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128 Cards in this Set

  • Front
  • Back
BIOMOLECULES
an organic compound normally present as an essential component of living organisms
DISTINGUISHING FACTORS OF LIVING ORGANISMS
- A high degree of chemical complexity and microscopic organization
- Systems for extracting, transforming, and using energy from the environment
- A capacity for precise self-replication and self-assembly
- Mechanisms for sensing and responding to alterations in their surroundings
- Defined functions for each of their components and regulated interaction among them
BIOCHEMISTRY
- describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing priciples we refer to collectively as the molecular logic of life
PLASMA MEMBRANE
- defines the periphery of the cell
- composed of lipid and protein molecules that form a thin, tough, pliable, hydrophobic barrier around the cell
- free barrier to inorganic ions and most other charged and polar molecules
- allows change of shape and size of cell because of flexibility
CYTOPLASM
- composed of the cytosol
- the cytosol is highly concentrated with enzymes and RNA molecules, amino acids and nucleotides, metabolites, coenzymes, and ribosomes
NUCLEUS
- where DNA is stored and replicated
- Eukaryotes have nuclear envelopes while prokaryotes do not
KINGDOMS
- eubacteria
- eukaryotes
- archaebacteria
EUBACTERIA
- inhabits soils, surface waters, and the tissue of other living or decay organisms
- Most well studied bacteria
ARCHAEBACTERIA
-most recently discovered
- less well characterized biochemically
- inhabit extreme environments (salt lakes, hot springs, highly acidic bogs, and ocean depths
- more closely related to eukaryotes than eubacteria
PHOTOTROPHS
- trap and use sunlight
- autotrophs- receive all needed carbon from CO2
- heterotrophs- need carbon from organic molecules
CHEMOTROPHS
- energy from oxidation of a fuel (organic nutrients)
- They can't fix carbon dioxide into organic compounds
- can't get carbon exclusively from carbon dioxide
- Lithotrophs- fuels that are oxidized are inorganic
- Organotrophs- fuels that are oxidized are organic
DIFFERENCES BETWEEN EUKARYOTES AND PROKARYOTES
- eukaryotes are bigger
DIFFERENCES BETWEEN PLANT AND ANIMAL CELLS
- animal cells have a nuclear envelope
- plant cells have chloroplasts and vacuoles
- plant cell have a cell wall
CELL FRACTIONATION
- cells or tissues in solution are disrupted by gentle homogenization
- leaves organelles in tact but ruptures plasma membrane
- homogenate is centrifuged
- organells sediment at different rates because of size
DIFFERENTIAL CENTRIFUGATION
- rough fractionation of the cytoplasmic contents
- organelles of different buoyant densities are separated on a density gradient
CYTOSKELETON
- protein filaments crisscrossing the eukaryotic cell
- forms n interlocking three-dimensional meshwork
- 3 types of filament: microtubules, actin, and intermediate filaments
- provide structure and shape to cytoplasm and shape to cell
- interactions between cytoskeleton and organelles are noncovalent, reversible, and subject to regulation in response to variousintracellular and extracellular signals
MACROMOLECULES
- subunits are usually joined by covalent bonds
- in supramolecular complexes macromolecules are held together by noncovalent interactions
METABOLOME
- the entire collection of small molecules in a given cell
PROTEINS
- long polymers of amino acids
- largest fraction of cells
- have catalytic activity, function as enzymes, serve as structural elements, signal receptors, or transporters
NUCLEIC ACIDS
- nucleotide residues are linked into DNA and RNA
POLYSACCHARIDES
- polymers of simple sugars
- energy yielding fuel stores
- extracellular structural elements with specific binding sites for particular proteins
LIPIDS
- hydrocarbon derivatives
- structural components of membranes
- energy rich fuel stores
- pigments
- intacellular signals
STEREOISOMERS
- molecules with the same chemical bonds but different stereochemistry
- exists when there is one double bond and has chiral centers
- a molecule has 2^n steroisomers. n being the number of chiral centers
CHIRAL CENTERS
- carbon with 4 different substituents
- clockwise rotation is R, counterclockwise rotation is S
- a molecule with a single chiral center can be named with the R-S naming system or the D-L naming system
