the 1st and 2nd shell?
- 2 in the first one, 8 in the second one
L1: true or false, it is the number of protons that distinguishes one element from another?
- true
L1: atomic number?
- the charge number of an atomic nucleus
- equals the number of protons
- the periodic table is organized by the atomic number
L1: what do the rows and columns correspond to?
Rows = number of electron shells
Columns = from left to right, the numbers of electrons in the outer shell (# of valence electrons)
L1: true or false, elements in the same column share properties but are not interchangeable?
true
L1: Atomic mass?
- indicates an atom's mass relative to the mass of other atoms
- protons and neutrons are nearly equal in mass (both are more than 1,800 times the mass of an electron)
- is the averages of the masses of different isotopes of an element
atomic mass = protons + neutrons
L1: Radioisotopes?
- will decay into lower mass forms
- unstable
- emit radiation as they decay
- used in medicine for cancer treatment, imaging
ex.) carbon 14 is unstable and will decay
L1: Mass vs. Weight?
Mass = the same in all locations, an absolute value
Weight = based on the gravitational pull on a given mass,
L1: Units - Dalton
(Da)
- measurement for atomic mass
- also known as atomic mass unit (amu)
- 1 Da = 1/12 the mass of a carbon atom
L1: Units - Mole
- 1 mole of any element contains the same number of atoms
- Avogadro's number
- 6.022 x 10 (to the 23)
- used to convert between mass and the number of protons
L1: Isotopes?
- multiple forms of an element that differ in the number of neutrons
ex.) C12 and C14
C12= 6 protons and 6 neutrons
C14 = 6 protons and 8 neutrons
L1: what is the building block of all living matter (the most abundant)?
carbon
L1: True or false: hydrogen, oxygen, carbon, and nitrogen make up about 95% of the atoms in living organisms?
True
(hydrogen and oxygen occur primarily in water)
(nitrogen is found in proteins)
L3: True or false, properties of a compound can be drastically different than the properties of the individual elements in the compound?
True
L3: Covalent bond (1/3)?
- electrons are shared (in order to fill valence shells)
can either be: polar covalent or nonpolar covalent
Polar covalent: more electronegative towards one atom
- between atoms of diff electronegativity
- unequal distribution creates a polarity (difference in electric charge) - mainly polar interactions
ex.) 0.4 to 0.8
Nonpolar covalent: 50 50 sharing
- between atoms with electronegativities
- no charge difference across molecule
- no possibility of hydrogen bonding with nonpolar covalent bonding
ex.) < 0.4
THE STRONGEST BOND!
L3: Hydrogen bond (2/3)
- hydrogen atom from one polar molecule is attracted to an electronegative atom from another molecule
- "not a sharing of the electrons, it's the attraction"
weaker but more numorous
- can be disrupted easily in water
- represented as dashed or dotted lines
L3: Ionic Bond (3/3)
electrons are transferred, forming ions
(one atom was so strong it pulled the atom from another towards it)
ex.) > 1.8
L3: what are Van der Waals dispersion forces?
- transient attraction (different than the other interactions)
- another type of weak molecular attraction
- created when electrons are located within orbitals in a random way
- FLEETING ELECTRICAL ATTRACTION: collective strength can be quite strong
- little spaces of charge
- mainly nonpolar interactions
L4: Cations? Anions?
Cations: have a net positive charge (+) -donate electrons
Anions: have a net negative charge (-) -mainly acquire the electrons
IONIC BONDS OCCUR WHEN A CATION BINDS TO AN ANION BY ELECTROSTATIC ATTRACTION
L4: Ca2+ = ?, Cl- = ?, H+ = ?, Mg2+ = ?
Ca2+ = lost 2 electrons
Cl- = gained one electron
H+ = lost one electron
Mg2+ = lost 2 electrons
L4: what does it mean to be SATURATED?
- having double bonds
L4: when referring to molecular shape/structure, RIGID means what?
- refers to how it is more difficult to rotate (not that it breaks easily)
L4: shape is determined by _____________ and ________ of ______ between atoms
determined by the arrangement and number of bonds between atoms
ex.) Carbon oxygen molecule with double bonds will have a planar arrangement
L4: True or false, noncovalent interactions may alter the shape of molecules?
