Biochemistry - Unified material Flashcards
Define the orientation of amino acids in humans.
ALL amino acids in humans are of L orientation.
What is sickle cell anemia (HbS)?
Abnormal protein aggregation
Mutation of DNA structure which abnormally impacts the primary structure of Hb turning glutamate into valine.
Hb normally biconcave
Can result in a sickle cell crisis
What is the normal value for hemoglobin (Hb)?
What is the normal value for hematocrit (HCT)?
Hb: 12-16
HCT: 41-53%; also called packed cell volume.
HCT is 3x Hb
Define hemolysis.
Destruction of RBC.
Can lead to hyperbilirubenemia, which in turn can cause the liver to secrete too much bilirubin into the bile. This can lead to gallstones, or cholecystitis.
What is bilirubin?
What is hyperbilirubenemia?
Bilirubin is a main component of bile. It is a pigment derived form the breakdown of heme (RBC).
Hyperbilirubenemia is too much bilirubin in the bile.
What is diabetic ketoacidosis (DKA)?
Inadequate uptake of glucose in DM1/2 can lead to liver metabolism of fatty acids to ketone bodies, acetoacetic acid and hydrobutryic acid.
These weak acids dissociate into [H+], which in turn lowers the pH. Bicarbonate will also be low.
Blood glucose will be higher than normal.
Patient will be hypotensive and dehydrated with a rapid pulse.
Acetone odor on breath.
Polyuria – more water in urine because of high osmolar glomeular filtrate with ketone bodies (osmotic dieresis)
Water loss from the blood leads to dehydration and eventually coma.
_________________ is blood from which RBC’s have been removed.
_________________ is the term for blood without clotting factors.
Plasma; serum
What is the treatment for DKA?
- IV saline to counteract osmotic dieresis fluid loss
2. IV insulin q 1 hr
What is the term for too much aspirin intake?
Salicylate toxicity.
Early signs: respiratory stimulation, upper GI distress, nausea/headache.
Normal serum levels: 120 mg/dl a day. 800 can be fatal
A drop in pH elicits an increase/decrease in breathing?
Increase.
___________________: deep labored breathing associated with severe metabolic acidosis.
Kussmaul
Normal paCO2?
35-45 mmHg
Water is _____% of body weight.
60%
Who has a greater percentage of water?
Men vs. Women
Obese vs. non-obese
Old vs. Young
Men
Non-obese
Young
Regarding body water:
What percentage is intracelluar vs. extracellular ?
60% intracelluar
IDDM or DM1 is a result of…
Beta-cells of pancreas inability to synthesize and secrete insulin.
Where is the breathing center in the brain?
Hypothalamus
Describe the fate of carbon dioxide in the body.
- Carbon dioxide dissolved in water
- Enzyme carbonic anhydrase helps convert into carbonic acid
- This breaks down to H+ the bicarbonate anion and trace carbonate
What is the major source of metabolic acid in the body?
Carbon dioxide produced principally from fuel oxidation in the TCA cycle.
What are the 4 major buffer systems in the body?
- Carbonic acid-bicarbonate buffer system in the blood
- Hb buffer in RBC’s
- Phosphate buffer in all cells
- Protein buffer in cells/plasma
In order to isolate plasma, one must administer a/an ____________________.
Anticoagulant
Otherwise, the blood will clot and you will be left with serum (blood without clotting factors).
What is the term for adding a carbohydrate to a molecule?
Glycolsalation
Define: hypoxia
Lack of oxygen
Define: ischemia
Lack of blood flow
Define this state:
pH: 7.31
PaCO2: 29
PaHCO2: 22
Uncompensated espiratory acidosis
What is normal physiological pH?
7.35-7.45
- The immediate precursor of the ammonia (NH3) produced by the kidney is
Glutamine
What is the pKa of an acid?
An indication of the strength of the acid
- The drug acetazolamide which is used to treat glaucoma also inhibits carbonic anhydrase of renal tubular cells. Administration of this drug is likely to cause:
Metabolic acidosis
The main form in which H+ is excreted by the kidney is as ____________________. This ion comes from ______________ & the reaction is catalyzed by _________________________.
Ammonium ion (produced from glutamine & catalyzed by glutaminase)
At a high altitude, there is more/less oxygen?
Less oxygen; someone would present with normal pH & low PCO2
What are the two major urinary buffering ions?
- Ammonia (predom) 2. Phosphate
The Hb-oxygen dissociation curve is what shape?
Sigmoidal
T/F Hb consists of primarily alpha-helix
True
Differentiate between the R & T states of Hb with respect to both oxygen & carbon monoxide.
Technically speaking, R & T refer to the conformation of Hb. R: oxy-Hb; T: deoxy-Hb (Except CO can make ‘R’ Hb because of it binds to Hb 200X stronger than oxygen. This technically isn’t oxy-Hb, but it stabilizes the conformation)
What is the composition of HbF (heme, alpha, beta, gamma chains)?
4 heme groups, 2 alpha peptide chains, 2 gamma peptide chains
HbF has greater/reduced affinity for oxygen than HbA
Greater (allows maternal blood to transfer oxygen across the placenta to the developing fetus)
Which binds more tightly to 2,3-BPG: HbA or HbF?
HbA
HbF becomes undetectable when?
6 months
What is HbA1C & why is it useful?
HbA1C is glycosylated Hb. When blood glucose levels are high, i.e. uncontrolled DM, more things (including HbA) will become glycosylated.
Differentiate between left and right shifts of the oxy-Hb dissociation curve.
Right – reduced affinity (metabolism, H+, 2,3,-BPG); Left shift – greater affinity (HbF, myoglobin)
Describe the extra-cellular matrix related to fibrous proteins.
- Fibrous proteins (collagen & elastin); specialized proteins – fibrillin, fibronectin, laminin; 2. Ground substance (GAG’s)
What is the AA composition, structure & function of collagen?