ENANTIOMERS
- mirror images of each other
DIASTEREOMERS
- not mirror images of each other
RACEMIC MIXTURE
- 2 enantiomers that exhibit no optical rotation because the same amount of enantiomer exists in the mixture
- Compounds without chiral centers do not rotate the plane of polarized light
CONFORMATIONS
- staggered is most stable, while eclipsed is least stable
SYSTEM
- all reactants and products present, the solvent that contaisn them, and the immediate atmosphere
CLOSED
- if it exchanges both energy and matter with its surroundings
OPEN
- if it exchanges both energy and matter with its surroundings
- living organism
ISOLATED
- if the system exchnages neither matter nor energy with its surroundings
OXIDATION REDUCTION REACTIONS
- all reactions involving electron flow
- one reactant is oxidized while the other is reduced
ENTROPY
- change in S
- any change in randomness of the system
- positive when randomness increases
FREE ENERGY CONTENT
- G
= change H - [T * Change S]
- if G is negative it is a spontaneous reaction
ENTHALPY
- H
- reflects the number and kinds of bonds
ENDERGONIC REACTIONS
- energy requiring
EXERGONIC REACTIONS
- energy releasing
- the sum of G1 and G2 is negative
- decline in free energy from reactants to products
- ATP to ADP and Pi
Keq
- the reaction proceeds until the reactants have almost completely converted into the products
STANDARD FREE ENERGY CHANGE
- change G = -RT ln Keq
- J/mol
- negative when Keq>>1
CATABOLIC
- exergonic reactions
ANABOLIC
- endergonic reactions
- requires the input of energy
WATER
- most abundant substance in living systems (70% or more weight of living systems)
- Important physical and chemical properties
- Solvent for bioreactions
- bond angle is 104.5
- Tetrahedron
- When water is a liquid is bonds to less water molecules (3.4) than when it is with ice (4.0)
WEAK INTERACTIONS IN AQUEOUS SOLUTION
- hydrogen bonds
- ionic interactions
- hydrophobic interactions
- Van der Waals Interactions
HYDROGEN BONDS
- gives water its unusual propterties: high melting point, high boiling point, high heat of vaporization
- the electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another
- occurs between an electronegative atom (hydrogen acceptor) like oxygen or nitrogen with a lone pair of electrons and a hydrogen atom covalently bonded to another electonegative atom (hydrogen donor)
BOND DISSOCIATION ENERGY
- energy required to break a bond
SPONTANEITY
- Change of H (enthalpy) remains the same for melting and evaporation, so the increase in entropy (change in S) makes the change of G positive or negative
WHEN ARE HYDROGEN BONDS THE STRONGEST?
- molecules are oriented to maximize electrostatic interaction when the hydrogen atom and the two other atoms are in a straight line.
HYDROPHILIC
- compounds that dissolve easily in water
HYDROPHOBIC
- don't dissolve in water
- nonpolar molecules like lipids and waxes
FORCE OF IONIC INTERACTIONS
- magnitude of charges (Q1&Q2) divided by the distance and dielectric constant
- stronger in less polar environments
NONPOLAR COMPOUNDS
- unable to undergo energetically favorable interactions with water molecules
- small gain in enthalpy
- decrease in entropy
AMPHIPATHIC COMPOUNDS
- contains regions that are polar and regions that are nonpolar
- forces that hold nonpolar areas together are hydrophobic interactions
DISPERSION OF LIPIDS IN WATER
- each lipid molecule forces surrounding water molecules to become highly ordered
CLUSTERS OF LIPID MOLECULES
- only lipid portions at the edge of the cluster force the ordering of water
- fewer water molecules are ordered
- entropy increases
MICELLES
- circle of lipids
- hydrophobic groups are sequestered from water
- ordered shell of water molecules is minimized
Entropy increases
VAN DER WAALS INTERACTIONS
- any two atoms in close proximity
- dipoles from electrons near both nucleuses attract one another
COLLIGATIVE PROPERTIES
- depend only on the solute concentration, not the chemical properties of the solute
- vapor pressure
- boiling point
- melting point
- osmotic pressure
- solutes alter colligative properties by lowering the effective concentration of water
OSMOTIC PRESSURE
- water molecules diffuse from an area of high concentration to an area of low concentration
- PI = icRT