- true
L4: Free radicals
- molecule containing an atom with a single, unpaired electron in its outer shell
- highly reactive molecule (can "steal" an electron from other molecules)
- can form exposure to radiation and some toxins
- can cause cell damage, kill invading bacteria
- will react almost instantly
L4: Chemical reactions
Chemical reactions:
- when one or more substances are changed into other substances
- reactants to products
- require a source of energy (ex. heat, ATP)
- often require an enzyme as a catalyst (speeds reaction rate)
- occur in liquid (water) -like most things in bio
L4: Properties of water (solution, solute, solvent)
Solution = solutes in a solvent (the liquid, in bio it's water)
Solutes = dissolved substances
Solvent = the liquid
L4: SOLUTES: Hydrophilic, hydrophobic, amphipathic
HYDROPHILIC: "water-loving"
- readily dissolve in water
- ionic and/or polar covalent bonds
HYDROPHOBIC: "water-fearing"
- do not dissolve in water
- nonpolar molecules like hydrocarbons, oils
AMPHIPATHIC: "both loves"
- both polar/ionized and nonpolar regions
- may form micelles in water
ex.) detergent is an amphipathic molecule
- have hydrophobic and hydrophilic properties
L4: Concentration?
- amount of a solute dissolved in a unit volume of solution
generally in gram/liter
L4: Molarity?
= number of moles of a solute dissolved in 1 Liter of water
L5: Heat of vaporization? Heat of fusion?
Heat of vaporization: energy to boil
Heat of fusion: energy to melt
- water is extremely stable as a liquid, due to high heats of vaporization and fusion, and high specific heat
L5: what is Specific Heat?
- the amount of heat energy to raise the temperature 1 degrees Celsius
L5: what influences the temperature at which a solution freezes or boils?
- by the amounts of dissolved solutes
adding solutes to water:
- lowers the freezing point (below 0)
- raises the boiling point (above 100)
L5: name some of water's functions in living organisms?
- participants in chemical reactions
- force or support
- removes toxic waste components
- evaporative cooling
- cohesion (molecules of same type attract each other) and adhesion (unlike molecules attract each other)
- surface tension (measure of attraction between molecules at the surface of a liquid)
- lubrication
L5: Acids?
molecules that release hydrogen ions in solution
- strong acid releases MORE H+ than a weak acid
L5: Bases?
lowers the H+ concentration
- some release OH-
- others bind H+
L5: the pH scale?
pH 0-6 = Acidic solutions (0 is most acidic) ex.) stomach fluid, lemon juice
pH 7 = Neutral solutions
pH 8-14 = Alkaline solutions (14 is most basic) ex.) bleach, baking soda
L5: what can the pH of a solution affect?
- the shapes and functions of molecules
- rates of chemical reactions
- ability of two molecules to bind to each other
- ability of ions or molecules to dissolve in water
L5: what do BUFFERS do?
- buffers help to maintain a constant pH (organisms usually only tolerate only small changes in pH)
L5: what is an ACID-BASE BUFFER system?
can shift to remove or release H+ to adjust for changes in pH
L6: what are MACROMOLECULES
- large, complex organic molecules
L6: True or false, organic molecules contain CARBON?
true
L6: functional groups? - list them (5)
groups of atoms with special chemical features that are functionally important
- each type of functional group exhibits the same properties in all molecules in which it occurs
ex.) Amino, Carbonyl, Aldehyde, Carboxyl, Hydroxyl
L6: what are some functional groups that bond to carbon? (list the 4)
- methyl (CH3) - nonpolar
- Phosphate (PO4 2-) - backbone of DNA molecules - polar
- Sulfate (SO4-) - polar
- Sulfhydryl (SH) also known as thiol - polar
L6: what are isomers? difference between Structural isomers and Stereoisomers?