AA: Glycine (every 3rd AA – allows tight winding), proline (leads to kinks for tight winding— like a rope), lysine
Collagen: insoluble extracellular protein of ECM – forms fibrils (mesh like network)
- Triple helical structure with three tightly-wound alpha-chains
Describe the fibril-associated collagens.
Type I: skin, bone, tendon, cornea
Type 2: cartilage (inter-vertebral disk & virteous body)
Type 3: (reticular) blood vessels, fetal skin
- 3-D mesh, components of basement membrane, below stratified squamous epithelia
How many genes do humans contain for pro-alpha chains of pro-collagen?
2 genes
How many pro-alpha chains are used to form procollagen?
3 pro-alpha chains
What is the function of propeptides in procollagen?
- Lock three pro-alpha chains via disulfide bonds (allows fast winding)
- Lock N-terminals to prevent unwinding
- Necessary for intracellular solubility
What is procollagen?
Soluble form of collagen inside fibroblasts
What is tropocollagen?
Formed extracellular by enzymes from procollagen; it is insoluble after the cleavages of propeptides – several tropocollagens are cleaved to form collagen
How is tropocollagen formed from procollagen?
Procollagen is cleaved to tropocollagen by cleavage of the N-terminal & C-terminal propeptides catalyzed by extracellular enzymes, procollagen peptidases.
Vitamin C deficiency is also known as _____________
Scurvy
Vitamin C is a conenzyme for which 2 enzymes involved in collagen synthesis in the fibroblast?
Prolyl hydroxylase & Lysyl hydroxylase
What is hydroxy-proline & what enzyme is important for its formation?
Needed for stabalization of pro-collagen triple helix; allow many H-bonds (Vit C is coenzyme for prolyl hydroxlase)
What is hydroxy-lysine? What enzyme is important for its formation?
Residues reach out of the triple helix; not used for stabalization
- Used for eventual extracellular cross-linking
- (Vit C is coenzyme for lysyl hydroxlase)
Which enzyme is involved in extra-cellular cross linking in collagen synthesis? What is its co-factor?
Lysyl oxidase (extracellular & needs copper)
The cofactor for hydroxylysine formation is…
Vitamin C
- Is the enzyme lysyl hydroxylase or is the enzyme lysyl oxidase needed for the eventual syntheses of both, collagen and elastin?
Lysyl oxidase is needed for the eventual synthesis of both, collagen and elastin. A deficiency of lysyl oxidase or also of copper leads to defective cross-linking in both, collagen and in elastin.
Lysyl hydroxylase is mainly needed for eventual collagen synthesis and nearly not used for elastin synthesis.
Differentiate between vitamin C & copper deficiencies.
Deficiency in vitamin C leads to defective collagen synthesis but to mostly normal elastin synthesis. (prolyl & lysyl hydroxylase)
Deficiency in copper leads to defective cross-linking in both collagen & elastin (lysyl oxidase)
Collagen deficiency manifests as…
Ehlers-Danlos syndromes. Can result from mutation in pro-alpha chain (lethal vascular problems); EDS can result from deficient enzymes (prolyl/lysyl hydroxylase, lysyl oxidase, procollagen peptides)
What is Ehlers-Danlos Syndrome?
Type III collagen deficiency
Classic presentation - fragility of skin/vascular vessel walls; hypermobility/hyperextensibility of joints/skin
What is osteogenesis imperfecta and what are classic signs?
Brittle bone disease – TYPE 1 COLLAGEN deficiency; long bone fractures in infancy, retarded wound healing, rotated spine, BLUE SCLERAE, short stature, hearing loss, dentiogenesis imperfecta
Differentiate between Type I, II, IV OI.
Type 1 - mildest [mutation in collagen I pro-alpha chain; glycine substituted for a more bulky AA which prevents tight winding; if cystein is there, disulfide bonds may form]
Type 2 - most severe
Type 4 - common, NORMAL SCLERAE
What are 2 common signs of OI?
Fractures (type I defective – bone, cornea) & blue sclerae (thin collagen layer of cornea so the pigmented layer shines through)
What is the inheritance of OI?
Autosomal dominant
What is the inheritance of EDS?
Autosomal dominant
What is the inheritance of Marfan’s snydrome?
Autosomal dominant
What is elastin?
Insoluble extracellular protein that has rubber-like properties which forms a network that can bend and stretch in any direction.
Thick yellow fiber (fibrillin + amorphous elastin)
T/F Marfan’s is a result of defective tropoelastin gene.
FALSE - Marfan’s is a genetic defect related to fibrillin-1 protein, a glycoprotein which functions as scaffold for tropoelastin.
What is Marfan’s syndrome?
Type IV connective tissue disorder (elastin) which results from defect in fibrillin.
Leads to long limbs, eye dislocation, aortic root dilation
What are desmosine & isodesmosine?
Special cross-linkages in elastin; allow rubber-like properties.
[Desmosine – yellow color]
-Formation catalyzed by lysyl oxidase, needs copper as co-factor
Describe the formation of elastin.
Tropoelastin –> fibrillin (scaffold) –> elastin cross-linked (with lysyl oxidase enzyme)
700 AA’s – alternating hydrophillic/hydrophillic
- Rich in glycine, alanine, lysine, proline
What is the clinical manifestation of a lack of copper?
Defective cross-linking can lead to aneurysms; large amount of elastic fibers found in walls of large arteries.
What is the key equation tying together delta G, delta H & delta S?
G = H - TS
How can you force a reaction forward?
Continuously remove products
T/F Endergonic reactions push exergonic reactions forward
False – exergonic reactions push endergonic reactions forward; this is necessary for coupled thermodynamic reactions
If a reaction is close to equilibrium, what ratio will be 1?
Keq = 1
What is log(1)?
0
T/F A negative delta g results in an exergonic reaction.
True
In alpha-amino acids, does the alpha-carbon represent Carbon #1?
