Midterm Flashcards
What are macromolecules composed of? Give some examples
Composed of monomeric subunits
Eg. Protein -> amino acids
DNA -> deoxynucleotides
What is dynamic steady state?
When the rate of appearance of a cellular component is exactly matched to its rate of disappearance
Define isolated, closed, and open system
Isolated: organism exchanges neither energy nor matter with the environment
Closed: organism exchanges energy, but not matter with the environment
Open: organism exchanges both energy and matter with its surroundings
Define anabolic and catabolic pathways
Anabolic: requires input of energy (synthesis)
Catabolic: release energy (degradation)
Describe prokaryotic cells
Lack cell membranes
Unicellular
No nucleus or suncellular organelles
Cell wall
Describe eukaryotic cells
High organized system of membranes
Multicellular with nucleus
Contain organelles
What are the bulk elements of cells?
Oxygen = 65% Carbon = 18% Hydrogen = 10% Nitrogen = 3%
What are the major elements in the cell that are cations?
Account for 4%
Calcium - framework
Sodium - animal extracellular fluid, membrane integrity, nerve impulse activity
Potassium - irremplaçable intracellular cation, membrane integrity, nerve impulse activity
Magnesium - associated with bone structure, membrane integrity
What are the major elements of the cells that are anions?
Phosphorus:
1. Organophosphate - compounds which contain oxidized phosphate radical, nucleic acids, phospholipids, energy metabolism
2. Inorganic phosphate - animal skeletons, major intracellular anion in animal cells
Chloride - major extra cellular anion
Sulphur - sulphites
What are the minor elements present in cells?
Iron - hemoglobin and cytochromes
Iodine - thyroid hormone
What are the trace elements in cells?
Copper, zinc, magnésium, Mo
Very specific activities in the cell
Activators of specific enzyme systems
Name and rate the bond types in terms of strength from highest to lowest.
Covalent Ionic Dipole-dipole Hydrogen Charge transfer Hydrophobic Vander waals
What are some of the biological properties of water?
- Transport medium: intake of nutrients, excretion of toxic waste
- High solubility capacity
- Temperature regulator
- Structural component
What is the dielectric nature of water?
Dipole nature permits electrostatic interactions between ions
Build up of water sheath will lead to prevention of interaction between oppositely charged particles (solvation sphere)
Dielectric constant is very high
What are the consequences of higher dielectric nature?
- High solubilisation capacity towards ionic compounds
2. High solubility towards polar compounds
What is a colloid?
A state of matter typified by large molecules
What are hemotherms?
Organisms that maintains its body temperature at a constant level, usually above that of the environment, by its metabolic activity
Water hydrogen bonds with proteins and is prevented from becoming ice
What are some dynamic properties of water?
- High specific heat of capacity
- energy going into covalent bonds - High heat of vaporization
- Hydrogen bonding between water molecules and polar compounds leads to segregation of any non-polar compounds interacting via a polar forces
- Maximum density = 4C
What are amphiphilic molecules?
Neither polar nor non polar
Form micelles in solution
Micelles repel one another due to negatively charged surfaces and thereby maintain relative stability in solution
Describe a buffer system
- Weak acid
- buffers OH- which increases the pH with the addition of OH-
- as H2O and A- goes up, HA goes down
- produces water and therefore there is no change in pH
- you can keep pulling out H+ until HA is exhausted - Salt of weak acid
- buffers H+
- conjugate base component
What is buffer capacity?
Total capacity to buffer on a quantitative basis against the addition of H+ and OH-
A system has a buffering capacity of 1 when the addition if 1g/mol of H+ or OH- produces a unit change of pH
Describe traits of very weak acids in biological systems
- Have very small dissociation
2. [undissociated acids] = [weak acids]
What is buffer efficiency?
Buffer should be able to buffer in either direction
Maximum buffer efficiency should be able to buffer [OH-] as equally well as [H+]
In general, buffer over a range of +- 1 pH of a pK value
What is pK?
A measure of a systems capacity to yield H+
What is the Henderson-hasselbach equation?
pH = pK + log[A]/[HA]
What are some examples of buffer systems?