- c is the molar concentration, I is the van't Hoff factor, R (0.0821 liter-atm/mole degree K) is the gas constant, and T is the absolute temperature
- Pi is given in atmospheres
ISOTONIC
- no net water movement
HYPERTONIC
- water moves out and cell shrinks
- inside the cell has a smaller concentration of molecules than outside the cell
HYPOTONIC
- water moves in to the higher concentration
- creates outward pressure
- cell swells and eventually bursts
IONIC PROPERTIES OF WATER
- pure water is slightly ionized
- water = H+ + OH-
- H exists as a hydronium ion which gives up a proton in proton hopping
- very rapid
EQUILIBRIUM CONSTANT
K = [A][B]/[C][D]
- water is: k= [H][OH]/[water]= 1.8 X 10^-16M
ION PRODUCT OF WATER
Kw = (55.5M)(k) = [H][OH] = 1.0 x 10^-14 M^2
pH
- the ion product of water forms the basis for the pH scale
- -log[H]
- pOH is -log[OH]
STRONG ACIDS
- completely ionized
- hydrochloric, sulfuric, and nitric
- pH = -log[acid]
STRONG BASES
- completely ionized
- NaOH and KOH
- pH = 14-log[base]
WEAK ACIDS
- don't completely dissociate in water
- acids give up protons
- acetic acid
WEAK BASES
- don't completely dissociate in water
- bases accept protons
- ammonia
CONJUGATE ACID-BASE PAIR
- HA = H+ + A-
- HA is the conjugate acid
- A is the conjugate base
- Ka = [H][A]/HA
STRONG ACIDS
- completely ionized
- hydrochloric, sulfuric, and nitric
- pH = -log[acid]
STRONG BASES
- completely ionized
- NaOH and KOH
- pH = 14-log[base]
WEAK ACIDS
- don't completely dissociate in water
- acids give up protons
- acetic acid
WEAK BASES
- don't completely dissociate in water
- bases accept protons
- ammonia
CONJUGATE ACID-BASE PAIR
- HA = H+ + A-
- HA is the conjugate acid
- A is the conjugate base
- Ka = [H][A]/HA
pKa
= log (1/ka) = -log Ka
= to the midpoint of the titration curve
- measure of the tendency of a group to give up a proton
- the molecules with the lowest pk loses its protons first
TITRATION CURVE OF WEAK ACID
- a plot of PH against the amount of NaOH added
- a weak acid and a conjucate acid-base pair acts as a buffer
- involves the gradual addition and removal of protons
HENDERSON-HASSELBALCH EQUATION
Ka = [H][A]/[HA]
logKa = log[H] + log[A]/[HA]
-log[H] = -logKa + log[A]/[HA]
pH = pK + log[A]/[HA]
BUFFERS
- resist change in pH
- mixtures of weak acids and their conjugate bases resist change in pH upon addition of either stron acid or base
- A buffering region is along the plateau (when the weak acid is 100% titrated)
BUFFERING IN BIOLOGICAL SYSTEMS
- phosphate and bicarbonate buffer systems maintain intracellular and extracellular fluids at their optimum pH
- optimum pH is close to 7
- Enzymes generally work at optimum pH
CONDENSATION REACTION
- water is eliminated
- ADp + Pi = ATP
- endergonic reactions
HYDROLYSIS REACTION
- addition of water elements
- responsible for enzymatic depolymerization of proteins, cabs, and nucleic acids
- exergonic reactions
AMINO ACIDS
- organic compounds that contain both an amino group and a carboxylic acid
PROTEINS
- most abundant biological macromolecule occurring in all cells and all parts of cells
- molecular instruments through which genetic info is expressed
- polymers of amino acids that are bounded by covalent bonds. Loses water when aa join together (amino acid residue)
STEROISOMERS
- The alpha carbon is the chiral center of the amino acids as long as there are 4 different groups
- amino acids have new steroisomers because they are nonsuperimposible mirror images (enantiomers) and optically active
D,L SYSTEM
- Its L if the amino group is on the left
- Its D if the amino group is on the right
- Amino acid residues in proteins are L stereoisomers
POLARITY
- tendency to interact with water at biological pH near 7.0
NONPOLAR, ALIPHATIC R GROUPS
- tends to cluster within proteins, stabilizing protein structure by means of hydrophobic interactions
AROMATIC R GROUPS
- relatively nonpolar
- all can participate in hydrophobic interactions
POLAR UNCHARGED R GROUPS
- more soluble in water (hydrophilic)
- functional groups form hydrogen bonds with water
CYSTINE
- covalently linked dimeric amino acid
- 2 cysteine molecules or residues are joined by a disulfide bond
- disulfide bonds are nonpolar and hydrophobic
POSITIVELY CHARGED (basic)R GROUPS AND NEGATIVELY CHARGED (Acidic) R GROUPS
- most hydrophillic R groups are either positively or negatively charged