No – carbon #1 belongs to the most oxidized group, which is carboxyl group (COOH). The alpha-carbon is actually C-2.
Describe an amino acid.
Alpha-C bound to COOH (acid), NH3 (amino), R group & H
Which amino acid has an alpha-carboxyl group & a gamma-carboxyl group?
Glutamate
At physiologic pH, what does an AA look like?
Carboxyl group (pKa 2) negatively charged; amino group positively charged (pKa 9-10)
Which of the 20 standard AA’s can contain 3 pK’s?
The acidic (Glu, Asp) and basic AA’s (His, Lys, Arg)
Which AA serves as a buffer in RBC’s?
Histidine (pKa 6)
What are the 20 AA’s and what are their categories?
NP (B - LIV /UB - GAP), P (UC) - TAGS, S - CM, Aromatic - PTT, Acid - GA, Base - HLA
What is the overall charge at the isoelectric point?
Net charge of 0
What enzyme is found in RBC’s?
Carbonic anhydrase
Which are the 3 AA’s with an OH on the side chain?
Serine, threonine, tyrosine (S & Threonine used for phosphoyrylation or glycosylation)
In patients with phenylketonuria, the hydroxylation of phenylalanine is defective. Which AA cannot be formed?
Tyrosine
In Maple Syrup Urine disease, the eventual degradation of the branched-chain amino acids is defective. Into which group do branched-chain amino acids belong, amino acids with nonpolar, polar uncharged, or charged side chains? Name the three branched-chain amino acids.
Leucine, Isoleucine, Valine
- Alanine and methionine both contain a methyl group. What is special in the methionine structure that allows methionine in its activated form to serve as the major methyl donor in metabolism?
Sulfur
How many disulfide bonds are found in the insulin molecule?
3 disulfide bonds
- Which amino acid side chain contains a sulfhydryl group that can form a disulfide bond with another amino acid of the same kind? Is the disulfide bond a covalent or a noncovalent bond?
Cysteine; yes covalent
How are biologically active amines formed?
Decarboxylation of alpha-carboxyl group (requires PLP from vitamin B6)
What is GABA & how is it formed?
GABA - inhibitory neurotransmitter; formed by decarboxylating the alpha-carboxyl group; the R-group carboxyl group becomes the new alpha-carboxyl group
How is histamine formed? Which responses or functions are mediated by histamine?
Histamine formed by decarboxylation of histidine; leads to gastric acid secretion & mediates allergic/inflammatory responses - a strong vasodilator
Tryptophan is hydroxylated and then decarboxylated to the physiological active amine serotonin. Which of the two reactions needs PLP? What is the biomedical importance of serotonin?
The decarboxylation of hydroxytryptophan to serotonin needs PLP.
Serotonin is needed for the regulation of sleep, temperature and blood pressure.
It is involved in pain perception and causes a feeling of well-being. Serotonin blood levels are related to mood disorders.
Give three examples of catecholamines. What does their synthesis require?
Dopamine, NE, Epi; Tyrosine
Dopamine is formed from DOPA. Sometimes the drug Levo-DOPA is given to patients. Why is it given as L-DOPA, meaning in its optical active form as L-amino acid?
DOPA is formed by hydroxylation of L-tyrosine. Tyrosine is a hydroxylated phenylalanine, and instead of hydroxy-tyrosine, the name refers to phenylalanine.
The L-form of the amino acid dihydroxy-phenylalanine (DOPA) needs to be given, as in humans the amino acids found are in the L-configuration which is recognized by human enzymes.
- Which catecholamine acts mainly as hormone and is released from the adrenal medulla into the blood?
Epinepherine; synthesis starts with tyrosine & forms dopamine & NE as intermediates.
- Fight/flight hormone; leads to increase of glucose & HR; degradation of triacylglycerols in fat cells
Which parts of amino acids are involved in a peptide bond?
COO of first AA & NH3 of second AA (dehydration synthesis, so the bond is CO-NH)
Describe the peptide bond.
40% double bond character; rotation, but no bending (rigid & planar)
How is a peptide bond formed?
Dehydration synthesis
Name 3 fibrous structural proteins.
Collagen, elastin, keratin
Is albumin a fibrous or a globular protein? What is its function in addition to regulate osmolality? Would you expect disulfide bonds in its structure?
Globular; transport protein in blood; Yes- di-sulfide bonds (extra-cellular proteins usually stabalized by disulfide bonds)
Describe primary, secondary, tertiary, quarternary structure of proteins.
Primary – sequence; Secondary – alpha/beta (H bonding); Tertiary – 3D folding; Hb formed by multimeric proteins
Arrange in order of strength (strongest to weakest): Covalent bonds, ionic bonds, hydrogen bonds, hydrophobic forces, VDW forces
As noted on front of card
In a globular protein, hydrophobic forces are ____________ & hydrophillic forces are _______________.
Phobic - inside
How are the insulin chains linked?
The insulin A- and B-chains are linked to each other via two disulfide bonds.
The A-chain has also an intra-chain disulfide bond which leads to a specific configuration needed for the insulin receptor.
In an alpha-helix, where are the side chains?
Directed outside helix
Which AA side chains would interrupy the alpha-helix when they would be 3-4 residues apart of glutamate residues?
Asp, Glu, Lys, Arg, His
How can proline residues in the primary structure affect the respective secondary structure of the alpha-helix?
Peptide bond formed with proline leads to kink in the polypeptide chain; disrupts secondary structure of helix
Describe the alpha-helix.
Alpha-helix: one polypeptide chain wound around an imaginary axis, hydrogen bonds formed from peptide bonds in the direction of the axis, amino acid side chains oriented to the outside of the spiral
Describe the beta-sheet.
At least two polypeptide chains linked to each other via hydrogen bonds formed with peptide bonds of the other chain, side chains are alternately above and below the plane
Name two diseases where an abnormal protein is not degraded, but accumulates and damages the brain.