two molecules with an identical molecular formula but different structures and characteristics
Structural isomers: contain the same atoms but in different bonding relationships
Stereoisomers: identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers
-> Cis-trans isomers: positioning around the double bond
-> Enantiomers: mirror image molecules (clearly see that they are different) -diff. in orientation leads to diff. binding abilities
L6: polymer formation by CONDENSATION reactions (also known as dehydration reactions)
- a molecule of water is removed (each time a new monomer is added)
- process repeats to form long polymers
- process catalyzed by enzymes
- produces a larger organic molecule plus a water molecule
L6: breakdown of a polymer by HYDROLYSIS reactions (also known as hydration reaction)
- molecule of water is added back (each time a monomer is released)
- process repeats to break down long polymer
- process is catalyzed by enzymes
L6: what are the 4 major classes of organic molecules found in living cells
Carbohydrates (composed of carbon, hydrogen and oxygen atoms) Cn(HnO)n -the n's have to have the same number
Lipids
Proteins
Nucleic acids
L6: what are monosaccharides?
- means one sugar
- most common are 5 (pentoses) or 6 carbons (hexose)
L6: a- and b-glucose (stereoisomers of glucose)
- hydroxyl group of carbon 1 is above or below ring
alpha = hydroxyl is on opposite side as carbon 6
beta = hydroxyl is on same side as carbon 6
L6: D- and L-glucose (stereoisomers of glucose)
- enantiomers with mirror image structure
D-glucose = commonly found in living cells
L-glucose = rarely found in living cells
L6: what are disaccharides?
- composed of 2 monosaccharides
- joined by dehydration or condensation reaction
-> glycosidic bond
ex.) sucrose, maltose, lactose
L7: what are polysaccharides?
- many monosaccharides linked together to form long polymers
ex.) energy storage(starch, glycogen), structural (cellulose, chitin)
L7: Lipids
- are NOT polymers
- mainly hydrogen, carbon and some oxygen atoms
- are NONPOLAR (therefore very insoluble in water)
L7: Fats
- fats and oils are essentially the same thing (fats are solid)
also known as TRIGLYCERIDES
- formed by bonding glycerol to 3 fatty acids
- joined by dehydration (resulting bonds are ester bonds)
Energy storage
Structural: provide insulation
L7: Saturated vs. Unsaturated fatty acids?
Saturated - all carbons have the maximal amount of hydrogens
- tend to be solid at room temp.
Unsaturated - contains one or more double bonds (=not all the possible amount of hydrogen on the carbons)
- tend to be liquid at room temp.
Cis forms naturally, trans formed artificially(linked to disease)
- Cis bonds creates kinks in the fatty acid
L7: what is a PHOSPHOLIPID comprised of?
- two fatty acids and a phosphate group
- amphipathic molecule
Phosphate head: polar/hydrophilic (polar heads will face outside)
Fatty acid head: nonpolar/hydrophobic
L7: STERIODS
- four interconnected rings of carbon atoms
- insoluble in water
ex.) cholestrol
L7: WAXES
- all contain 1 or more hydrocarbons and long structures that resemble a fatty acid attached by its carboxyl group to another long hydrocarbon chain
- very NONPOLAR (barrier to water loss)
L7: PROTEINS
- composed of carbon, hydrogen, oxygen, nitrogen and small amounts of other elements like sulfur
- amino acids are the building blocks
L7: Amino Acid structure (name the 4 parts)
the carbon makes 4 bonds to:
1. a hydrogen
2. amino acid side chain (represented by a R) *20 diff amino acids*
3. carboxyl group (C03)
4. Amino group (NH3)
L8: what is a POLYPEPTIDE?
- POLYMERS OF AMINO ACIDS (amino groups joined by dehydration reaction)
- PROF THINKS THAT PROTEINS ARE POLYPEPTIDES
L8: which amino acid is the N-terminus or the C-terminus?
N-terminus = the amino acid at the beginning of the protein
C-terminus = the last amino acid
L8: Protein hierarchy of structure (4 progessive levels)
1. Primary
- linear sequence of the amino acids
2. Secondary
- sequences of amino acids together
- either a spiral (alpha helix) or sheet (beta pleated sheet)
3. Tertiary
- secondary structures and random coils folded into a 3D shape
4. Quaternary
- 2 or more polypeptides binded together
- form a functional protein
L8: what are 5 factors that promote protein folding and stability?
