Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
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 |