Prion disease & Alzheimer’s disease
Describe what happens to the secondary structure of proteins in Prion disease.
Prion disease shows an abnormal change from the alpha-helix to the beta-pleated sheet. The amino acid sequence is the same, only the secondary structure is changed and leads to the disease. Prion is a normal protein found on neurons with abundant alpha-helices.
Arrange in order of strength (strongest to weakest): Covalent bonds, ionic bonds, hydrogen bonds, hydrophobic forces, VDW forces
As noted on front of card
Arrange in order of strength (strongest to weakest): Covalent bonds, ionic bonds, hydrogen bonds, hydrophobic forces, VDW forces
As noted on front of card
In a globular protein, hydrophobic forces are ____________ & hydrophillic forces are _______________.
Phobic - inside
In a globular protein, hydrophobic forces are ____________ & hydrophillic forces are _______________.
Phobic - inside
How are the insulin chains linked?
The insulin A- and B-chains are linked to each other via two disulfide bonds.
The A-chain has also an intra-chain disulfide bond which leads to a specific configuration needed for the insulin receptor.
How are the insulin chains linked?
The insulin A- and B-chains are linked to each other via two disulfide bonds.
The A-chain has also an intra-chain disulfide bond which leads to a specific configuration needed for the insulin receptor.
- Which catecholamine acts mainly as hormone and is released from the adrenal medulla into the blood?
Epinepherine; synthesis starts with tyrosine & forms dopamine & NE as intermediates.
- Fight/flight hormone; leads to increase of glucose & HR; degradation of triacylglycerols in fat cells
Which parts of amino acids are involved in a peptide bond?
COO of first AA & NH3 of second AA (dehydration synthesis, so the bond is CO-NH)
Describe the peptide bond.
40% double bond character; rotation, but no bending (rigid & planar)
How is a peptide bond formed?
Dehydration synthesis
Name 3 fibrous structural proteins.
Collagen, elastin, keratin
Is albumin a fibrous or a globular protein? What is its function in addition to regulate osmolality? Would you expect disulfide bonds in its structure?
Globular; transport protein in blood; Yes- di-sulfide bonds (extra-cellular proteins usually stabalized by disulfide bonds)
Describe primary, secondary, tertiary, quarternary structure of proteins.
Primary – sequence; Secondary – alpha/beta (H bonding); Tertiary – 3D folding; Hb formed by multimeric proteins
Arrange in order of strength (strongest to weakest): Covalent bonds, ionic bonds, hydrogen bonds, hydrophobic forces, VDW forces
As noted on front of card
In a globular protein, hydrophobic forces are ____________ & hydrophillic forces are _______________.
Phobic - inside
How are the insulin chains linked?
The insulin A- and B-chains are linked to each other via two disulfide bonds.
The A-chain has also an intra-chain disulfide bond which leads to a specific configuration needed for the insulin receptor.
In an alpha-helix, where are the side chains?
Directed outside helix
Which AA side chains would interrupy the alpha-helix when they would be 3-4 residues apart of glutamate residues?
Asp, Glu, Lys, Arg, His
How can proline residues in the primary structure affect the respective secondary structure of the alpha-helix?
Peptide bond formed with proline leads to kink in the polypeptide chain; disrupts secondary structure of helix
Describe the alpha-helix.
Alpha-helix: one polypeptide chain wound around an imaginary axis, hydrogen bonds formed from peptide bonds in the direction of the axis, amino acid side chains oriented to the outside of the spiral
Describe the beta-sheet.
At least two polypeptide chains linked to each other via hydrogen bonds formed with peptide bonds of the other chain, side chains are alternately above and below the plane
Name two diseases where an abnormal protein is not degraded, but accumulates and damages the brain.
Prion disease & Alzheimer’s disease
Describe what happens to the secondary structure of proteins in Prion disease.
Prion disease shows an abnormal change from the alpha-helix to the beta-pleated sheet. The amino acid sequence is the same, only the secondary structure is changed and leads to the disease. Prion is a normal protein found on neurons with abundant alpha-helices.
What are heat shock proteins?
Chaperones for specific folding of proteins (HSP 70-prevents aggregation of unfolded protein; HSP-60 have a barrel shape and help folding/unfolding)
How does one get Prion disease?
Prion disease can be acquired by eating infected tissue that contains abnormal prion protein.
Does protein denaturation lead to a destruction of primary structure?
NO – only tertiary & secondary. Dietary enzyme pepsin works best at pH 1-2 in stomach & catalyzes denatured dietary proteins.
In the laboratory, how do we break hydrophobic interactions of proteins?
Detergent (SDS)
In the laboratory, how do we break ionic bonds?
Strong acids/bases
In the laboratory, how do we break disulfiede bonds?
Mercaptoethanol
What are the properties of the active site of an enzyme regarding its size, structure & specificity?
Active site (relatively small); cleft formed by AA’s apart from each other in primary structure; specificty is high
Human enzymes use L/D AA & L/D Carbohydrates.
L-AA & D-Carbs
What is the difference between a holoenzyme and an apoenzyme?
Holoenzyme = apoenzyme plus co-enzyme; Some apoenzymes need metal ions in order to become the holoenzyme
What happens after the substrate binds to the active site?
E-S complex is formed; goes to high energy transition state
T/F Enzymes change the delta G of a reaction.
False! Enzymes reduce the energy of activation, but have no affect on delta G.
How can the delta-G of a reaction be changed?
Change [substrates] & [enzymes]
- Is the reaction catalyzed by lactate dehydrogenase (LDH) reversible? Which coenzyme (cosubstrate) is needed for LDH in order to form lactate from pyruvate?
Lactate dehydrogenase catalyzes a reversible reaction.
LDH needs NADH when pyruvate is used as substrate and in this direction, LDH forms lactate and NAD+ as products.