- hydrogen bonds
- ionic bonds and other polar interactions
- hydrophobic effects
- Van der Waals forces
- Disulphide bridges
L8: protein-protein interactions
- specific binding at surface
- two or more different proteins interact
L9: Anfinsen's beliefs on proteins
- proteins contain all the info necessary to fold into their proper conformation
- proteins spontaneously assume their most stable conformation
SINCE THEN HAVE LEARNED THAT PROTEINS DO REQUIRE ASSISTANCE IN FOLDING
L9: what are 4 domains of proteins?
1. Ligand binding
2. DNA binding
3. Nuclear localization domain
4. Activation domain (a protein fold that activates genes)
PROTEINS THAT SHARE A PARTICULAR DOMAIN ALSO SHARE THE ASSOCIATED FUNCTION
L9: Nucleic acids: what are they and what are the 2 classes?
responsible for the storage, expression, and transmission of genetic information
1. Deoxyribonucleic acid (DNA)
-> stores genetic info encoded in the sequence of nucleotide monomers
2. Ribonucleic acid (RNA)
-> decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain
L9: what is a nucleotide made of? what are they linked by?
- made of a PHOSPHATE GROUP
- a FIVE-CARBON SUGAR (either ribose or deoxyribose)
- a SINGLE OR DOUBLE RING (of carbon and nitrogen atoms) = known as a base
- nucleotides are linked into a polymer by a SUGAR-PHOSPHATE BACKBONE
L9: what are PURINES and PYRIMIDINES?
Purines: nucleotides of ADENINE (A) and GUANINE (G)
-> double cyclic
Pyrimidines: nucleotides of CYTOSINE (C) and THYMINE (T)
-> single cyclic
L9: DNA
- consists of two stands of nucleotides coiled around each other in a double helix
- held together by hydrogen bonds (between a purine base in one strand and a pyrimidine base in the opposite strand)
A PAIRS WITH T, AND C PAIRS WITH G
L9: DNA vs. RNA
DNA:
- deoxyribonucleic acid
- deoxyribose
- thymine (T)
- A, G, C used in both
- 2 strands, double helix
- 1 form
- does not have oxygen on the 2nd carbon
RNA:
- ribonucleic acid
- ribose
- Uracil (U)
- A, G, C used in both
- single strand
- several forms
- has an oxygen on the 2nd carbon
L10: what are the two main life goals of living organisms?
survive and reproduce
L10: What are two or more atoms of the same kind called?
- a molecule
L10: what are two or more atoms of different kind called?
- a compound
L10: energy relationships involving interactions among the electrons or reacting atoms
= chemical bonds
L10: the sum total of all chemical reactions that occur within an organism?
= metabolism
L10: matter may be changed _____________ and _______________
Physically:
- changes do not alter the basic nature of a substance
ex.) changes in the state of matter (solid, liquid, gas)
Chemically:
- changes alter the chemical composition of a substance
L10: the ability to do work
= energy
- has no mass and does not take up space
L10: Kinetic energy
= energy is doing work
- associated with movement
ex.) hand with hammer swinging down
L10: Potential energy
- energy held up by an object because its position relative to other objects (hand raised above a nail, not swinging the hammer)
L10: Thermodynamics
- study of energy interconversions
(energy being converted from one form to another)
L10: what is the First Law of Thermodynamics?
energy cannot be created or detroyed, but can be transformed from one type to another
L10: Second Law of Thermodynamics?
transfer of energy from one form to another increases the entropy (degree of disorder) of a system
- as entropy increases, less energy is available for organisms to use to promote change or do work
L10: what is free energy and what symbol represents it?
Free energy = amount of energy available to do work
= (G)
also called Gibbs free energy
Gibbs free energy = to predict whether a chemical process is spontaneous or non-spontaneous
L10: H = G + TS
H = enthalpy or total energy
G = free energy or amount of energy for work
S = entropy or unusable energy
T = absolute temperature in Kelvin (K)
L10: what makes a reaction spontaneous?
occur WITHOUT input of additional energy to proceed naturally
- may need to provide some activation energy
-> once the reaction has started, the rest will proceed without the need of a continous input of an external source of energy
eg.) Combustion
-just because it is spontaneous doesn't mean that it is fast
L10: a non-spontaneous reaction?
- a continuous energy input is necessary for the reaction to proceed
eg.) photosynthesis: requires constant source of energy (in the form of sunlight) to drive chemical reactions