HCO-/H2CO3 = biocarbonate system (pK = 6.1)
HPO4-2/H2PO4 = phosphate system
Protein-/H+protein (pK = 6-7)
HbO2-/HbO2H = oxyhemoglobin system (pK = 6.6)
Hb-/HbH = hemoglobin system (pK = 8.2)
Does the bicarbonate system have any buffering capacity at all?
Acids interact with bases to nullify increase in pH
pK = 6.1 but actual pH of cell is 7.2
Difference is approximately 1 pH therefore there is 10X more conjugate base is present
[A]/[HA] = 10/1
Poor buffering capacity: conjugate acid will buffer against addition of OH but not H
What are some colligative properties?
Diffusion
Osmosis
Describe diffusion
Passage of particles from high concentration to low concentration
Complicated by the presence of cell membrane
- size of particle vs membrane permeability: different colligative properties in the inside and outside
- lipophilic nature of membrane facilitates passage of non-polar lipid like molecules
- polar charged molecules will not diffuse readily: membrane carries a positive charge which repels the molecule or membrane carries a negative charge which binds the molecule
PH interferes with the passage of polar molecules
How can you change the ability of a membrane to allow charged molecules to pass?
Changing the charge in the membrane by changing the pH
Describe osmosis
Diffusion of water molecules
What is osmotic pressure?
Reflects the # of particles in solution
Pressure must be applied to a solution separated by a semipermeable membrane from water in order to prevent a volume change in solution
What are the three types of movement of water?
- Plasmolysis: less water in extracullular fluid than in intracellular fluid so water flows out of the cell
- Plasmoptysis: more water in extracellular fluid than intracellular fluid so water flows into the cell
- Water balance: water in extra cellular fluid = water in intracellular fluid
What are the to phases of the colloid state?
1) discontinuous dispersed phase (like solute)
2) continuous dispersion medium (like solvent)
What is emulsion?
Liquid dispersed in a liquid
What are the different classifications of size of solid molecules?
- Solute when dispersed in a solution: 1x10^-9 m or less
- Colloid state: 1x10^-9 m to 1x10^-7 m
- Suspension or precipitate: 1x10^-7 m or more
What is needs for stabilization of the colloid state to prevent aggregation and precipitation?
- Presence of electric change - mutual repulsion
- Degree of interaction with water:
- hydriphilic colloid = more stable
- hydrophobic colloid = less stable
What does neutralization do to colloid state?
Interference of colloid stabilizing factors could lead to distraction
What is the colloid state associated with?
- Large molecules: large molecule mass eg. Proteins
- Aggregates of smaller molecular mass: interacts with one another (h-bonds), exist not in solution but in colloid state
What are colligative properties?
The influence of the solute on the solvent
Alteration of solvent properties
Governed by number of particles in solution and not by their chemistry
What are some colligative properties?
Freezing point depression
Boiling point elevation
Lowering of vapor pressure
Osmotic pressure effects
What is colloid state?
Composed it a dispersion phase and a dispersion medium
Macromolecules have charge and thus repel each other, staying in solution
Properties are conferred by the solutés and not the solvent of the solution
What are proteins?
Compounds containing C,H,O,N, and usually some S of high molecular weight and are composed largely or entirely of amino acids joined via peptide bonds
What is a peptide linkage?
Bond formed on the removal of water resulting in a covalent bond formed between a carboxyl and an amino group
Forms between amino and carboxyl ends of amino acids, releasing a water molecule
What are some general properties of proteins?
- No group solubility: no one solvent that will extract all proteins, some exist in colloid state
- Many proteins exist in the colloid state in the cell and will have properties of the colloid state
What are the biological properties of proteins?
- Major cellular component: level of protein standard for cell type
- Protein itself is not a dietary component
- Not a primary energy reserve
- Structure and organization
- Locomotion
- Défense
- Transmission of hereditary factors
- Mediators of biological reactions
- Regulators of certain biochemical reactions
- Respiration
Are amino acids L or D?
Most belong to L
Organism can us D amino acids but does so in abnormal fashion, usually resulting in death
Describe optical isomers
Process the same general properties with the exception of the ability to rotate planar polarized light
In what order do we loose proteins as pH rises?