Is pyruvate oxidized/reduced to lactate?
The structure of pyruvate is changed to the structure of lactate by uptake (gain) of
hydrogen (from NADH + H+). Therefore, pyruvate is REDUCED to lactate.
In this reaction, NADH is oxidized to NAD+
T/F When the substrate is oxidized, then the coenzyme is reduced. When the substrate is reduced, then the coenzyme is oxidized.
True
Why is Vmax reached at very high substrate concentrations?
All the free enzyme is used up; no more E-S complexes can be formed, even at further increased [substrate]
What is the velocity of an enzyme-catalyzed reaction?
Product formation over time
What is Km?
Km is a CONSTANT & it is the substrate concentration at half Vmax
Which is affected by the enzyme concentration in the assay?
Vmax; Km is not changed as it is a CONSTANT. Vmax is larger in an assay that contains more enzyme
Enzyme A has a smaller Km than enzyme B for the same substrate. Does enzyme A have a higher or smaller affinity for the substrate than enzyme B?
Enzyme A with the smaller Km for the same substrate, has a higher affinity for the substrate than enzyme B. Less substrate is needed to achieve half Vmax
[an example is hexokinase (enzyme A) which has a much smaller Km for glucose than glucokinase (enzyme B). Hexokinase, which is found in most cells, has a much higher affinity for glucose than glucokinase which is found mainly in the liver and -cells of pancreas. Glucokinase is a special type of hexokinase that has a large Km and large Vmax for glucose.]
Describe an allosteric enzyme. Do allosteric enzymes follow Michaelis-Menten kinetics and show a hyperbolic curve? If not, how does the curve look like? Is Vmax reached?
Allosteric enzymes consist of several protein subunits and show cooperative substrate binding. Their kinetics do not show a hyperbolic curve, the curve is sigmoidal.
As it is an enzymatic catalysis, a Vmax is reached where all enzyme is in the ES complex. The substrate concentration at half Vmax, is named K 0.5 (instead of Km), and is an indicator for the affinity of the allosteric enzyme for the substrate.
Why do allosteric enzymes show sigmoidal curves?
Cooperative substrate binding
Does a competitive inhibitor directly interfere with E-S complex or produce formation?
E-S complex
How can we overcome competitive inhibition?
Add more substrate
What is Km in competitive inhibition?
Apparent Km is higher
Describe Vmax & Km in noncompetitive inhibition.
Vmax is lower; Km is the same
In a double-reciprocal plot (L-B), what is the x-intercept, y-intercept?
Y-intercept is 1/Vmax
X-intercept is -1/Km
Is the structure of statins similar to the structure of HMG CoA (enzyme involved in cholesterol synthesis) or HMG CoA?
HMG CoA (this is competitive inhibition); cholesterol is the product after a lot of steps
Draw 2 plots each for competitive & non-competitive inhibition.
(Y-axis = 1/Vmax; X-axis = -1/Km)
Competitive inhibition: same Vmax, larger apparent Km. The higher the inhibitor concentration is, the larger the apparent Km becomes.
Noncompetitive inhibition: same Km, apparent Vmax is smaller. The higher the inhibitor concentration is, the smaller the apparent Vmax becomes.
Differentiate between reversible & irreversible enzyme inhibition.
A reversible inhibition of the enzyme allows the dissociation of the inhibitor, and the restoring of the original conformation of the protein.
In contrary to this, an irreversible inhibitor covalently binds to the enzyme. The binding can involve the active site, sulfhydryl groups or often binding and interference with metal cofactors for apoenzymes.
Draw 2 plots each for competitive & non-competitive inhibition.
See notes
Differentiate between reversible & irreversible enzyme inhibition.
A reversible inhibition of the enzyme allows the dissociation of the inhibitor, and the restoring of the original conformation of the protein.
In contrary to this, an irreversible inhibitor covalently binds to the enzyme. The binding can involve the active site, sulfhydryl groups or often binding and interference with metal cofactors for apoenzymes.
How doe we overcome irreversible inhibition?
Synthesize new enzyme
Discuss DFP (nerve gas) & its mechanism of action
Covalent modification of a serine residue at the active site
Discuss the mechanism of aspirin.
The target enzyme for aspirin is cyclooxygenase. This enzyme is needed for the formation of prostaglandins and thromboxane.
Aspirin irreversibly acetylates a serine residue in the channel of cyclooxygenase and prevents normal product formation. Aspirin is used as drug for pain treatment.
[At a low dose, however, it can be used as daily treatment for reducing thromboxane synthesis in platelets.
Thromboxane formed by platelets favors blood clotting whereas prostacyclin, a special prostaglandin formed mostly by endothelial cells, prevents blood clotting.
Aspirin inhibits cyclooxygenase in all cells and this inhibition can be overcome by synthesis of new enzyme.
Why is low-dose aspirin recommended for high patients at high risk of blood clot?
In endothelial cells, the modified cyclooxygenase is degraded and a new enzyme is synthesized. Platelets on the other hand do not contain a nucleus and
cannot synthesize new cyclooxygenase.
This leads to a higher than normal prostacyclin/thromboxane ratio in the blood and to less blood clotting.
Where is pepsin active & what is its optimal pH?
Stomach, pH 1-2
Where is trypsin active & what is its optimal pH?
Duodenum, pH 9-10
What can a deficiency pancreatic bicarbonate lead to?
Pancreas secretes less bicarbonate, thus the acidic chyme from the stomach is not neutralized in the duodenum; happens in patients with secretin deficiency, or CF
What are the 4 general concepts of enzyme regulation?
- Changes of [substrates] or [products]
- Modulation of [enzyme]
- Covalent modification of enzymes
- Modulation of a metabolic pathway
Which response is faster – covalent enzyme modification or enzyme induction?
Covalent modification is faster than induction; covalent regulation acts on present enzyme, whereas induction acts via increased amount of enzyme and needs transcription/translation
What is a protein kinase? Does it catalyze reversible or irreversible reactions?
