Past Qs 2 Flashcards
What results from an increase in volume in ECF?
Overhydration
What results from decrease in volume in ECF
Dehydration
What results from increase in volume in plasma?
Hypervolaemia
What results from decrease in volume in plasma?
Hypovolaemia
What results from increase in volume in ISF?
Oedema
What is Isosmosis?
Constancy of Osmotic Pressure
What is Osmotic pressure?
force which prevents osmotic movement
What is Osmotic concentration?
Osmolarity; measure of osmols per litre
What is freezing point depression?
Difference between freezing point of pure solvent and solution with solute
Na+
a) in ECF= 140mmol/l
b) in ICF=27mmol/l
K+
a) in ECF=5.0mmol/l
b) in ICF=95mmol/l
Ca2+
a) in ECF=2.5 mmol/l
b) in ICF=1.0 mmol/l
Mg2+
a) in ECF=1.0mmol/l
b) in ICF= 3.0mmol/l
Cl-
a) in ECF=103mmol/l
b) in ICF=30mmol/l
HCO3
a) in ECF=27mmol/l
b) in ICF= 10mmol/l
HPO4
a) in ECF=1.5-2.0 mmol/l
b) in ICF=cca.30mmol/l
Proteinate in ECF and ICF
a) in ECF=16mmol/l
b) in ICF= 40-60 mmol/l
What is Isohydria?
Constancy of pH of ECF (pH=7.4)
What is the Henderson/Hasselbach eq.?
Ka=[H+]*log[A]/[HA] (weak ac=high pK,vice versa)
What pH classified as Acidosis?
7.0-7.35
What pH classified as Alkalosis?
7.45-7.8
What do buffer systems/pairs resist?
Change in pH (prevent shifts in H+ conc.)
What type of buffer system found mainly in ECF?
Bicarbonate Buffer System (Inorganic)
Which chemicals involved in buffer system of ECF?
Carbonic Acid (HCO3), Sodium Bicarbonate (NaHCO3)
What is eq. for pH?
pK=6.1 -> pH=6.1+ log20/1= 1.3+6.1= 7.4
What type of Buffer System found in ICF?
Phosphate Buffer System (Inorganic)
Which chemicals involved in Buffer system in ICF?
Dihydrogenase phosphate (H2PO4), Monohydrogen Phosphate (HPO4-)
What is eq. for pH?
pK=6.8 -> pH=6.8+log4/1=6.8+0.6= 7.4
What type of buffer system in plasma and ICF??
Protein Buffer System
What substances involved in Buffer System in plasma and ICF?
Plasma Proteins and Haemoglobin
How is acid-base behaviour of protein found?
Ionisable groups of R and –amino, -carboxyl end groups
What is pKd of proteins?
4.9-6.4
Why is haemoglobin effective buffer?
Imidazole groups (8% histidine) with pKd≈7
Is oxygenated haemoglobin a stronger acid than deoxy?
Yes, Oxy= HbO2 -> pH:6.6 Deoxy≠O2 -> pH:6.8
What happens when Haemoglobin is oxygenated?
Decr. In pH or release of O2= proton uptake
What are the characteristic features of Prokaryotic cells?
No nucleus, have bacteria, unicellular, small
What are characteristics of Eukaryotes?
Nucleus, uni- and multicellular, smallbig size range
What is Plasma Membrane?
Barrier between cell and environment
What is Internal Membrane?
Separate subcellular organelles from cytoplasm
What are the major components of membrane/dynamic fluid?
Lipoids (40%), Proteins (60%)
What is a lipoid?
Phospholipid e.g. lecithin, cephalin
How is the basic structure of membrane/ dynamic fluid?
A lipoid bilayer allowing proteins to diffuse
What can be present in the glycoproteins/glycolipids?
Sugar moieties (<1%)
Name another lipoid component and its role;
Cholesterol- b/w lipid molecules for membrane stability
Name a major component of Membrane;
Phospholipid (glycerol, 2 fatty acids + phosphate grp.)
Which molecules linked to phosphate group give variety?
Polar Choline/Cholamine in Lecithin,Cephalin, Sphingosine w/ Choline -> Sphingomyelin
Is the tail of phospholipid Hydrophobic or –philic?
Hydrophobic (non-polar fatty acids)
Is the head of phospholipid Hydrophobic or –philic?
Hydrophilic (polar molecules e.g. glycerol)
What is an unsaturated fatty acid?
Has 1-3 double bonds at certain locations along chain
What does the “kink” from double bond do?
