Biochemistry Exam 1! Flashcards
aldehyde
aldehyde
Carbon-Oxygen Groups
Alcohol Aldehyde Ketone
Carbon-Oxygen Groups
Alcohol Aldehyde Ketone
Carbon-Oxygen Groups
Carboxylic Acid, Ether, Acid anhydride
Carbon-Oxygen Groups
Carboxylic Acid, Ether, Acid anhydride
Carbon-sulfur Groups
sulfhydryl group
A disulfide
Carbon-sulfur Groups
sulfhydryl group
A disulfide
Carbon-Nitrogen Groups
Amino group
Quaternary amine
Carbon-Nitrogen Groups
Amino group
Quaternary amine
Esters and Amides
Ester
Thioester
Esters and Amides
Ester
Thioester
Esters and Amides
Phosphoester
Amide
Esters and Amides (Good leaving groups)
Phosphoester
Amide
Major Types Functional groups found in biochemical compounds of the human body
Carboxylate group
phosphate group
sulfate group
Major Types Functional groups found in biochemical compounds of the human body
Carboxylate group
phosphate group
sulfate group
Small, Hydrophobic AAs
Small, Hydrophobic AAs
Nucleophilic AAs
Nucleophilic AAs
pKas are very high. Can dissociate and lead to hydrogen base.
Hydrophobic AAs
Hydrophobic AAs
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Methionine (Met)
Proline (Pro)
Aromatic AAs
Aromatic AAs
Phenylalanine (Phe)
Tyrosine (Tyr)
Tryptophan (Trp)
Acidic AAs
Acidic AAs
Generate acids pretty well because have a low pKa
Aspartic Acid (Asp)
Glutamic Acid (Glu)
Amide AAs
Amide AAs
Have an electrophylic carbon beneath double bonded O!
Asparagine (Asn)
Glutamine (Gln)
Basic AAs
Basic AAs
Histidine (His)
Lysine (Lys)
Arginine (Arg)
Titration Curve of Alanine
Titration Curve of Alanine
Respiratory
Increase CO2 –>__pH, Compensation:
Decrease CO2 –>__pH, Compensation:
Metabolic
Decrease HCO3- ==> __pH, Compensation
Increase HCO3- ===>__pH, Compensation
Respiratory
Increase CO2 –> Decrease pH, Compensation: Retain HCO3-
Decrease CO2 –>Increase pH, Compensation: Excrete HCO3-
Metabolic
Decrease HCO3- ==> Decrease pH, Compensation: Decrease CO2
Increase HCO3- ===>Increase pH, Compensation: Increase CO2
Different forms of Alanine
Different forms of Alanine
Anion Gap
Anion Gap = Na+ - Cl- - HCO3-
Normal values: 8-16mmol/L
Changes in pH, HCO3-/CO2, HCO3-, & pCO2 with…
metabolic acidosis
metabolic alkalosis
respiratory acidosis
respiratory alkalosis
Changes in pH, HCO3-/CO2, HCO3-, & pCO2 with…
metabolic acidosis
metabolic alkalosis
respiratory acidosis
respiratory alkalosis
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Dehydrogenase: Transfer hydrogen from substrate to coenzyme
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
Answer: Kinase: transfer phosphate from ATP to another molecule
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Isomerase: Interconverts isomers (These can be stereochemical transformations D to L form. Or, can be geometric transformations - from cis to trans).
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Kinase: Transfer phosphate from ATP to another molecule (add)
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Oxygenase: incorporate oxygen into substrate
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Dehydrogenase: transfer hydrogen from substrate to coenzyme
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Oxygenase: Incorporate oxygen into substrate.
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Transferase (aminotransferase): moves groups between substrates
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Isomerase: Interconverts isomers
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Synthase (the reaction is named for the reverse process – arrow should be bi-directional)
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Synthetase or carboxylase
Synthetase: ATP-coupled bond formation between substrates
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
Answer: Isomerase: Interconverts isomers
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
ANSWER: Synthase: binds 2 substrates without using ATP
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
- Identify the type of enzyme that catalyzes each of the reactions given below.
a) kinase e) dehydrogenase i) synthase
b) decarboxylase f) hydrolase j) synthetase
c) isomerase g) carboxylase
d) oxygenase h) transferase
Phosphatase
Phosphatase: remove phosphate from a substrate (add)
Protease
Protease
cleaves peptide bonds by addition of water
The intercept on the x axis is is -1/Km = -1. Km = .5mM.
Enzymes decrease the ______
Enzymes do NOT alter the _____ of a reaction
Enzymes decrease the energy of activation. Enzymes do not alter the “net energy change” of a reaction.
If Change G prime not is known, the actualy free energy change for a reaction can be calculated….
Change in G is used as a predictor of the spontaneity of the reaction
If Change G prime not is known, the actualy free energy change for a reaction can be calculated….
Change in G is used as a predictor of the spontaneity of the reaction
exergonic reaction - exothermic
endergonic reaction - endothermic
Also… Change in G = G(products) - G(reactants)
In an endergonic reaction, some energy stays in that molecule and the net energy change is negative (the ending Energy on the graph of a reaction is higher than the initial state).
Role of metals as cofactors
Role of metals as cofactors
- May link substrate to enzyme surface
- Act as “electron sinks” (eg Zn2+); redox agents (eg Fe2+, Cu2+)
Metals - prosthetic gropus - may attach directly to the enzyme…
- What is the relationship between DG, DG0/, and Keq (memorize, understand, do calculations using the equation)?
- What is the relationship between DG, DG0/, and Keq (memorize, understand, do calculations using the equation)?
- How do the “lock and key” and “induced-fit” models of enzyme action differ?
- How do the “lock and key” and “induced-fit” models of enzyme action differ?