An enzyme that phosphorylates. This is an irreversible reaction.
What is a phosphatase? Does it catalyze reversible or irreversible reactions?
An enzyme that dephosphorylates. This is an irreversible reaction
Is the activity of the human enzyme affected by temperature? Is there a clinical relevance?
Yes; increase in temperature leads to increase in velocity until the denaturation of human enzymes starts at high fever.
Why is cardiac surgery performed with cardiac arrest solutions?
Reduce enzyme activity and save energy
What precedes enzyme induction?
Hormonal activation; i.e. Glucagon signals low blood glucose and it leads to induction of key enzymes for gluconeogenesis (forms/releases glucose into the blood)
Give an example of enzyme induction.
Insulin signals high blood glucose levels and leads in the liver to induction of key enzymes for glycolysis.
What is proteolytic cleavage?
Covalent modification of pro-enzyme by cleavage of a protein & refolding into a smaller enzyme. This is irreversible.
Give 2 examples of enzymes that are activated by proteolytic cleavage.
- Blood clotting factors (prothrombin–>thrombin); 2. Digestive proteases and pancreatic phospholipase (tripsinogen is cleaved to trypsin by proteolytic cleavage; prevents premature formation of trypsin in pancrease)
Differentiate between homotropic and heterotropic effectors.
Homotropic is where the molecule that induces the effect is similar to the substrate
Heterotropic is when the molecule that induces the effect is different from substrate.
T/F Allosteric enzymes can perform a conformational shift after binding of heterotropic effectors.
True
For example, a pathway can be down-regulated when the end product (or a related compound) of the respective pathway binds to a specific binding site of the allosteric enzyme at the rate-limiting step.
This can induce a conformational shift which leads to less activity of the enzyme, (often the affinity for the substrate is reduced by the conformational change that follows after the binding of the respective heterotropic effector.)
T/F A low K0.5 indicates a smaller affinity for an enzyme.
False - A lower K0.5 leads to a higher affinity for enzyme.
What is the difference between feedback regulation and competitive inhibition?
Feedback regulation (natural compound which has a specific binding site at regulated allosteric enzyme; molecule does not compete with substrate binding)
Competitive inhibitor – a synthetic drug that competes with substrate binding
T/F Feed-forward activation of an allosteric enzyme leads to a conformational shift after bining of the respective heterotropic effector.
True - affininty of the enzyme for the substrate is increased (left-shift in a sigmoidal curve)
Why is an increase of normally intracellular enzymes in the blood an indication of increased cell damage or even cell death?
When cells get damaged, then a leakage of large amounts of respective intracellular enzymes into the blood can occur. These are non-functional plasma enzymes.
Why does creatine kinase (CK) peak in serum earlier than LDH?
CK is smaller and diffuses faster into the blood and has a shorter half-life in blood than LDH
What are isozymes?
Enzymes that catalyze the same reaction; different AA composition & can be separated by electrophoresis
What is the function of CK?
Creatine kinase is an enzyme that phosphorylates creatine to creatine phosphate. Most kinases are irreversible – this is not.
CK has ___ subunits.
2 (M or B)
What are the 3 isozymes of CK?
CK-MM (skeletal muscle), CK-MB (heart), CK-BB (brain, colon)
Which CK is indicative of an MI?
CK-MB (heart-30% CK-MB, 70% CK-MM), but 98% of CK-MB in the body is in the heart
What is the normal ratio of CK-MB to CK-total?
< 3%; thus about 3% can be indicative of an MI
T/F CK is also a marker of liver injury.
False
What is analyzed in addition to CK, cardiac troponins, and LDH-1?
Myoglobin - not specific, but elevated during general muscle damage
What are the early and late markers of an MI?
Early - troponin, CK-MB:CK-MM, myoglobin; Late - troponins (can last a week), LDH-1:LDH-2 (the flip, around 48 hours)
Regarding LDH, what is the flip?
LDH-1 is higher in the heart, lower in RBC’s. The flip occurs during an MI when LDH-1 becomes higher in the RBC’s.
Does defibrillation lead to leakage of CK-MB as found during an MI?
No heart damage should be observed with cardiac defibrillation, so CK-MB should not go up; sometimes chest muscles are damaged and CK-MB leaks out, but MUCH less than what you would see from heart.
What are the 2 major enzymes analyzed for liver injuries?
ALT (cytosol) & AST (cytosol & mitochondria)
AST:ALT >2 can indicate liver mitochondria damage (ETOH abuse)
Which enzyme increases with bile duct obstruction or liver cirrhosis? What is special about this enzyme and bone cancer?
ALP (alk phos); yes-bone cancer (different isozyme); if GGT & bilirubin go up, then it is likely that the damage was to the liver & not the bone.
Under what normal conditions are sALP elevated?
Pregnancy & bone growth of children
Which enzymes are elevated during pancreatitis?
Amylase & lipase
What is the expected pancreatic enzyme ratio for ETOH-induced pancreatitis?
Lipase:amylase > 2
T/F CK is also a marker of liver injury.
False
What is analyzed in addition to CK, cardiac troponins, and LDH-1?
Myoglobin - not specific, but elevated during general muscle damage
What are the early and late markers of an MI?
Early - troponin, CK-MB:CK-MM, myoglobin; Late - troponins (can last a week), LDH-1:LDH-2 (the flip, around 48 hours)
Regarding LDH, what is the flip?
LDH-1 is higher in the heart, lower in RBC’s. The flip occurs during an MI when LDH-1 becomes higher in the RBC’s.
Does defibrillation lead to leakage of CK-MB as found during an MI?
No heart damage should be observed with cardiac defibrillation, so CK-MB should not go up; sometimes chest muscles are damaged and CK-MB leaks out, but MUCH less than what you would see from heart.
What are the 2 major enzymes analyzed for liver injuries?