Looser packing and decr. melting point (fluidity, temp)
Name steroid found in Membrane;
Cholesterol (carbon skeleton of 4 fused rings)
What is the function of Cholesterol?
Stabilize the Membrane, Precursor to other synth. Steroids
What does high Cholesterol cause?
Atherosclerosis= decr. phosphol. movement + membrane fluidity
What does LDL Cholesterol have a role in?
Plaque formation in blood vessels
What percentage of membrane made up by proteins?
60% (made of same set of 20 amino acids)
What are Integral Proteins?
Transmembrane proteins (hydrophob= int. membr.;hydrophilic ends)
What are characteristics?
Immobile(attached to cytoskeleton), dynamic function, ion channels
What are Peripheral Proteins?
Not embedded in lipid bilayer at all
What are characteristics of Peripheral Proteins?
Loosely bind to membr. surface/exposed integral prot., static func., receptors
What do receptors do?
Detect chemical signals and transmit detection inside
What are membrane carbohydrates composed of?
Branched oligosaccharides with <15 sugar units
What bonds in glycolipids i.e. between oligosacc. and lipid?
Covalent
What are bonds in glycoprotein i.e. between oligosacc. and protein?
Covalent
Where are oligosaccs.located in plasma membrane?
External surface
What is oligosaccs.function?
Markers that distinguish one cell from another
What is Cell Membrane function?
Selective barrier, Control structure, metabolism, compartment environ.
What are characteristics of Cell Membrane?
Dynamic, Move, Components cont. synthesize/degrade, asymmetric, main component in “cell death”
Describe Asymmetry in Membrane;
Membranes have distinct inside and outside faces -> differ in lipid composition, plasma membrane has carbs on ext. only, asymmetrical distribution of proteins, lipids and carbs (determined by ER at membrane synthesis)
How does an ion/molecule move across the membrane?
Move down the conc. /electrochem. gradient and without using metabolic energy
What is Diffusion?
Ion/Molecule passed through membrane passively, without specific inhibitor
What are the 2 types of Passive Transport?
Simple Diffusion, Passive Diffusion
Describe Simple Diffusion;
Lipid-soluble, non-polar molecules diffuse passively through lipid components of cell membrane e.g. Water, Urea, Carbon Dioxide, Ethanol (Rate limiting step= movement of molecule from aq. Environment outside or inside cell into lipid bilayer) Ions don’t diffuse well
Describe Gibbs-Donnan Equation;
Unequal ion distribution on both sides of membrane
Describe its Solution Equilibrium;
Ions diffuse from high conc. -> low conc. Until equilibrium attained and final conc. on either side contains equal conc. I.e. K+ ion conc. =Cl- ion conc.
Describe the membrane at Equilibrium;
K+ ions move with Cl- ions from one side of membrane to other and equal no. of ions move back -> solutions either side maintain equal conc. and electric. Neutrality -> System becomes more complicated if non-membrane-permeable anion present
Describe the membranes Permeability Properties;
K+ and Cl- penetrate easily the membrane, Pr- can’t (anion), remains on one side
Describe Facilitated Diffusion;
Molecules can diffuse passively via proteins of cell membrane, which act as carrier proteins (permeases) or Hydrophilic pores/gates (very selective) E.g. Glucose, Chloride Ions
What is Active Transport?
Using energy in order to move molecules across membrane against their electrochem. gradient (can inhibit ATP synthesis)
Name the 2 types of Active Transport;
Primary Active Transport, Secondary Active Transport
What is Primary Active Transport?
Involves carrier protein that directly hydrolyses ATP
Give example of Primary Active Transport;
Na+/K+ pump. Na+-K+ ATPase= most imp. transport enzyme. -> resting membrane potential (nerve, muscle), drives secondary active trans., osmotic grad.
How does the Na+/K+ pump work?
High Na+ in cytoplasm, ATP hydrolysed -> phosphoryl. of cytoplasm loop and ADP release, confo. change in pump releases Na+ ions outside, pump binds 2 EC K+ ions -> released inside and α subunit dephosphoryl.
What inhibits the Na+/K+ pump?
Cardiac Glycosides, Digitalis Purpurea ( Inhib. of Na+ pump= incr. IC Na+ conc. -> incr. cardiac contractility)
What is Secondary Active Transport?
Transport across membranes fuelled by ATP ANDenergy stored in ion grad. (Cotransport)
What is Cotransport?
Free energy released by transport in electrochem. grad. is used to pump other ions up their electrochem. grad.
