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228 Cards in this Set

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a small enzyme that catalyzes protein digestion in the small intestine.
Carboxypeptidase A
(Fig. 29.5, pg 851)
Large binding proteins
Immunoglobulin G
(Fig. 29.6-29.7, pg 852-3)
Are immunoglobulins antibodies?
Yes
What binds antigens as a defense against disease?
Immunoglobulins or antibodies
Each of these has a distinct amino acid sequence in its antigen binding sites and therefore has sites of unique size and shape.
Immunoglobulin G
Proteins that traverse partly or completely a membrane bilayer
Integral membrane proteins
What keeps the integral membrane protein stable inside the nonpolar environment of the lipid bilayer?
Their quarternary structures in which the outer surface of the protein is largely nonpolar and interacts with the lipid bilayer
Do the polar groups of the integral proteins turn inward or outward?
inward
How are protein conformations stabilized in their native states?
by secondary and tertiary structures and through the aggregation of subunits in quaternary structures.
The process by which any physical or chemical agent destroys the stabilizing structures, changing the conformation of the protein.
Denaturation
The loss of secondary, tertiary, and quarternary structures of a protein by a chemical or physical agent that leaves the primary structure intact.
Denaturation
When a protein is denatured, which three types of bonds are broken resulting in a change of structure and function of the protein?
hydrogen, ionic, and disulfide bonds.
Which agents destroy the protein structure?
Heat, detergents, acids, bases, reducting agents, heavy metals, and alcohol.
Hydrolysis breaks down what type of bonds?
amide bonds
Heat as a denaturing agent breaks what type of bonds?
hydrogen bonds
Detergents as denaturing agents affect what regions?
hydrophobic regions
Acids and bases as denaturing agents affect what regions?
salt bridges and hydrogen bonds
Why do reducing agents affect disulfide bonds?
b/c disulfide bonds are formed by oxidation thus reduction destroys them.
Heavy metals such as lead and mercury as denaturing agents affect what bonds?
disulfide bonds
Alchol as a denaturing agent affects what regions?
hydration layers
What must happen in order for dietary protein to provide nutrition for the body?
dietary protein must have its primary structure destroyed before it can provide nutrition for the body.
What reactions are involved in digestion?
denaturation and hydrolysis
How are proteins denatured in digestion?
stomach acids destroy the secondary, tertiary, and quarternary structures.
How is hydrolysis involved in digestion?
Hydrolysis breaks the peptide linkages causing proteins to be converted into free amino acids which are then absorbed through the intestinal membranes into the blood stream.
In globular proteins, what causes the unfolding of the polypeptide chains?
Heat
what takes place after heat causes the unfolding of polypeptide chains?
subsequent intermolecular protein-protein interactions, precipitation or coagulation takes place.
What happens when an egg is boiled?
The egg solidifies partially b/c egg proteins, including albumin (egg whites) are denatured by heat.
How does alcohol denature proteins?
by coagulating them
Why is alcohol used in sterilizing the skin before injections?
ethanol penetrates bacteria and kills them by coagulating their proteins.
Is Denaturation a reversible or irreversible process?
It can be reversible or irreversible
What is an example of an irreversible denaturation process?
A hard boiled egg cannot be unboiled.
How is the process of denaturation reversed?
chaperons help a partially heat-denatured protein to regain its secondary, tertiary, and quarternary structures thereby regaining their biologically active conformation.
What four tests are used to detect and differentiate between amino acids, peptides and proteins?
Xanthproteic test, biuret test, bradford test, and ninhydrin test.
__________ tests for proteins containing aromatic amino acids.
Xanthproteic test
___________ test specific for polypepetides and not amino acides or peptides.
Biuret test
test used to detect proteins.
Bradford test
test used to detect amino acids
Ninhydrin test
Proteins that catalyze biochemical reactions. i.e. they increase the rate of reactions without themselves undergoing any change.
Enzymes
Are all biological catalysts proteins?
No
These ribonucleic acids called _________ also catalyze some biochemical reactions.
Ribozymes
The limitation of an enzyme to catalyze specific reactions with specific substrates is known as:
substrate specific
an enzyme that cleaves the peptide bonds of protein molecules- but only those on the carboxyl side of lysine and arginine residues.
Tyrpsin
specifically catalyze the hydrolysis on only the last amino acid on a protein chain- the one at the C-terminal end.
Carboxypeptidases
the nonprotein part of an enzyme necessary for its catalytic function. These may be metallic ions (Zn2+, Mg2+) or organic compounds
Cofactor
organic cofactors or nonprotein organic molecules that act as a cofactor (B vitamins, the heme group)
Coenzymes
the protein portion of the enzyme. It cannot catalyze a reaction without its cofactor, nor can the cofactor function without it.
apoenzyme
an enzyme that consists of both the protein and nonprotein parts.
holoenzyme
the compound on which the enzyme works, and whose reaction it speeds up. It usually binds to the enzyme surface while it undergoes the reaction.
substrate
the specific portion of the enzyme where the substrate binds during a reaction
active site
If the enzyme has coenzymes, where are they located?
at the active site.