ALT (cytosol) & AST (cytosol & mitochondria)
AST:ALT >2 can indicate liver mitochondria damage (ETOH abuse)
Which enzyme increases with bile duct obstruction?
ALP
Under what normal conditions are sALP elevated?
Pregnancy & bone growth of children
Which enzymes are elevated during pancreatitis?
Amylase & lipase
What is the expected pancreatic enzyme ratio for ETOH-induced pancreatitis?
Lipase:amylase > 2
What is a serum marker for HCC? This same marker can be used for testicular and ovarian tumors.
AFP (alpha-fetoprotein)
What is a serum marker for prostate cancer?
PSA
What is an enxyme tested for early indication of alcohol abuse?
GGT
What non-enzyme LFT’s can be tested?
Albumin, bilirubin
Which are the purines vs. pyrimadines?
Pyr- CT(U); Pur- AG
What is the difference between purines & pyrmidadines?
Pur-2 rings; Pyr-1 ring
RE: purines & pyrimadines, who bonds to whom & with how many bonds?
AT: 2 H bonds, CG: 3 H bonds
What are the three components of a nucleotide?
Pentose sugar, phosphate, N-base
What is the difference between nucleosides & nucleotides?
Nucleotides have the phosphate - necessary for polymerization
What is the bond called between 2 DNA bases?
Phosphodiester bond
If your molecule contains 50 A’s, how many T’s?
50
T/F Purines = pyrimadines in a molecule of DNA
True
T/F An AT rich part of the chromosome will have weaker bonds than a GC rich part
True
Define the primary, secondary, tertiary and quarternary structure of DNA
1- 5’/3’ base pairing, 2-3D structure, 3-supercoiling with histones; 4-interaction of nucleic acids and proteins
Describe mRNA
Single-stranded, carries codons for translation
Describe tRNA
Folded stem-loop structures with H-bonding; carries AA to ribosome
Describe rRNA
MAJOR RNA; complexes with protein to form ribosome
Describe snRNA
Small nuclear RNA; remove introns, keep exons
Describe miRNA
Micro-RNA; silencing of gene expression
List 3 nucleoside analogs & describe their mechanism of action
AZT, Didanosine (HIV reverse transcriptase inhibitors NARTI’s); Acyclovir (herpes/varicella) DNA Polymerase inhibitor – utilize viral kinase for phosphorylation and then incorporated into ds-DNA
** No 3’ OH group
List 2 nucleotide analogs & describe their mechanism of action
Adenosine arabinoside (acute lymphoblastic leukemia) Cytosine arabinoside (acute myeloid leukemia); OH in a different plane – causes chain termination
List 2 cytidine analogs & describe their mechanism of action
Decytidine, 5-azacytidine; these are hypo-methylating agents; in cancer, tumor suppressor genes are turned off (methylated), and need to be hypo-methylated
List 2 quinolines & describe their mechanism of action
Ciprofloxacin, nalidixic acid (Inhibit topoisomerase II - aka DNA gyrase in bacteria) - used for RTI, UTI, anthrax
List 1 courmarin & describe its mechanism of action
Novobiocin (identical to cipro)
List the inhibitors of DNA gyrase.
Cipro, nalidixic acid, novobiocin, etoposide
List an inhibitor of Topoisomerase I
Camptothecin
List 2 transcription inhibitors
Rifampin (TB treatment) & actinomycin D (anti-cancer - prevents unwinding of DNA)
What toxin inhibits RNA polymerase II in humans?
Toxin from mushroom a. phalloides (toxin alpha amanitin) – can be lethal!
What is the mechanism of systemic lupus erythematosus?
Autoimmune prevention of normal splicing of mRNA’s. Characterized by fatigue, arthritis, fever, skin rash & renal problems
What are the function of topoisomerases?
Topo I & DNA gyrase; prevent supercoiling of DNA
In order for extremely large DNA to be packaged in the nucleus, DNA is organized into _______________. These are composed of ____________________. The most important protein is ___________________.
Chromosomes, chromatin, histones
Histones are rich in basic proteins & are +/- at physiological pH. Therefore, DNA, which is +/- charged wraps around the histones. ds-DNA and histones associate to form a __________.
+ histones; - DNA; nucleosome
Differentiate between euchromatin & heterochromatin (include methylation & acetylation)
Euchromatin – de-condensed, transcriptionally acitive (hypomethylation, acetylated); heterochromatin– highly condensed, tightly packed & transcriptionally inactive (hypermethylated, de-acetylated)
Histone acetylation reduces/increases affinity between DNA & histone.
Reduces; thus it increases transcription
How many DNA polymerases do prokaryotes have? What are their functions?
2 DNA Polymerases
DNA Pol 3: Main replicative enzyme
DNA Pol 1: Removes RNA primer & replaces with DNA
How many DNA polymerases do eukaryotes have? What are their functions?
2 DNA polymerases
DNA Pol Delta: main replicative enzyme
DNA Pol Alpha: synthesizes RNA primer
Differentiate betwen the removal of RNA fragments in prokaryotes & eukaryotes.
Proks - DNA Pol 1; Euks - RNAseh & FEN-1 protein
Differentiate between prok & euk chromosomes & origin of replication.
Prok- circular, 1 origin of replication;
Euk- linear, many origins of replication
What enzyme puts Okazawi fragments together?
DNA ligase
What is the function of DNA helicase?
Unzip DNA; helicase inhibitor delivers it to the DNA template
What enzyme lays down an RNA primer on a DNA strand to begin initiation? What other proteins help out?
DNA primase; initiator proteins
What is at the end of the chromosome? It is repeated hundreds of times. They get smaller as we get older.
Telomeres
What is a reverse transctipase enzyme which holds a short sequence complementary to the telomere?
Telomerase
As we age, telomerase activity goes down. Cancer cells have very high telomerase activity, and if you put them in culture, they will be immortal and divide forever. Thus, a target of cancer therapy is telomerase.