Name the 2 forms of Secondary Transport;
Symport (Same Direction), Antiport(Opposite Direction)
Give example of Secondary Active Transport;
1 Glucose/2 Na+ symport (Lumen -> intestinal ep.), uses energy stored in Na+ grad. (produced by Na+/K+ ATPase)
What are peptides, polypeptides+ proteins classed in mammal?
Polymers of α-L-amino acids
What do the peptides, polypeptides + proteins in mammals consist of?
(Polymers of alfa-L-amino acids)
Carboxyilic (-COOH) and Amino (-NH2) group attached to the α- Carbon
What differentiates the peptides, polypeptides + proteins in mammals?
(Polymers of alfa-L-amino acids)
Distinct R-groups at end
What is a Chiral amino acid?
Has a C-atom with 4 distinct constituents (asymmetry) (Gly≠Chiral)
What conformation do all amino acids show?
L-glyceraldehyde (L=Levarotary)
Are there D-amino acids?
Yes, but only exist in nature NEVER PROTEINS
Name Monoamino Monocarboxylic Acids with Aliphatic R-group;
Gly, Ala, Val, Leu, Iso
Name Non- Aromatic Amino Acids with Hydroxyl R-Groups;
Ser, Thr
Name Amino Acids with Sulfur-containing R-Groups;
Cys, Met
Name Monoamino Dicarboxylic acids;
Asp, Glu, Asp acid, Glu acid
Name Diamino Monocarboxyilic Acids;
Arg, Lys, His
Name Amino Acids with Aromatic Ring;
Phe, Tyr, Try
Name Imino Acid;
Pro
What forms a peptide bond?
Condensation of 2 amino acids
What bonds do proteins in amino acids have?
Peptide bonds
How are proteins classified?
Shape/Solubility, Composition, Function
Describe a Globular protein;
water soluble, tightly folded peptide chains in spherical shape e.g. albumin, globulin
Describe a Fibrous protein;
non-water soluble polypeptide chains in parallel layers e.g. collagen, elastin, keratin
Describe Intermediate product;
long, rod-like water soluble structures e.g. myosin
Describe Simple proteins;
yield only amino acids (or derivatives) by hydrolysis
Describe Conjugated proteins;
Simple protein with nonprotein compound e.g. glycoprotein
What are derived proteins?
Come from chemicals, enzymes and other phys.force of other aminos
Name some possible functions of proteins;
Contractile, Transport, Enzymes, Hormones etc.
What is the primary structure of protein?
Amino acid residues
What is the secondary structure of protein?
α helix, β sheet
What is the tertiary structure of protein?
Folding of Polypeptide chain
What is the Quarternary Structure?
Assembled subunits forming overall structure e.g. Haemoglobin
What is direct sequencing of proteins?
Edman degradation (amino acids at terminal identified, Only N-Terminal residue removed, rest remains intact, carboxy-peptidases then identify carb. terminal)
How can we determine Amino Acid sequence of entire peptide?
Peptide Mapping, Overlapping Sequence Information
Give characteristics of Tertiary structure;
repeating units, unregular parts, position of side chains
Which type of protein mainly has tertiary structure?
Globular
What is Native Confirmation?
A 3D structure that’s stable and active under certain temp. and pH
How are functions of proteins determined?
Chain conformation
What is Denaturation?
Weak bond stabilizing chain conformation and quart. structure unfold protein
What causes denaturation?
Heat, Acids/Bases,Red/Ox.Agents,H-bonding solvents,Heavy Metal ions
Is denaturation reversible?
Yes, Renaturation= correct restoring of folding and bio. activity, but Irreversible possible also.
What process made easier by denaturation?
Hydrolysing proteins
What methods are used to examine Protein Structure?
Mass Spec., X-Ray Crystallography, NMR Spectroscopy.
What forces stabilize the proteins?
Covalent bonds and Non-Covalent bonds
Name the Covalent bonds;
Peptide bonds and Disulfide bonds
What is a Peptide Bond?
Connects 2 amino acids in polymer by α amino acid and α carboxyl grp.
What is the reaction between two Peptide bond called?
Condensation –> Liberates H2O molecule
What is a Disulfide Bond?
Covalent bond between 2 S atoms (restricts flexibility of polype. chain)
What does Disulfide bond result from?
Oxidation of –SH groups of 2 Cys molecules= Cys
Where else is Disulfide bond found?