1) loose protons from COOH first
2) loose protons from NH3+ second
What are the non polar amino acids?
Gly, Ala, Val, Leu, Île, Met, Cys, Phe, Trp, Pro
What are the uncharged polar amino acids?
Ser, Thr, Try, Asn, Gln
What are the negatively charged polar amino acids?
Asp, Glu
What are the polar amino acids with definite positive charge?
Arg, Lys
What is the polar amino acid with fractional positive charge?
Imidazole group of histidine
Describe high preformance liquid chromatography
Separates amino acids according to size, charge, and hydrophobicity
High pressures reduce diffusion of proteins in column and improve resolution
Stationary phase and mobile phase
Describe ion exchange chromatography
Separates proteins according to charge
Takes ions out of solution and holds them to resin
Wash proteins off by changing salt concentration
What is the difference between anion exchangers and cation exchangers in ion exchange chromatography?
Anion exchangers: have bound positive groups (bind - charged proteins)
Cation exchangers: have bound negative groups (bind + charged proteins)
Describe gel filtration (size exclusion) chromatography
Separates proteins according to molecular weight
Small proteins associate with beads more (move into pores) while large proteins move around them
Describe affinity chromotography
Separates proteins according to their affinity for a ligand
Ligand is covalently attached to a solid matrix
Binding of protein depends upon the affinity for the bound ligand and the capacity of the bead
Elution of protein by changing conditions or excess of free ligand
What is two dimensional gel electrophoresis?
Proteins separated first by charge then by molecular weight
Describe nanotechnology
Requires the binding of biomacromolecules to solid surfaces
Take advantage of crosslinkers that can make covalent bonds with amine, sulfhydryl, aldehyde, and carboxylate containing molecules
Spacer arms (long chains of carbon atoms) may be cleanable or non-cleavable
Describe SDS-PAGE
Seperation according to size
Matrix formed of acrylamide monomers and bisacrylamide crosslinkers
Proteins run through a discontinuous pore size and pH
Proteins saturated with SDS move towards the positive electrode
What are the acidic amino acids?
Asp, Glu
What are the basic amino acids?
His, Lys, Arg
What are large positive hydropathic indexes indicative of?
Regions of protein with large positive hydropathic index are indicative of hydrophobic regions and are likely buried in the centre of the globular proteins
What is the ISO electric point?
pH at which the charge is 0
What are post-translation modifications?
A nascent polypeptide is often covalently modified before it achieves its nature form
Some are reversible
What are some examples of post-translational modification?
Protéolytic cleavage Hydroxylation Methylation Acetylation Phosphorylation Sulfation Carboxylation Formylation Glycosylation Acylation Prenylation Uniquitunation Disulfide bond formation/ breakage Some very specific modifications
What is a peptide?
Amino acid residues joined via peptide linkage
What is an oligopeptide?
2 to 10 residues
What are the nomenclature rules for polypeptides?
1) read from left to right
2) amino acids residues use the short form eg. Glycyl for glycine
3) use full name for c-terminal amino acid
What are major and minor peptides?
Major: proteins
Minor: by themselves with specific biological activity
Under what conditions do you get cleavage of the peptide bond?
- Acid hydrolysis
- Base hydrolysis
- Cyanogen bromide
- Hydrazine
- Enzyme hydrolysis
Describe enzyme hydrolysis
Operates under mild conditions
Peptidases and proteases show specificity for certain peptide bonds
What are the different types of enzyme hydrolysis?
- Carboxypeptidase: cleaves c-terminal grouping, can be spontaneous but must be controlled so as to not go past C-terminal
- Aminopeptidase: cleaves n-terminal grouping
- Chymotrypsin: cleaves after aromatics amino acids as well as after leucine
- Trypsin: cleaves after basic amino acids having a positive charge, lysine and arginine, modify charge in the medium, and trypsin will no longer show activity
Describe the edman’s method sequencing
Phenylisothiocyante
- dilute alkali
Phenylthiocarbamyl peptide
- inductive effects caused by S atom, susceptible to dilute acid, the rest remains stable and does not react
- dilute acid
Phenylthiohydantoin derivative
- isolate and identify what the chemical nature of R1 unit is, add to molecule in notes and repeat the procedure
How does double bond affect the structure of the peptide bond?