ZWITTERION
- dipolar ion
- can act as a acid or base
- also called ampholytes because of this duel nature
ISOELECTRIC POINT
- at sufficiently low pH all amino acids are positively charged
- At sufficiently high pH all amino acids are negatively charged
- At some pH all amino acids have no charge
- The isoelectric point is the pH at which the amino acid has no net charge
- pI = 1/2(pk1 + pk2)
* Must be the two pks that surround the molecule with no net charge
DIFFERENCES IN PKs
- The basic diprotic titration is exhibited in the amino acids with a single alpha amino group and a single alpha carboxyl group, and an R group that doesn't ionize
- The normal range is pk (COOH) 1.8 to 2.4 and pK (NH3) 8.8 to 11.0
- Amino acids with a ionizable R group have a 3 stage titration curve
PEPTIDES
- polymers of amino acids
- peptide bond is the only bond
- written with amino terminus at left and carboxyterminus at right
- aa are called residues
PEPTIDE BOND
- covalently bonds 2 amino acids with a substituted amide linkage
- removes water
- joins alpha carboxyl group of one aa with the alpha amino group of the other
- hydrolysis is exergonci but its slow because of high activation energy
- peptide bonds are stable and have a half life of 7 years
- characteristic titration curve and isolectric pH
OLIGOPEPTIDE
- few amino acids are joined
POLYPEPTIDE
- many amino acids are joined together
- molecular weight below 10,000. Proteins have molecular weight above 10,000
ISOELECTRIC PH FOR PEPTIDES
- determined by loss of charge in alpha carboxyl and alpha amino groups, the interactions with other peptide R groups, and environmental factors
- approximate number of amin o acid residues by dividing its molecular weight by 110.
MULTISUBUNIT
- 2 or more polypeptide chains bonded noncovalently
- If they are identical polypeptides the protein is oligomeric and the units are protomers
SIMPLE PROTEINS
- only amino acid residues and no other chemical constituents
CONJUGATED PROTEINS
- proteins with permanently associated chemical ponents in addition to amino acids
- classified based on prosthetic groups
PROSTHETIC GROUP
- non amino acid part of the conjugated protein
- lipoproteins, glycoproteins, metalloproteins
PROTEIN STRUCTURE
- Primary - amino acid sequence and includes any disulfide bonding that exists
Covalent bonds between amino acids and proteins
- Secondary- stable arrangements
- Tertiary- 3 dimensional folding of a polypeptide
- Quarternary- two or more polypeptide subunits
- protomers are the smallest units
PROTEIN PURIFICATION
- Assay (know how much protein your starting with by enzymatic activity, immunological activity, color, size or any property you can measure)
- breaks open tissue and microbial cells and releases it into crude extract
- Separate - differential centrifugation can be performed to prepare subcellular fractions or isolate specific organelles
- purify proteins through fractionation (separated on size and charge) The best way to do this is by column chromatography
- combine fractions with the protein
- Repeat with a new separation Method
DETERMINING AMINO ACID COMPOSITION FROM PEPTIDE
- hydrolyze peptide to free amino acids
- separate mino acids from acid hydrolysis or base hydrolysis (use other methods to determine Q, N, W, and C
- quantitate amino acids through spectrophotometric method
A = e[c]l
A is absorbance, c molar concentration, and e is molar extinction (object absorbed light if incident light is greater than the transmitted light
AMINO ACID COMPOSITION
- composition of peptide or protein is number of moles of each amino acids present in one mole of the peptide
- only whole numbers because its the number of each aa/ # of protein
DETERMINING CYSTEINE
- oxidize with performic acit to cysteic acid
Alkylate with iodoacetate or iodoacetamid to make carboxymethylcysteine or carboxamidomethylcysteine
- these are stable for acid hydrolysis
DTT
- helps understand protein
- Reduce disulfide bond to form free disulfidal groups
- only works in basic conditions because sulfhydral group needs to be a nucleophile
- intramolecular reaction
- only molecule that reacts with iodoacetate
SIZE-EXCLUSION CHROMATOGRAPHY
- separates proteins according to size
- the smaller the protein then it has more volume accessible to it since it can get inside the tube easier.