Intrachain disulfide bonds form Cyclic structures)
Name types of Non-Covalent bonds;
Van Der Waals forces, Hydrophobic forces, H-bonding, Ionic
Describe Van der Waals forces;
weakest intermolecular force, molecule given temp. partial neg.charge which induces temp. dipole of neighbour atom. Only significant with numerous atoms
Describe Hydrophobic forces;
Hydrophilic/-phobic R-group interact with aq. environment = shape protein structure (spontaneous folding)
Describe H-Bonding;
attractive force between H atoms covalently bonded to very electroneg. atom e.g. H has a large partial pos. charge and O, F, N have a large partial neg. charge
Describe Ionic Bonds;
Formed between Carboxyl group of acidic amino acid (Glu, Asp) and amino group of Basic amino acid (Lys, Arg, His)
What is Keratin?
Structural protein in skin, hair, nails, hooves and feathers.
Characteristics of Keratin;
Insoluble in cold/hot water, not attacked by proteolytic enzymes, numerous disulfide bonds (due to Cys= 24%)
What is Keratin split into?
α and β
Describe Alpha Keratin;
Strong and Inelastic e.g. hair, wool, nail, hoof
Describe Beta Keratin;
Stronger than alpha, folded into beta sheets e.g. scales, feathers
Describe the structure of Wool;
Alpha keratins twist together=protofibrils, microfibrils and macrofibrils
How are polypeptide chains of keratin stabilised?
S-S bonds, H-bonds and Ionic interactions
What are keratin containing cells called?
Keratinocytes
What part of cell contains keratin?
Stratum Corneum
Can Keratin be degraded?
Yes, but not in an organism.
What is Collagen?
abundant fibrous fibrous protein in skin, bone, tendon, cartilage and vessels
Describe its basic unit structure of Collagen;
triple helix= tropocollagen , Gly, Pro and Hydroxypro found
What does the high level of Pro/Hydroxypro cause?
Cant form alpha helix or beta sheet
What is polypeptide structure?
Left handed helix conformation (forms triple helix)
What stabilises the polypeptide structure?
H-bonds between pro/hydroxypro which lock chains in confo.
What enzyme performs hydroxlations on Pro?
Prolyl Hydroxylase (requires Vit. C cofactor)
What enables H-bonding between triple helixes?
Hydroxy-Lys (catalysed by Lys Hydroxylase)
How is Collagen synthesised?
Transcription, Translation (at central part of chain, every 3rd amino acid are Gly= allow 3 strands to twist together), Pro amino acids changed into hydroxypro, they twist together= ProcollagenEC C and N terminus propeptides cut off= Tropocollagen, Crosslinks form between Tropocollagen= Type 1 Collagen
What is Elastin?
Elastic protein in Connective Tissue, composed of Gly, Val, Ala, Pro
How is Elastin made?
Linking many soluble tropoelastin molecules to make insoluble, durable crosslink array.
Where is Elastin found?
Large elastic blood vessels e.g. Aorta, Lungs, Elastic Ligs, Skin, Bladder and Elastic Cartilage
What is an Enzyme?
Protein that speeds up a chemical reaction in living organism, converts substrates to products.
Give example of Cofactors;
Metal Ions e.g. iron sulphur clusters, Water-soluble vitamins e.g. NAD+,PALP
What are Coenzymes?
Intermediary carriers of electrons, specific atoms or funct. group
Give example of Coenzymes;
Water-soluble vitamins e.g. Thiamine, Riboflavin
What is a Holoenzyme?
Complex of Enzyme + Enzyme
What is Apoenzyme?
Enzyme – Coenzyme
What are prosthetic groups?
Tightly bound organic cofactors
What is Active Site?
Crevices containing catalytic residues, bind substrate and carry out reaction.
What does the active site consist of?
Substrate binding site and catalytic site
What do Serine Proteases do?
Hydrolyse peptide bonds of proteins e.g. Chymotrypsin, Trypsin, Elastase
Chemotrypsin function;
(Ser189, Gly216) Catalyses the cleavage of peptides and esters of Phe, Tyr, Try
Trypsin function;
(Asp189, Gly216) Asp forms salt bridge at end of substrate, acts on Lys, Arg
Elastase function;
(Ser 189, Val 216) Accommodates small hydrophobic side chains e.g. Ala
What does their reactivity depend on?
Arrangement of Serine side chain with 2 other polar chains.
How can Serine Proteases be inhibited?
Di-isopropylphosphofluoridate (DIPF)
Describe “Lock and Key” Model;
Binding pocket is complementary to substrate, no confo. Changes upon binding and protein enzyme is rigid structure.
Describe “Induced Fit” Model;
Binding substrate is structurally interactive, binding site alters active site structure to fit the substrate.