- What are the 4 modes of enzyme catalysis? How do “modes of catalysis” differ from “models of enzyme action”?
- What are the 4 modes of enzyme catalysis? How do “modes of catalysis” differ from “models of enzyme action”?
- What is the role of myoglobin? Of hemoglobin? What are their locations in the body?
>>>More info about T & R forms…
- What is the role of myoglobin? Of hemoglobin? What are their locations in the body?
Myoglobin is an intracellular oxygen storage protein., while hemoglobin transports oxygen from the lungs to tissue. Together, these hemo-proteins diffuse oxygen into the cellular environment.
Hemoglobin: Must be able to bind oxygen at relatively high PO2 in the lungs and release oxygen at the relatively low PO2 in the tissues. Oxygen binding curve for hemoglobin is sigmoidal because oxygen binding is cooperative.
Hemoglobin alternates between high oxygen affinity (R) form and a low oxygen affinity (T) form as the RBCs move through circulation.
Mygolobin: binds oxygen well as low oxygen tension. The oxygen binding curve for myoglobin is a rectangular hyperbola.
>>>>
The hemoglobin oxygen binding dissociation curve is sigmoidal since it it must be able to bind oxygen at relatively high Po2 (inhalation) in the lungs and release oxygen at relatively low Po2 in the tissues (exhalation?).
Meanwhile, the myoglobin oxygen binding dissociation curve is rectangular since it binds oxygen as a low Po2 (low oxygen tension). This makes sense since myoglobin is found in muscle cells where it stores oxygen for use in mitochondria.
- Describe the global structure of myoglobin. How does hemoglobin differ in structure from myoglobin?
- Describe the global structure of myoglobin. How does hemoglobin differ in structure from myoglobin?
Myoglobin is compactly folded, single polypeptide chain of 153 Amino acids residues. 75% of the structure consists of 8 helical segments. The polar residues tend to be located on the outside of the molecules, while non-polar residues are on the inside of the molecule. Heme functions as the prothetic group that enables the binding of oxygen to myoglobin and hemoglobin. Heme fits in the hydrophobic pocket of the protein.
Meanwhile, hemoglobin is a tetramer of four non covalently linked subunits that are similar to myoglobin. It has a quarternary (not tertiary structure like myoglobin) structure. Each subunit has a hydrophobic pocket that contains heme. Several different forms of hemoglobin exist because of variation in the primary structure of subunits.
- What is heme? What is the oxidation state of the heme iron in hemoglobin? Why is the oxidation state important? Define methemyoglobin and carbaminohemoglobin.
- What is heme? What is the oxidation state of the heme iron in hemoglobin? Why is the oxidation state important? Define methemyoglobin and carbaminohemoglobin.
Heme is a prothetic group that enables the binding of oxygen to myoglobin and hemoglobin. Heme is made of ferrous iron and a porphyrin group, composed of four linked pyrrole units. Iron is bound to the center of porphyrin by four nitrogens. Heme iron in hemoglobin is Fe2+ (ferrous iron) since oxygen only binds to Fe2+.
Methemoglobin- is the oxidized form of hemoglobin that does not carry oxygen (since Fe is in the Fe3+ form).
Carbaminohemoglobin - is a compound of haemoglobin and carbon dioxide, and is one of the forms in which carbon dioxide exists in the blood. 10% of carbon dioxide is carried in bloodthis way (85% carried in blood as bicarbonate [hydrogen carbonate], 5% carried as free CO2, in solution).
- Where does oxygen bind in hemoglobin and myoglobin? How many oxygen molecules can associate with each heme unit in hemoglobin?
- Where does oxygen bind in hemoglobin and myoglobin? How many oxygen molecules can associate with each heme unit in hemoglobin?
Oxygen binds to the heme in both hemoglobin and myoglobin. Each heme unit in hemoglobin carries one oxygen molecule, and it occupies the sixth bond. So, hemoglobin inserts a heme into one of its four units, meaning hemoglobin carries 4 oxygen molecules.
- How does fetal hemoglobin differ from adult hemoglobin? Describe the developmental production pattern for human hemoglobins.
- How does fetal hemoglobin differ from adult hemoglobin? Describe the developmental production pattern for human hemoglobins.
Fetal hemoglobin is the first hemoglobin formed during embryogenesis. (5?) are replaced by alpha subunits in the first six months. Also, during these first six months of development, the epsilon subunits are replaced by the gamma subunits. The gamma subunits are replaced by beta subunits in later embryonic development and just after birth!
- What is the Bohr Effect? What is meant by the “R” and “T” forms of Hb? Relate these forms to the oxygen dissociation curves.
- What is the Bohr Effect? What is meant by the “R” and “T” forms of Hb? Relate these forms to the oxygen dissociation curves.
The Bohr effect is a physiological phenomenon first described in 1904 by the Danish physiologist Christian Bohr, stating that hemoglobin’s oxygen binding affinity is inversely related both to acidity and to the concentration of carbon dioxide.
Picture: R form at top - High oxygen affinity (in lungs)
T form - bottom - Low oxygen affinity (in muscles)
- How do reversible inhibitors alter kinetic curves?
- How do reversible inhibitors alter kinetic curves?
Reversible inhibition:
Competitive Inhibition - Change in Km
Non competitive inhibition: Change in Vmax
- What are the key features and parameters of the Michaelis-Menten kinetic theory of enzyme action (as shown in the curve)?
- What are the key features and parameters of the Michaelis-Menten kinetic theory of enzyme action (as shown in the curve)?
If Km = [S], then v = 1/2Vmax
Km is a measure of the affinity of an enzyme for its substrate: smaller the value of Km, greater the affinity of the enzyme for substrate.
M / M Equation