Any process that initiates or increases the action of an enzyme. It can be the simple addition of a cofactor to an apoenzyme or the cleavage of a polypeptide chain of a proenzyme.
activation
an inactive protein that becomes an active enzyme after undergoing a chemical change.
proenzyme
any process that makes an active enzyme less active or inactive. This process is achieved by inhibitors.
Inhibition
inhibitors that bind to the active site of the enzyme surface, therby preventing the binding of substrate. Its ability to bind to the active site is due to the fact that it chemically resembles the structure of the natural substrate.
competitive inhibitors
these inhibitors bind to some other portion of the enzyme surface. They may sufficiently alter the tertiary structure of the enzyme so that its catalytic effectiveness is reduced.
noncompetitive inhibitors
Both ________________ and ____________ inhibition are reversible, but some compounds alter the structure of the enzyme permanently and thus make it irreversibly inactive.
competitive and noncompetitive
Pepsin, trypsin, and chymotrpsin are all enzymes located where?
The digestive tract
In the IUB system, enzymes are classified into six major groups according to what?
the type of reaction they catalyze
What are the 6 major classes of enzymes?
oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases or synthesases.
enzymes that catalyze oxidations and reductions
oxidorecuctases
enzymes that catalyze the trasfer of a group of atoms from one molecule to another.
transferases
enzymes that catalyze the hydrolysis of esters, carbohydrates, and protiens.
hydrolases
enzymes that catalyze the addition of two groups to a double bond (addition) or the removal of two groups from adjacent atoms to create a double bond (elimination).
Lyases
enzymes that catalyze isomerization reactions (i.e. interconversion of steroisomers and structural isomers) cis to trans.
Isomerases
enzymes that catalyze the joining or linkage of two molecules.
Ligases or synthesases
Enzyme activity is a measure of what? i.e. what is the effect of concentration, temp, and pH on enzyme activity?
how much reaction rates are increased
If we keep the concentration of substrate constant and increase the conentration of enzyme, the rate of reation increases _________.
linearly
If wee keep the concentration of enzyme constant and increase the concentration of substrate we get a __________ _____.
saturation point
What happens after a saturation point is reached?
substrate molecule are bound to all available active sites of the enzymes.
True or False: increasing the substrate concentration can no longer increase the rate b/c the excess substrate cannot find any active sites on which to bind.
True
What are 3 factors that influence ENZYME activity?
enzyme and substrate concentration, temperature, and pH.
In ____________ reactions, the rate usually increases as the temp. increases.
uncatalyzed reactions
At a _______ _________, an increase in temp first causes an increase in rate.
low temp
temperature at which the enzyme has maximum activity.
optimum temperature
what happens after the optimum temperature has been reached?
enzyme shape and conformation are altered.
What happens as a result of the changing shape and conformation of an overheated enzyme?
the substrate may not properly fit into the changed enzyme surface, so the rate of reaction decreases.
most enzyme from bacteria and higher organisms have an optimal temperature around ______.
37 degrees celsius
the inactivation of enzymes at low temps is used in what?
the preservation of food by refrigeration
each enzyme operates best at its_________pH.
optimum pH.
within a narrow pH range, changes in enzyme activity are _____.
reversible
What happens at extreme pH values (either acidic or basic)?
enzymes are dentarued irreversibly, and enzyme activity cannot be restored by changing back to the optimum pH.
After a small temperature increase above the optimum, how could the decreased rate again be increased?
by lowering the temperature.
True or False: over a narrow temperature range, changes in enzyme conformation are reversible?
True
How do catalysts speed up reactions?
by combining with the substrate to form some kind of intermediate compounds.
In an enzyme catalyzed reaction, the intermediate compound is called:
enzyme substrate complex
How do enzymes really spped up the reaction?
enzymes catalyze reactions by lowering the activation energy between the reactants (substrates) and the products. In other words, they lower the amount of energy requeired.
an enzyme regulation process in which formation of a product inhibits an earlier reaction in the sequence, especially in a complex system in which enzymes work cooperatively.
Feedback control
In this regulation process, the last product in the chain, D, may inhibit the activity of enzyme E1 by competitive, noncompetitive, or some other type of inhibition).
Feedback control
In this enzyme regulation process, when the concentration of D is low, all three reactions (A-B- C) proceed rapidly, and as the concentration of D increases, the action of E1 becomes inhibited and eventually stops, thus the accumulatin od D serves as a message that tells enzyme E1 to shut down b/c the cell has enough D for its present needs.
feedback control process
Enzymes manugactured by the body in inactive forms
proenzymes
Proenzymes are also called
zymogens
What must be removed from proenzymes in order to make them active?
A small part of their polypeptide chain.
What is an example of a zymogen?
trypsinogen (manufacutred from trypsin).
This is a mechanims involving regulation that takes place by means of an event that occurs at a site other than the active site but that eventurally affects tha active site.