Fractional charges
No rotation between C and N
High degree of rotation restriction
How does the coplaner nature of the peptide bond effect the structure?
R groupings can rotate through a characteristic angle
As it rotates gives 3D structure to the protein
What does the degree of rotation of a peptide bond depend upon?
Will depend upon R-group; 1) bulk 2) charged state 3) water reaction: polar=rotate out to h-bond with water Nonpolar=on inside of molecule
How is a peptide bond structured?
Coplanar nature
Transconifuration
Compare single and conjugated proteins
Single proteins: contain only amino acids
Conjugated proteins: contain non-protein components
What are the differences between passive and dynamic proteins?
Passive: structural proteins (keratin)
Dynamic: enzymes (catalysts)
What is homology?
Different amino acids in a given position but part of the same functional group
Similarity of structure which may be associated with a biological activity
What is the primary stucture of proteins?
Dictates secondary structure
Specific sequences of amino acids in polypeptide
What are the techniques for determining the primary structure of a protein?
C-terminal assay:
- hydrazine
- carboxypeptidase
N-terminal assay:
- aminopeptidases
- Sanger: can label n-terminus, stable bond
- edman: slices amino acids sequentially off of chain, peptide sequencing, must work with fragments
How do you fragment the primary sequence of an protein?
Partial acid hydrolysis: peptides of a certain chain length
Cyanogen bromide
Enzymes
What is paper synthesis of the primary structure of proteins?
Reconstruct protein from polypeptides
Must work with only one polypeptide chain
What is mass spectrometry?
Take a protein and break it down to characteristic components, each with a specific mass
Describe tandem mass spectrometry
Proteins are fired from electro spray ionization source to a meta plate with a hole (MS-1)
Those that get through hit a collision cell which fragments the protein into amino acids
Pieces are fragmented down further and can identify the amino acids before they hit the detector
What is a proteins secondary structure?
The physical shape of a polypeptide chain along one axis
Can be determined by X-ray diffraction
Describe the 3 states of proteins secondary structure
- Alpha helix
- constrained right handed helix with extreme registry of peptide bond
- held in place with hydrogen bond - Pleated sheet
- present in single extending polypeptide chain
- anitparallel: intrachain H bond, gives extreme strength to silk
- parallel: chain running in same direction, intrachain H bonding, tend to have long random loops - Triple helix: collagen, lefthanded, h-bonding,
What are some alpha helical breakers?
- Shape of r group: glycine (free rotation=unstable), proline (not an alpha amino acid therefore lefthanded, chain bends back upon itself), serine and asn (bulky)
- Charged state of r group: same charges repel one another
- Interaction of r group with water: preference for polar groups, disrupts natural spiral
Describe the tertiary structure of proteins
Concerned with physical shape
Incorporation of the various forms of secondary organization in a polypeptide chain
What is the axel ratio?
Axial ratio = length of molecule/breadth of molecule
>10 = fiberous proteins
<10 = globular proteins
Describe the quaternary structure of proteins
Incorporations of individual polypeptide chains and subunits leading to the total protein molecule
Considers:
1. Nature of polypeptide chain (similar or different in chemical nature)
2. Degree of polymerization (how many units in the chain)
What are the forces of incorporation for quaternary structures?
- Electrostatic
- H bonding
- Disulfide bridge
What are fibrous proteins used for?
Scaffold proteins (cell structure) Molecular motors
What are globular proteins used for?
Enzymes Antibodies Transcription factors Membrane pores Receptors Gas transport
Define protein dénaturation
Any factor (physical or chemical) that results in the loss of native structure of the protein molecule with probable loss of biological activity Make proteins unable to interact with water
What factors are involved with protein dénaturation?
- Electrolyte addition: interference with the colloid state
- Insolvable salt formation
- Organic solvents (ethanol)
- Heat denaturation (more energy breaks bonds)
- pH (destroys charge and ability to interact with water
- Destruction of hydrogen bonding (urea)
What are the physico-chemical properties of proteins?