Describe “Fluctuation Theory”;
Conformation of enzyme’s active site always change and substrate bound only if binding site is complementary.
Michaelis- Menten Theory;
E+S ⇌ES→E+P
What is Activation Energy?
Free energy between initial and transitional state.
Can enzymes slow down reaction?
No, they ONLY speed up rate of reaction
How do enzymes affect activation energy?
Lower it by creating a new pathway with lower trans. State
What happens when a reaction rearranges atoms?
Hydrate hull removed, existing bonds in reactants broken and new bonds of products formed
What is initial investment to start reaction?
Activation Energy ( usually heat)
What is meant if a reaction is exergonic?
More energy released than was invested in breaking bonds
Name 3 levels of Specifity in Enzymes;
Reaction Specifity, Substrate Specifity and Stereospecifity
What is Reaction Specifity?
Broad, peptide bonds are broken e.g. chymotrypsin, trypsin, pepsin
What is Substrate Specifity?
Strick, Only Glucose-6-phosphate is degraded e.g. Glucose-6-phosphatase
What is Stereospecifity?
Very Strick, only L or D degraded e.g. L-glutamate dehydrogenase, D-amino acid oxidase
Why must heat be added to a system?
At typical temp, not enough energy to reach activation energy
What effects occur in cell with heat addition?
Reaction speeds up but high temperature kills cells
What effect does increasing the temp. have on enzyme?
Increases enzyme velocity
How does enzyme speed up reaction?
Lowers activation energy so reaction can occur at moderate temp.
How is an enzyme denatured through temperature?
Heated beyond its optimal temp. H-, Ionic and weak interactions that stabilise shape are disrupted.
What is the optimal temperature for enzymes?
35-40˚C
What are optimal pH values for enzymes?
pH 6-8 (with exceptions e.g. pepsin, alkaline/acidic phosphatase)
What are reaction velocities proportional to?
Substrate concentrations (reaction rate decr. w/ substrate decr.)
What is the Michaelis Constant?
Km is substrate conc. where velocity of reaction is half of max. value (Vmax/2) Enzyme is saturated in half by substrate Please look at Graph
Do active enzymes have a higher or lower Km value?
Lower
What happens as Km increases?
Enzyme activity decreases ( vice versa, 10-1 -10-6 mol/l)
Name main units of enzyme activity?
IU (µmol/min), Kat(al) (mol/sec), Turnover no. (no.of substrate/sec)
Do enzymes alter the equilibrium?
No, they only speed up rate of reaction forwards/backwards
• Describe a Reversible Reaction;
Glucose-1-P ([S]) -> K=19([S], [P] no change),
K>19([S]has to incr.),
K<19([P]has to incr.)
Example of Irreversible Reaction;
ATP degradation &synthesis, degradation of Trypsin, Pepsin,Amylase etc.
6 types of Enzyme inhibiton;
non-specific, specific,competitive, non-competitive, irreversible, reversible
What is non-specific inhibition?
Denaturation (heat, pH etc.)
What is specific inhibition?
One group of enzyme is inhibited
What is competitive inhibition?
Inhibitor resembles normal substrate and competes for and binds to active site, reducing productivity of enzymes reversibly e.g inhibition of Succinate Dehydrogenase by Maloanate
What is non-competitive inhibition?
Don’t directly compete for active site, but impede enzymatic reaction by binding to another part of enzyme, changing its shape and shape of active site
What is irreversible inhibition?
Enzyme inactivated if substrate can no longer bind to active site (inhibitor bound to site or binding very tightly = slow dissociation)
Examples of Irreversible Inhibition;
CN- ion inhibit Cytochromoxidase (enzyme of resp. chain), Heavy Metals (Hg++, Cd++, As++, Pb++) bind to –SH or –OH groups on active site.
What is reversible inhibition?
Allosteric (rapid equilibrium of enzyme and inhibitor)
Where do you find Allosteric inhibitors and Effectors?
Oligomeric enzymes
How can you control the action of an enzyme?
Regulation of its concentration (by repressing/inducing synth)
What is a constitutive enzyme?
enzyme is permanently produced without reg. of enzyme synth.
How is activity of individual enzyme molecule reduced?
Inhibitors (incr. by effectors)
How does Genetic Control of enzymes work?
Gene that codes enzyme can be regulated to no. of copies of mRNA and therefore, the number of enzymes produced.
What is Gene Induction?
“Turning On” transcription incr. mRNA production
What is Gene Repression?
“Turning Off” transcription reduction in mRNA
How does Allosteric Regulation work?
Molecules bind to allosteric site, separate from active site, inhibit/stimulate enzyme activity.