- Bigger proteins go in first and the smaller ones go in last.
CATION-EXCHANGE CHROMATOGRAPHY
- separation of protein based on charge
- Fill the column with a solid matrix of either positve or negative charged molecules.
- If the column has negatively charged molecules the positive charge proteins migrate through the matriz more slowly
- Resolution improves when the column is longer
TYPES OF FUNCTIONAL GROUPS ON COLUMNS
- amino group (NH3+)
- Carboxyl group (-COO-)
- Sulfonic acid (SO3-)
- Phosphate Groups (PO42-
HYDROPHOBIC INTERACTION CHROMATOGRAPHY
- hydrophobic groups on column interact with hydrophobic surfaces on protein
- interaction is favored by high salt concentration
- Sample applied in high salt, and then the salt concentration is steadily decreased
- Proteins elute in decreasing order of hydrophobicity
AFFINITY CHROMATOGRAPHY
- beads in the column have covalently attached chemical groups. A protein with this affinity will attach to that particular group and its migration will stop.
ACTIVITY
- total units of enzyme in a solution
SPECIFIC ACTIVITY
- the number of enzyme units per milligram of total protein
- a measure of enzyme purity
SDS POLYACRYLAMIDE GEL ELECTROPHORESIS
- separates based on size and the smallest protein moves the fastest towards the positive pole
- one hour to run
- Run a standard mixture in one lane and samples in the others
- A dye is included so you can see how far the smallest component goes
ISOELECTRIC FOCUSING
- an electrophoretic technique that separates proteins based on isoelectric point
- a stationary pH gradient is established
- Proteins are allowed to migrated in an electric field
- They migrate until they reach their isoelectric pH
- pH = pI
TWO DIMENSIONAL ELECTROPHORESIS
- 1st dimension is isoelectric focusing so proteins are separated based on isoelectric pH
- 2nd dimension is SDS gel electrophoresis and separates everything by size
- SDS has to come after isoelectric because it turns every protein into negatively charged proteins
PROTEIN SEQUENCING
- determine amino acid sequence present because proteins have a large number of amino acids
- determine the sequence of both ends first through FDNB
- Cleave protein into smaller pieces and determine some sequence using Edman Degradation
- purify fragments
- partial sequencing of fragments is performed
Combine all data on overlapping peptide sequences to complete the sequence
FDNB
- FDNB reacts with any amino group to form a stable derivative that has a distinctive yellow color
- determines how many amino groups are present
- hydrolysis stage destroys polypeptide so no more sequencing can be done
- analyzes protein primary structure
EDMAN DEGRADATION
- procedure labels and removes only the amino terminal residue from a peptide leaving all other peptide bonds intact
- cyclic molecule
- coupling step
- cleavage step
- extract ioin
- repeat as many times as necessary
SEQUENCING LARGE PROTEINS INTO SMALLER SEGMENTS
- Break disulfide bonds
- Cleave the polypeptide Chain
- Sequence peptides
- Order peptide fragments
- locate disulfide bonds
MASS SPECTROMETRY
- detects changges in mass of proteins due to the presence of bound cofactors, bound metal ions, covalent modified cations, and so on.
- A protein solution is dropped into a high voltage electic field
- droplets evaporate and ions enter the spectrometer
- Spectrum generates peaks corresponding to charged species
TANDEM MS
- extracts sequence information
- protein solution is treated with protease or chemical reagent to hydrolyze it into shorter peptides
- Injected into a device
- peptide mixture is sorted and ionized fragments are manipulated so only one type of peptide emerges at the end.
- Peptide is fragmented with high energy impact with collision gas. Most breaks occur at peptide bonds
- Peaks are generated for peptide fragments
FMOC
- synthesizes a peptide while keeping it attached at one end to a solid support
- the support is a insoluble polymer contained within a column
- at each step protective chemical groups block unwanted reactions
- protecting group is removed by flushing with mild organic base
- Alpha amino group of amino acid 1 attacks activated carboxyl group of amino acid 2 to form peptide bond
- Completed peptide is deprotected as in reaction 2
- HF cleaves ester linkage between resin