1) amphoteric nature: ion transportation
2) buffering ability: involves the imidizole group of HIS
3) solubility: characteristic for each protein, lower most polarity
4) shape
What is the ISO electric point?
The pH at which a molecule carries no net electric charge
pI = 0.5(pk1 + pk2)
What is isoelectric focusing?
Separation of proteins according to charge along immobilized pH gradient strip
pH gradient set up by ampholytes
Electric field applied such that one pole is + and one pole is -
Proteins migrate in the pH gradient until their net charge = 0
What are enzymes?
Proteins in which their biological activity in living systems is to catalyze thermodynamically possible reactions
Permits reactions to occur in the living cell under mild controlled conditions
Associated with virtually all physiological processes and their accompanying biological processes
Define enzyme catalysis?
Involves alteration in the rate of a reaction without changing the chemical nature of the end products of the reaction
What are the important aspects of
Catalysis?
- Turnover number: number of reaction processes that each active site catalyzes per unit time, kcat = vmax/[E]t where Et = [enzyme], units s^-1
- Catalytic efficiency: kcat/km units M^-1s^-1
- Molecular activity: katals/mol of enzyme
- Specific activity: katals/kg of protein
What are katals?
Quantity of activity requiring conversion of 1 mole substrate/second by enzymes
What is enzyme specificity?
- Recognition of reaction type
2. Substrate specificity: reflected in the shape of the substrate molecule
What are holoenzymes?
Complex protein
Nonprotein cofactor + protein apoenzyme
Includes cofactors (directs course of chemical reactions) and apoenzyme (catalyst)
What are multienzyme complexes?
High degree of organization
Substrate tunnelling: sequential enzymes in a pathway occur in complexes
What are simple proteins?
Yields only amino acids upon hydrolysis
What is the active site of the enzyme?
Site of interaction of enzyme and substrate
Composed of catalytic site and specificity site
What is the allostérie site of an enzyme?
Outside catalytic site where small enzymes can bind to changing shape of protein
Site of regulation of enzyme protein shape and hence enzyme activity
What denatures enzymes?
pH
Temperature
Salt concentration
What are the different types of biological distribution for enzymes?
- Common universal reaction: generally wide spread eg. Electron transfer
- Specialized system: restricted distribution, specific biological function (visual enzymes in eye tissues)
- Specific intracytoplasmic distribution: differences in cellular membranes, specific location between outer and inner membrane surfaces, eg. Marker enzymes (identify tissue organization of cellular components)
How does alpha 1-antitrypsin lease to disease in protein folding?
Secreated by liver and can block elastase action in the lungs
Elastase cleaves elastin of the alveoli if it tries to leave site of inflammation
Causes elastase to bind to a critical methionine on an open loop
Dragged to opposite side of alpha 1-antitrypsin where it is distorted and inactivated
Complex is then broken down by proteases
What to defects in alpha 1-antitrypsin cause?
Serious lung and liver damage
Results in protein being poorly secreated from the live or function poorly in the lungs
Mutations in loop make vulnerable to aberrant conformational changes
Z mutation in the loop causes a diner of alpha 1-antitrypsin to form
Repetition of events cause polymer of protein to form in liver leading to cirrhosis and death or emphysema
What is the activation energy?
The quantity of energy that must be put into the system in order to raise it to a higher energy state
How do you reduce the activation energy?
- Concentration and proximity effects: concentration of substrate at the enzyme active site
- Orientation effects: proper alignment of atoms and bonding electrons to favour reaction,
- Every reaction has a characteristic equilibrium state: number of molecules of reactant and product,
What is the Keq?
Dépendant upon concentration of reactants and products
Distribution of energy between reactants and products
What is the michaelis-menten hypothesis?
Biochemical pathways only move as fast as their rate limiting steps allow them
Two assumptions:
1. ES formation is reversible
2. E + S -> ES is the rate limiting step
What is the Michaelis-menten equation?
V=Vmax[S]/[S]+Km
V = observed rate of reaction
Is the rate limiting step reversible?
Yes
What occurs with a very high substrate concentration?
Vmax=k2[ES]
But all enzyme is working, therefore [E]=[ES] measure all the relative quantity of ensure present independent of [S]
V varies with [S] but Vmax does not
Vmax is proportional to [E]
What is involved in Km?