What are allosterically regulated enzymes made from?
2+ polypeptide chains with their own active site
What is an Allosteric Activator?
Binding of allosteric molecule promotes a shift to relaxed state
What is an Allosteric Inhibitor?
Binding of Allosteric molecule promoted shift to tense state
Describe Sigmoidal Plot of Allosteric Regulation;
Plots of [S] vs reaction velocities are sigmoidal rather than Michaelis-Menten (rectangular hyperbola)
What does Sigmoidal plot indicate?
co-operating effect (binding of substrate to one enzyme promotes binding of 2nd substrate to another enzyme) and intermolecular communication (adj. molecules in contact)
Give an example of Allosteric Regulation;
Feedback Inhibition (Final product of metabolic pathway is an allosteric inhibitor (feedback molecule) of 1st enzyme and shuts down pathway when product accumulates)
How is Covalent Modification of Enzyme induced?
Addition of a specific functional group e.g. phosphorylation or Removal of functional group
What is effect of Covalent Modification?
Activate or Inhibit enzyme activity e.g. Glycogen Synthetase and Glycogen phosphorylase regulated by phosphorylation
What is a Zygomen?
A pro-enzyme or enzyme in inactive precursor form
What form do Zygomens take?
Long polypeptide
How does The Zygomen form work?
Cleavage at activation site( termini or internal location of polypeptide) releases a polypeptide known as “pro-sequence” activation of enzyme and therefore, makes cleavage a regulatory mechanism.
What are Isoforms?
Monomeric units produced by the body, differ slightly in amino acid sequence and catalytic properties
How are Isoforms produced?
Multimeric assemblies and Isomeric forms provide mechanism by which catalytic properties of active multimer can be “tailored” to suit needs
What are 2 forms of Km in Isofroms?
High Km= works best in tissue with high substrate conc., Low Km= works best in tissue with low substrate conc.
Name a Modulator protein;
CAP (Catabolite Activator Protein)
Describe biochemical characterization of the Nucleus;
(600g, 10min) Consists of histone and nonhistone proteins (eukaryotic cells only)+DNA, Enzymes of DNA replication and transcription; DNA polymerase, DNA Ligase and RNA polymerase
Describe biochemical characterization of the Mitochondria;
(15000g, 5 min) consists of Outer membrane , inner membrane and matrix, Enzymes of Citric Acid Cycle, Fatty Acid Oxidation, Respiratory chain etc.
Describe biochemical characterization of the Lysosomes;
(15000g, 5min) differentiated by marker enzyme: acid phosphatase, Enzymes of Citric Acid Cycle, Fatty Acid Oxidation, Respiratory chain , Degradative Enzymes, Acid Hydrolases, Ribonuclease, deoxyribonuclease, protease, glucosidase, lipase, catespin.
Describe biochemical characterization of the Matrix;
Enzymes of Citric Acid Cycle, Fatty Acid Oxidation, Enzymes if Urea Cycle, L-Glutamate dehydrogenase
Describe biochemical characterization of the Inner Membrane;
enzymes of resp. chain, oxidative phosphorylation, carnitin- fatty acid transferase (fatty acid oxidation), ß-hydroxy-butyrate dehydrogenase
Describe biochemical characterization of the Intermembrane space;
Adenylate kinase (rephosphorylation AMPADP)
Describe biochemical characterization of the Outer Membrane;
Acyl CoA synthetase (fatty acid oxidation)
Describe biochemical characterization of the Microsomes; (Ribosomes [RNA+protein], Endoplasmic Reticulum, Golgi)
(100000g, 60min) contains enzymes of protein synthesis: peptidyl transferase etc.
Describe biochemical characterization of the Cytosol;
Soluble fraction of cytoplasm, contains enzymes of glycolysis, gluconeogenesis, pentose-phosphate cycle, activation of amino acids, synthesis of fatty acids etc.
How are Enzymes named?