Who has faster DNA replication? Euks or Proks?
Proks
What is the function of single-stranded binding proteins?
Prevents unzipped DNA from re-annealing.
Differentiate between the sense and anti-sense strand of RNA processing.
Sense: the non-template strand (i.e. this strand matches the new mRNA; it just has T’s instead of U’s)
Anti-sense: the template strand
T/F RNA Polymerases need primers like DNA Polymerases
FALSE - RNA polymerases do not need primers
How many RNA polymerases do proks & euks have?
Proks-1; Euks-3 (I-rRNA, II-mRNA, III-tRNA)
In prokaryotes, what is the term of the RNA polymerase that binds to the sigma factor (helps promorter bind to the right place on DNA)?
Holoenzyme
Where is the promoter found in proks?
-10 to -35 bp; Upstream is before the promoter, downstream is after
What are the 3 steps of transcription?
Initiation, elongation, chain termination
DNA & mRNA are written in the ___’ to ___’ direction & read in this direction __’ to __’
Written in 5’ to 3’; read in 3’ to 5’
50+ proteins bind to the RNA polymerase at the promoter site in eukaryotes. Some regions are called: GC box, TATA box, CAAT box. What are the 5 most important transcription factors?
TAT box binding protein, TFIIH (helicase), TFIIB (start site recognition), TFIID (alters DNA helix structure), TFIIE (involved in positioning the RNA polymerase)
Differentiate between intrinsic & extrinsic termination sequences in eukaryotic transcription.
Intrinsic – GC rich at base; stem loop structure formed, separates RNA polymerase from the template;
Extrinsic – Rho protein uses helicase activity to separate the template & mRNA
Differentiate between prokaryotic & eukaryotic mRNA
Prok- completely unmodified, is polycistronic
Euk - 5’ cap, 3’ poly A tail; splicing to remove introns; alternative splicing to increase diversity
Beta-thalassemia results from
Abnormal splicing post-transcription; this is a hemoglobinopathy
Discuss 5’ capping of eukaryotic mRNA
Guanylyl transferase adds a G onto the 5’ end of the RNA (actually happens during, not after transcription because RNA Pol II is responsible for this)
- Regulates export of mRNA out of the nucleus
- Initiation factors require cap for translation
- Stabalizes and prevents exonuclease activity
Discuss 3’ poly-adenylation of eukaryotic mRNA
Poly-A polymerase adds 200 A’s; it is like a telomer, protects the end from exonuclease degradation, and is necessary for translation
What is the function of guanylyl transferase?
Transfers G to the 5’ cap of mRNA
What is the key post-transcriptional modification?
Splicing (exons in, introns out) & alternative splicing (25,000 genes –> 100,000 proteins)!
Describe 2 examples of RNA base editing.
- APO-lipoprotein in liver/intestine (creating a stop codon) – cytodinedeaminase changes C’s to U’s
- Glutamine –> arginine in the brain (adenosine deaminase) – necessary for brain development
Give 3 examples associated with mRNA errors.
- SLE
- B-thalassemia
- Limb girdle muscular dystrophy
Describe the impact of cholera toxin, E. coli, & pertussis toxin and signal transduction
Cholera toxin & E. coli can bod ADP-ribosylate G-subunit; pertussis toxin ADP-ribosylates G
(ADP-ribosylation of G-alpha results in inactivation of GTP-ase activity; we’re perpetually in a GTP state & adenlyl cyclase is active)
Describe Trypanosome (Chagas disease) & Leishmania (Leishmaniasis). These are parasitic infections.
Extensive editing; addition of a lot of U’s into mRNA (uses guide mRNA, which has a region complimentary to the target, so it can bind)
What is the function of guanylyl transferase?
Transfers G to the 5’ cap of mRNA
What is the key post-transcriptional modification?
Splicing (exons in, introns out) & alternative splicing (25,000 genes –> 100,000 proteins)!
Describe 2 examples of RNA base editing.
- APO-lipoprotein in liver/intestine (creating a stop codon) – cytodinedeaminase changes C’s to U’s
- Glutamine –> arginine in the brain (adenosine deaminase) – necessary for brain development
Give 3 examples associated with mRNA errors.
- SLE
- B-thalassemia
- Limb girdle muscular dystrophy
Describe the impact of cholera toxin, E. coli, & pertussis toxin and signal transduction
Cholera toxin & E. coli can bod ADP-ribosylate G-subunit; pertussis toxin ADP-ribosylates G
(ADP-ribosylation of G-alpha results in inactivation of GTP-ase activity; we’re perpetually in a GTP state & adenlyl cyclase is active)
Describe Trypanosome (Chagas disease) & Leishmania (Leishmaniasis). These are parasitic infections.
Extensive editing; addition of a lot of U’s into mRNA (uses guide mRNA, which has a region complimentary to the target, so it can bind)
Pertussis is also known as ________________.
Whooping cough
- Which fatty acid has the lowest melting point out of the group of oleic acid, linoleic acid and alpha-linolenic acid?
Alpha linoleic acid; lowest meting point because it has the most double bonds
Which are the fat-soluble vitamins?
A, D, K, E
Why are omega-3’s important?
DHA is important for brain functions and the visual cycle in the retina
What the derivatives of linolenic acid & alpha-linolenic acid?
Linolenic (omega-6) –> arachadonic acid
Alpha-linolenic (omega-3) –> DHA, EPA
What is the main storage form of fatty acids?
TAG
During fasting, what happens to TAG’s?
They are cleaved and the free fatty acids and glycerol are released into the blood
What is phosphatidylcholine?
- Major component of cell membranes
- Secreted by liver into bile for cholesterol transport
- Provides lung surfactant (dipalmitoyl) in alveoli of lung
- Used for synthesis of shingomyelin
What fatty acid is used for lung surfactant?
Dipalmitoyl