Frequently Km can be interpreted as a measure of equilibrium constant for ES dissociation into E + S
Reflects the nature of the enzyme and does not depend on concentration
High Km=high dissociation, low affinity of E for S
Low Km=low dissociation, high affinity of E for S
Depends on temperature and pH
What is assumed with the michaelis-menten equation?
- When S is very large, all E exists as ES
2. Overall rate limiting step is ES -> E + P
What are the disadvantages of the lineweaver Burke double reciprocal plot?
- Undue emphasis on the least reliable data point
- Poor data point distribution (most at the origin)
- Not a good way to determine the slope of a line (use of top point)
- Radical change in values
- When dealing with reciprocales, the Hughes 1/V and 1/[S] are more likely to have errors
What is the easiest Hofstee plot?
Plot V vrs V/[S]
Data points uniformly distributed
Can work out Km value
What did the lineweaver burk double reciprocal plot?
Plot 1/V vrs 1/[S]
What factors effect enzyme activity?
- Time: disappearance of substate and appearance of product, as time goes less able to produce product due to depletion of substrate, reversal of equilibrium, enzyme dénaturation
- Substrate concentration: will effect velocity
- Cofactor concentration:
- Temperature: initially an increase as lowers Ea, enzyme dénaturation at 55C
- pH: vary in sensitivity to pH, active site of enzyme (affinity for substrate changes with pH, more than one charge at the active site, importance of enzyme shape to activity
- Oxidation state
- Enzyme concentration
What are the two general types of inhibitors?
- Non-specific inhibitors: protein dénaturants, leads to inactivation of all enzymes, eg. Sterilization, pasteurization, trichloracetic acid
- Specific inhibitors: chemically reactive with specific portions of specific enzymes
What are the two major types of specific inhibitors?
- Competitive inhibition: bonding of a compound structurally similar to the substrate at the enzymes active site, reversible, inhibitors blocks active site, substance that competes directly with the substrate for the enzyme active site, 1/V (Vmax) constant, Km increases
- Non competitive inhibition: binding of a compound on the enzyme at a site other than the active site, effective reduction in [E] and therefore a decrease in molecular activity, 1/[S] remains constant, Vmax decreases, Km does not change
How can inhibition be overcome?
- Lowering inhibitor concentration
2. Increasing substrate concentration
What is uncompetitive inhibition?
Bonds to the enzyme substrate complex but not the free enzyme
Changes the affinity of an enzyme for substrate
Changes shape of enzyme such that binds enzyme tighter
Vmax decreases
Km decreases
What is the shape of an enzyme immediately associated with?
- Enzyme catalysis
- Enzyme specificity
- Enzyme regulation within the cell
How do enzymes caralyze reactions so quickly?
- Physical basis: surface effects or concentration effects at the surface of the enzyme, proximity and orientation effect (making and breaking bonds), Strain distortion (making and breaking bonds)
- Chemical basis: general acid/base catalysis, proton donating group, proton accepting group, nucleophilic activity
What is nucleophilic activity?
Leads to formation of covalent bond through a covalent intermediate
What are the three enzyme specificity theories?
- Lock and key
- Induced fit theory
- Combination
What is the lock and key theory?
Enzyme = lock Substrate = key
What is the induced fit theory?
Approaching substrate causes a change in enzyme conformation to accommodate the substrate
What controls enzyme regulation?
- Isozymes
- Allosteric enzymes
- Covalent modification
What are isozymes?
Same enzymes that show subtle differences in chemical structure leading to subtle differences in shape
Results in altered enzymatic activity
Give an example of isozymes
Lactate dehydrogenase
Found in smooth muscle
Oligomeric of 4 subunits
Possibility of 5 different enzymes (5 different permutations)
Blood system: transport nutrients and waste
Hepatitis: death of liver cells release enzymes
Heartattack: altered patterns of isozymes
Tumors: patterns and localization
Practical use: each tissue has a particular isozyme composition
Describe allosteric enzymes
Enzymes which show shape alteration with altered enzymatic activity as a result of a reversible interaction of a compound at the allosteric site of the enzyme
A) modifier nature can vary
- homotropic modification: modifier is the substrate itself
- heterotropic modification: modifiées differs from the substrate
B) all weak interactions at the allosteric site
C) positive modification = activation
Negative modification = inhibition
D) mode of action of the modifier can be examined by altered affinity of E for S (change in Km), and altered catalytic activity (change in Vmax)
What is covalent modification?