Trivial name e.g. trypsin, Substrate +-ase e.g. maltase, Substrate + chemical reaction e.g. Glucose-6-phosphatase, International Enzyme Comission
Name 6 Major classes of Enzymes;
Oxidoreductase, Transferase, Hydrolase, Lyase↔Synthase, Isomerase, Ligase=Synthetase (ATP)
Describe Oxireductase;
One substrate is oxidised, another is reduced -> dehydrogenases, amino acid oxidases, catalase
Describe Transferase and subclasses;
Transfer certain groups from one substrate to another ->
i) aldehyde-, ketotransferases (transketolase)
ii) acyltransferase (thiolase) iii)aminotransferases(transaminases) iv)phosphotransferases (hexokinase)
Describe Hydrolase and subclasses;
Hydrolytic cleavage of different bonds ->
i) Esterases(lipase,phosphatase) ii)Glycosidases
A) α-glycosidase(amylase, maltase) B) ß-glycosidase(Succrase, lactase) C) N-Glycosidase
iii)Peptidases (endo- & exopeptidases; pepsin, trypsin, elastase, rennin)
iv) Amidases(hydrolyse nonpeptide C-N bond; asparaginase, glutaminase)
Describe Lyase↔Synthase and subclasses;
Eliminate/Add non-hydrolytic cleavage of different bonds/synthesis without breakdown of ATP ->
i) C-C:amino acid decarboxylases,aldolases
ii) C-O: Carbonic Anhydrase, Enolase
iii) C-N: Arginosuccinase iv)Glycogen synthase
Describe Isomerase;
Isomerization -> phosphohexose isomerase, phosphoglucomutase
Describe Ligase=Synthetase (ATP);
Joining 2 molecules with breakdown of ATP -> Aminoacyl-tRNA, DNA Ligase
What is the origin of pyruvate?
Glycolysis, Transamination (ALT), Lactate
What is role of pyruvate?
Anaerobic Glycolysis (lactate-dehydrogenase -> lactate, mitochondria -> pyruvate-dehydrogenase -> acetyl-coA, mitochondria -> pyruvate-carboxylase -> oxaloacetate, transamination -> alanine)
What is origin of Acetyl- coA?
Oxidation of pyruvate, ß-oxidation, Ketolysis
What is role of Acetyl- coA?
Citric Acid Cycle, Fatty Acid Synthesis, Cholesterol synthesis, Ketogenesis
What are branching points of Citric Acid Cycle?
Citrate, α-ketoglutarate, Succinyl-coA, Fumarate, Malate
What is Citrate used for?
Fatty Acid Synthesis (transfers acetyl- coA to cytoplasm)
What is α-ketoglutarate used for?
Transamination(ALT,AST),Oxidative deamination (L-Glu-dehydrogenase) entering amino acids into GNG (Gluconeogenesis)
What is Succinyl-coA used for?
Starts Heme Synthesis, enters propionate and some amino acids into GNG
What is Fumarate used for?
Purine Synthesis and Urea Cycle
What is Malate for?
GNG
What are branching points of Pentose Phosphate pathway?
Ribose-5-phosphate, NADPH+H+
What is the origin of ribose-5-phosphate?
Glucose -> oxidative part, degradation of nucleic acids
What is role of ribose-5-phosphate?
Non-oxidative part Glucose, PRPP synthetase5-ribophosphyl-1-pyrophosphate synthesis of nucleic acids
What is the role of NADPH+H+?
anabolic pathway -> fatty acid and cholesterol synthesis
What is origin of UDP?
Glucose-1-P -> UDP-glucose-pirophosphorylase
What is role of UDP?
Glycogen synthesis, 4-epimerase -> UDP- Galactose -> Mucopolisacc., Lactose synt.
What is role of HMG-coA in Cytoplasm?
Synth. Of cholesterol
What is role of HMG-coA in Mitochondria?
Ketogenesis
What substances involved in amino acid metabolism?
Gluconeogenic Amino Acids, Arginine, Methylations
What is role of Gluconeogenic Amino Acids?
GH -> built into proteins, Glucocorticoids -> GNG -> Glucose
What is role of Argenine?
Creatine Synthesis, Urea cycle
What is role of Methylations?
SAM -> SAH, synthesis of creatin, lecithin
Name Anaerobic FAD-dependent enzymes;
Succinate dehydrogenase, Acetyl-coA dehy., NADH dehyd.
Name Aerobic FAD-dependent enzymes;
Xantinoxidase, Monoamino-oxidase
Name NADP+ dependent enzyme;
Glucose-6-phosphate dehydrogenase
Name NAPH+H+ dependent enzymes;
HMG-coA reductase, Enoyl reductase
Name PALP dependent enzymes;
aminotransferases (ALT,AST), Aminoacid decarboxylases
Name Biotin dependent enzymes;
Pyruvate carboxylase, acetyl-coA carboxylase
Name TPP-dependent enzymes;
Pyruvate dehydrogenase, Trans-ketolase
Where is DNA stored in Eukaryotes?
Nucleus
What makes up Nucleic Acid in DNA?
Sugar, Phosphate and Bases
What makes up a Nucleoside?
