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
L10: Exergonic and Endergonic reactions
Exergonic = spontaneous
- change in G is less than zero (neg. free energy change)
- energy is released by reaction
Endergonic = not spontaneous
- change in G is greater than zero (pos. free energy change)
- requires addition of energy to drive reaction
L11: True or false, an endergonic reaction can be coupled to an exergonic reaction so that the two reactions overall is thermodynamically favored
true
L11: True or false, ATP is the major 'energy' molecule produced by metabolism: it's dispatched to wherever a non-spontaneous reaction needs to occur within the cell
True!
L11: do cells use ATP hydrolysis to drive reactions?
Yes!
- typical cells use millions of ATP molecules per second to drive endergonic processes
L11: what are CATALYSTS?
- an agent that speeds up the rate of a chemical reaction without being consumed during the reaction
L11: what are ENZYMES?
- protein catalysts in living cells
- act as biological catalysts
- increase the rate of chemical reactions
- bind to substrates at an active site to catalyze reactions
- can be recognized by their suffix: hydrolase, oxidase
L11: what are RIBOZYMES?
RNA molecules with catalytic properties
L11: what is HYDROLASE (an enzyme)?
enzymes that facilitate the cleavage of bonds in molecules with the addition of the elements of water -they help to break down
L11: ACTIVATION ENERGY
what is it: initial input of energy to start reaction
- allows molecules to get close enough to cause bond rearrangement
how to overcome it:
- large amounts of heat
- using enzymes to lower activation energy
L11: how do enzymes lower activation energy?
- straining bonds in reactants make it easier to achieve transition state
- positioning reactants together to facilitate bonding
- enzymes bring reactants together, so they don't have to expend energy moving about until they collide at random
L11: Location where reaction takes place?
ACTIVE SITE
L11: reactions that bind to active site?
SUBSTRATES
L11: formed when enzyme and substrate bind?
ENZYME SUBSTRATE COMPLEX
L11: enzyme affinity and saturation?
Affinity: degree of attraction between an enzyme and its substrate
Saturation: plateau where nearly all active sites are occupied by substrate
L12: Enzyme inhibitors: Competitive and Non-competitive
Enzyme inhibitors: molecules that interact w/ enzymes in some way and reduce the rate of an enzyme-catalyzed reaction or prevent enzymes to work in a normal matter
Competitive: inhibitor molecules binds to active site
- direct competition with the substrate
- inhibits ability of substrate to bind = Km needs to increase as more substrate needed
- in the system is swamped with substrate, it would knock out the inhibitor
Non-competitive: lowers Vmal without affecting Km
- inhibitor binds to allosteric site(another spot on the enzyme), not active
- causes a shape change in the enzyme
L12: Small molecules permanently attached to the enzyme and aids in enzyme function
prosthetic groups
ex.) FAD
L12: Usually inorganic ion that temporarily binds to enzyme to promote a chemical reaction
Cofactor
L11: organic molecule that participates in reaction but is left unchanged afterward
Coenzyme
ex.) NAD
L12: difference between ANABOLIC metabolic pathways and CATABOLIC metabolic pathways?
Anabolic:
- synthesis of cellular components (to build bigger molecules)
- endergonic (must be coupled to exergonic reactions
ex.) Amino acids --> proteins (through dehydration reactions)
Catabolic:
- breakdown cellular components(reactants)
- used for recycling building blocks
- used for energy to drive endergonic reactions
- exergonic
ex.) Glycolysis (breakdown of sugar)
L12: what are two ways to make ATP?
1. Substrate-level phosphorylation: The enzyme directly transfers phosphate from one molecule to another molecule
2. Chemiosmosis: energy stored in an electrochemical gradient is used to make ATP from ADP and P
L12: how are electrons shuttled? Redox reactions!
- the reactions in which NAD+ and FAD gain or lose electrons
LEO says GER
(losing electrons = oxidation)
(gaining electrons = reduction)
cellular respiration involves many reactions in which electrons are passed from one molecule to another
L12: Regulation of metabolic pathways: gene regulation, cellular regulation, biochemical regulation, recycling of organic molecules
Gene regulation: turn genes on or off that encode for the creation of enzymes
Cellular regulation: cell-signaling pathways like hormones (i.e. targeted on and off switch via chemical messenger)
Biochemical regulation: feedback inhibition: product of pathway
Recycling of organic molecules:
- most large molecules exist for a relatively short time
- RNA and proteins are made when needed and broken down when not needed
L12: Half-life?
time it takes for 50% of the molecules to be broken down and recycled
L12: Proteasome
large complex that breaks down proteins using protease enzymes
- they cleave bonds between amino acids (tags a target protein with ubiquitin and breaks up the protein into individual monomers)
L12: what does UBIQUITIN TAGGING allow for? (3 answers)
1. degrade improperly folded proteins
2. rapidly degrade proteins to respond to changing cell conditions
3. recycle amino acids for new proteins
L12: function of LYSOSOMES?
1. contain hydrolases to break down proteins, carbohydrates, nucleic acids, and lipids
2. digest substances: taken up by endocytosis
3. Autophagy: recycling worn-out organelles using an autophagosome -> this process delivers the organelles to the lysosomes
L13: what is definition of cellular respiration and what is its aim?
a process by which living cells obtain energy from organic molecules and release waste products
Primary aim: to make ATP
L13: Difference between EUKARYOTES and PROKARYOTES?
Eukaryotes
- have a nucleus and membrane-bound organelles
- larger
- more complex cell structure
- DNA in nucleus
- plants, animals, fungi
Prokaryotes
- lack a nucleus and membrane-bound organelles
- simple structure
- DNA in cytoplasm
- bacteria, archaea
L13: basic overview of glucose metabolism
- when glucose is broken down, some of the energy is lost as heat but much of it is used to make 3 energy intermediates: ATP, NADH, FADH2
L13: what are the 4 metabolic pathways?
1. Glycolysis - in cytosol
2. Breakdown of pyruvate - in mitochondrial matrix
3. Citric acid cycle - in mitochondrial matrix
4. Oxidative phosphorylation - in mitochondria (inner membrane)
L13: One turn of the Citric Acid cycle produces what?
- 2 CO2, 1ATP, 3 NADH, 1 FADH2
L15: what are the two main goals of the ETC?
1. oxidizing high energy intermediates (which releases protons)
2. Uses energy to pump the protons into the outer membrane space
**moves against the gradient** going from inner to outer membrane
L15: what does ATP and ADP stand for?
ATP = Adenosine Triphosphate
ADP = Adenosine Diphosphate