Involved making or breaking of a covalent bond
Shape alteration
What occurs with entropy with the formation of ES complex?
Loss of entropy
What is the iron-sulfur cluster of aconitase?
When iron is high, cluster forms and it acts as the enzyme aconitase
When iron is low cluster does not form and it acts as a RNA-binding protein known as the iron-responsive protein, a protein that binds to the iron-responsive element and controls iron-responsive gene expression
What are the three major types of cofactors?
- Cofactor: low molecular weight, non protein component that interacts loosely with the apoenzyme
- Prosthetic group: low molecular weight, non-protein component that interacts strongly with the apoenzyme
- Metal: covalent bonding, loosely or strongly, chemical reactant or structural component
Describe pyridine nucleotide cofactors
- NAD+ = energy metabolism, cofactor for most dehydrogenases
- NADP+ = biosynthetic processes, cofactor for most reductases
Both show capacity to accept hydride ion - Flavin mononucleotide (FMN)
- Flavin adening dinucleotide (FAD)
Both are prosthetic groups bound to apoenzyme
What is a vitamin?
Growth factor that must be supplied in the diet
What are FMN and FAD derived from?
Riboflavin (vitamin B)
Describe coenzyme A
Nucleotide cofactor
SH is functional group
Involved in metabolism of carbs, proteins, and lipids
Describe thiamine pyrophosphate
Involved in pyruvate oxidation and the citric acid cycle
Thiamine is strongly bound to apoenzyme
Pryophophate is the aldehyde transfer group
Describe tetrahydrofolate (THF)
Derived from folic acid
One carbon carrier for serine hydroxymethyl transferase reaction
Describe pyridoxal-5-phosphate (PLP)
Capable of forming schiff bases with amino acids and proteins
- Can cleave Calpha-Cbeta bond in threonine
- Can remove OH group from serine to eventually form pyruvate
Describe some other cofactors
Cytochrome c: stable, heme protein, function dépendant upon the valent state of iron
Cytochrome a and a3: catalyze the passage of electrons in to molecular oxygen
Cytochromes: function depends upon valent state of iron
Coenzyme Q: ubiquinone, not an enzyme cofactor
Describe exergonic reactions
Energy is released
Catabolism
Describe endergonic reactions
Energy is absorbed
Anabolism
What is the equation for the change in free energy and what does it mean?
G = H-TS
The maximum useful work that can be obtained from a chemical reaction by operating in a perfectly reversible fashion under standard conditions of temperature and pressure
Define metabolism
Sim of all reactions going on within cell
What is redox potential?
Measure of a systems affinity for electrons
Electrons flow from lower to higher
What are the two major forms of energy?
- Storage: fat (mobile organisms) and carbs (immobile organisms)
- Immidate energy currency
- low energy phosphate (10000-12000 J/mol)
- high energy phosphate (30000-60000 J/mol)
When would you get a high G?
When molecule has two or more like charges that repel each other
Ex ATP has 3 negative phosphate groups that repel one another, most energy is released with loss of first group as repulsion is strongest
What is phosphorylation quotient?
Inorganic P -> organic O/#O2 concumed
If 3/1 = x type transport chain
If 2/1 = y type transport chain
Name the different complexes in the ETC
Complex 1: NADH CoQ reductase
Complex 2: Succinate-CoQ reductase
Complex 3: CoQ-cytochrome c Reductase
Complex 4: Cytochrome c Oxidase
What are the inhibitors of the ETC and where do they act
Complex 1 = rotenone (causes paralysis) and Amytal (causes death)
Complex 3 = antimycin myxothiozol (causes build up of electrons along ETC)
Complex 4 = CO, cyanide azide (interacts with iron in cytochrome oxidase)
ATPase = oligomycin
What occurs when you block complex 3?