Pentose+Base
What makes up a Nucleotide?
Phosphate+ Pentose+ Base
What are Bases divided into?
Purines, Pyrimidines
What bases are found in Nucleotides?
A, G, C,U, T, Ribose and Deoxyribose
What is the diff. in a keto- and -enol form?
Keto -> = O or - NH , enol -> -OH , =N
What bonds are found in Nucleosides?
N-Glycosidic Bonds
What bonds are found in Nucleotides?
Phosphoester- Phosphodiester bond
What is structure of Polynucleotide?
Sugar phosphate backbone+ single strand of polynucleotide with ribosome sugar and nitrogenous base; Adenine, Uracil, Guanine and Cysteine
What enzyme used in PRPP Synthesis?
Phosphoribosylpyrophosphate synthetase (PRPP Synthetase)
Describe Synthesis of Purine Nucleotide; (de novo)
IMP (Inosine Monophosphate) begins with 5-phosphoribosyl-1-pyrophosphate, PRPP Use Glutamine to form 5-PR-1-Amine by PRPP-amido transferase -> using ATP, tetrahydrofolate (THF) derivatives, CO2, Glutamine, Glycine and Aspartate = IMP
Describe Synthesis of GMP;
IMP oxidised, adding a ketone group -> attacked by ammonia on glutamine in next reaction= GMP (cost to cell=1 AMP)
Describe Synthesis of AMP;
IMP combines with aspartate and in 2nd reaction, combination split into fumarate and AMP. (cost to cell=GTP)
How is Purine Nucleotide Synthesis regulated?
Aminotransferase reaction is regulated in PRPP-amido transferase (feedback inhibited by allosteric binding of ATP, ADP and AMP at 1 inhibitory site and GTP, GDP and GMP at another. Activity of enzyme is stimulated by PRPP)
What does catabolism of purine nucleotides lead to and what species does it affect?
Production of Uric acid which is insoluble in some species (Hu, Pr, Av, Dalmatians) and is excreted in urine as sodium urate crystals or to Allantoin production in liver only
What are Salvage Pathways?
Synthesis of Nucleotides from purine bases and nucleosides
What actually takes place in Salvage pathways?
Free purine bases; Adenine, Guanine, Hypoxanthine are converted to their corresponding nucleotides by phosphorylation.
Name 2 key transferase enzymes involved in purine salvage;
Adenosine Phosphoribosyltransferase (APRT) [Catalyses Adenine+PRP↔ AMP+PPi], Hypoxanthine-guaninephosphoribosyltransferase (HGPRT) [catalyse x2 reactions; hypoxanthine +PRPP↔IMP+PPi and guanine+PRPP↔GMP=PPi]
Describe Synthesis of UMP;
Carbamoyl Phosphate synthesized from glutamine instead of ammonia and synthesized in cytosol. Reaction catalysed by Carbamoyl phosphate synthetase II (CMP-II) -> incorporated via aspartate transcarbamoylase (ACTase) -> N-Carbamoyl aspartate -> Cyclized to form 6 membered ring of pyramidines -> PRPP combines with ring to form orotidine 5’phosphate -> CO2 removal = UMP -> 2 kinase reactions (addition of phosphate)= UTP (uses up 4 ATP) -> addition of amino =CTP (CTP synthetase) (costs one ATP)
What are uridine nucleotides precursors to?
De novo synthesis of Thymidine Nucleotides
Describe Pyrimidine Nucleotide Synthesis;
1st step occurs in Eukaryotes (not microbes), Carbamoylphosphate synthetase II (CPS-II) activated by ATP (PRPP) (inhibited by UDP, UTP, dUTP and CTP). CTP synthetase is feedback inhibited by CTP/ activated by GTP
Describe De Novo Pathway of Synthesis of Thymine (dTTP);
dUMP converted to dTMP by thymidylate synthase -> methyl group donated by tetrahydrofolate
Describe Salvage Pathway to dTTP;
Thymidine kinase uses thymidine/ deoxyuridine as substrate -> 2x reactions; thymidine+ATP↔TMP+ADP and deoxyuridine+ATP↔dUMP+ADP
What is activity of Thymidine Kinase like?
Fluctuates with cell cycle, rising to peak activity in DNA synthesis, it’s inhibited by dTTP
Describe formation of Deoxyribonucleotides;
Reduction of rDNPs by ribonucleotide reductase enzyme -> Phosphorylation= dNTPs
What catalyses the phosphorylation of dNDPs to dNTPs?
Nucleodisediphosphat kinases (uses ATP)