Electrons still flow but build up in 1 and 3 and get reduced
Bind with oxygen and create radical known as superoxide
Leads to generation of other free radicals
Can damage cell
What do uncouplers do?
Insert themselves into inner motchondrial membrane and dissipate proton gradient
Brought forth for variety of reasons, including cold termperatures
Many metabolic systems will use to dertermine how much energy mitochondria is generating
What is the chemiosmotic theory?
ETC on the inner surface of mitochondrial membrane
Most important thing is passage of protein passed against a concentration gradient
Gradient requires energy from
ETC to maintain
Energy provided when moving from low redox to high pulls OH off of Pi and H off of ADP so ATP can be formed more easily, catalyzed by ATPase
What occurs in anaerobic organisms?
ATP - terminal phosphate is generally used
ADP - only in dire cases
ETC on inner surface of mitochondria
Store energy according to demand
Generally describe the citric acid cycle
- Provides a mechanism of oxidation of acetyl coA
- Unity of mechanism - similar across all organisms
- Located in mitochondrial matrix and inner membrane
- Aerobic process: oxygen is ultimate electron acceptor in ETC
What is the committing step?
Thermodynamics of system pulls the reaction in the forwards direction, pulls entire CAC in forward direction
In CAC is citrate synthesis from acetyl coA and oxaloacetate
What is citrate synthase?
Enzyme used to condense citrate
Citryl-CoA formed as an intermediate and is hydrolysis to citrate
Requires large expenditure of free energy = exergonic = negative G
Describe isomérisation of CAC
Dehydration followed by rehydration both catalyzed by aconitase
Citrate to cis-aconitate to isocitrate
Reversible
Describe oxidation of CAC
Isocitrate to oxalosuccinate catalyzed by isocitrate dehydrogenase
Formation of NADH
Important for aerobic organisms and could be turned off by ATP
Thermldynamically favorable
Describe decarboxylation of CAC
Oxalosuccinate to alpha ketoglutarate catalyzed by isocitrate dehydrogenase
Formation of CO2
Thermodynamically favorable
Isocitrate dehydrogenase required Mn2+ or Mg2+ as a cofactor
Describe oxidation, decarboxylation of alpha Keto acid in CAC
Alpha letoglutarate to succinyl CoA catalyzed by alpha ketoglutarate dehydrogenase with formation of NADH and CO2
Depends on Mg2+, TPP, lipoic acids and CoA
Sulfure makes bond more energy rich
Thermodynamically favorable
Decarboxylation first and oxidation second
Describe substrate phosphorylation of CAC
Succinyl CoA to succincte catalyzed by succinyl CoA synthétase with formation of GTP and CoASH
Free energy change is close to 0 and is therefore readily reversible
Succinyl CoA couples cleavage o high energy succinyl CoA to synthesis of high energy nucleoside triphophate
Describe oxidation of succincte in CAC
Succincte to fumarate catalyzed by succincte dehydrogenase with formation of FADH2
Possibility of isomerism
Reversible
Succinate dehydrogenase strongly inhibited by Malonate
Describe hydration of fumarate in CDC
Fumarate to L-Malate catalyzed by fumarase with consumption of water
Reversible
Describe the oxidation of L-Malate in CDC
L-Malate to oxaloacetate catalyzed by Malate debydrogenase with formation of NADH
Endergoic reaction so substrate favoured
Large thermodynamic brake
Strong regulation
How many ATP are produced in one cycle of CAC?
12 ATP
How does NAH regulate CAC?
Accumulates and causes negative feedback inhibition
So that we don’t deop to much ATP as it turns the system off and causes the production of AMP nad ADP
What allosteric enzymes regulate the CAC?
- Citrate synthase: negatively modified by NADH
2. Isocitrate dehydrogenase: negatively modified by NADH and ATP, positively by AMP
What four things regulate the CAC?
- Thermodynamics: commitig steps (-G) and thermodynamic break (+G)
- Allosteric enzymes
- Availability of cofactors: NAD+, TTP, lipoic acid, CoA, O2, Pi
- Membrane permeability: governs retention of oxaloacetate or inner membrane and rest to initiate CAC