Allosterism
An enzyme regulated by allosterism is call an ____________ enzyme.
allosteric
The substance that binds to the allosteric enzyme is called a?
regulator
the site to which the regulator attaches is called the ___________.
regulatory site
What does the binding of a regulator to a regulatory site do to the allosteric enzyme?
It modeifies the enzyme's ability to bind the substrate in the active site by changing the shape of the active site.
What regulatory mechanism usually involves a change in the primary strucutre by addition of a functional group covalently bound to the apoenzyme?
Protein modification
The activation or inhibition of enzymes by phosphorylation as in pyruvate kinase is an example of what kind of enzyme regulation?
protein modification
Is Pyruvate Kinase from the liver active or inactive when it is phosphorylated?
inactive
What happens when the activity of PK is not needed?
It is phosphorylated to PKP by a protein kinase using ATP as a substrate as well as a source of energy.
What happens when the system wants to turn on PK activity?
The phosphate group, PI, is removed by another enzyme, phosphatase, which renders PK active.
Name the two kinds of nucleic acids found in cells and where they are located.
DNA- located in the chromosomes in the nucleus and RNA- located in the cytoplasm
Both nucleic acids (DNA and RNA) are polymers made up of ?
nucleotides (monomers)
Nucleotides are composed of what three simpler units?
Carbohydrates, Bases and phosphates.
What are the two classes of bases?
Purines and pyrimidines
What two bases are purines?
Adinine and Guanine
What three bases are pyrimidines?
cystosine, Thymine, Uracil
What bases are found in both DNA and RNA?
AGC
What bases are found in DNA?
AGCT
What bases are found in RNA?
AGCU
Both DNA and RNA contain four bases: 2 ________ and 2 ________.
purines and pyrimidines
In RNA, the carbohydrate is:
D-Ribose
In DNA, the carbohydrate is:
D-2-deoxyribose (pg. 897)
The combination of a carbohydrate and a base is known as a :
nucleoside (see pg. 31.1 for names of nucleosides)
What kind of bond links the purine bases to C-1 of the monosaccharide through N-P of the 5-membered ring?
Beta-N-glycosidic bond
True or False: the pyrimidine bases are linked to C-1 of the monosaccharide through their N-1 by a beta-N-glycosidic bond.
True (see pf. 895 and 897, Fig 31.2)
Base + Carbohydrate + Phosphate group=
nucleotide
The phosphoric acid links to the nucleoside by a ____________ bond.
phosphoester
AMP, ADP, and ATP are examples of what?
nucleotides ( see figures 31.3 and 31.4)
A chain of nucleotides:
DNA, RNA
base + sugar=
nucleoside
base + sugar + phosphate=
nucleotide
The order or sequence of nucleotides provides what?
the primary structure
The primary structure of DNA is divided into what two parts?
The backbone and the bases
alternating phosphate and deoxyribose groups make up what part of DNA?
The backbone
Side-chain groups carrying all of the information necessary for protein synthesis make up what part of DNA?
The bases are the side-chain groups.
Each phosphate group is linked the the ______ carbon of one deoxyribose unit and simultaneously to the _____ carbon of the next deoxyribose unit.
3' carbon and 5' carbon
at which positions do each of the monosaccharide units form a phosphate ester?
3' and 5' positions
What are two ends of the backbone of DNA chains?
3' - OH and 5'- OH.
At which terminus does the sequence of nucleotides begin?
The 5' terminus
DNA is composed of two strands entwined around each other in what is called a ________________.
double helix
True or False: In the DNA double helix, the two polynucleotide chains run in the same direction.
FALSE- the two polynucleotide chains run in opposite directions.
The sugar-phosphate backbone is on the outside, exposed to eth aqueous environment. Is it hydrophilic or hydrophobic?
hydrophilic
The bases point inward- are they hydrophilic or hydrophobic?
hydrophobic
How is the double helix stabilized?
by the hydrophobic interactions btwn the bases.
A on one strand pairs with what on the opposite strand?
T
G on one strand pairs with what on the opposite strand?
C
The paired bases form what kind of bonds with each other?
hydrogen
how many hydrogen bonds link A-T
two
how many hydrogen bonds link G-C?
three
A-T and G-C are __________ bases.
complimentary
True or False: If the sequence of one strand is known, the sequence of the other strand can be inferred.
True
True or False: the cell is not able to chemically "read" one strand in order to synthesize its complementary partner.
False- the cell IS able to chemically read one strand in order to synthesize its complementary partner.
the study of the transformation, distribution, and utilization of energy by living organisms.
Biogenetics
The chemical reactions occurring inside cells are the major source of what?
Biological energy
the sum of all chemical reactions that occur within a living organism
metabolism
Metabolism is subdivided into what two contrasting categories?
anabolism and catabolism
the process by which simple substances are synthesized (build up) into complex substances.
anabolism
the process by which complex substances are broken down into simpler substances
catabolism
these reactions usually involve carbon reductions and consume cellular energy.
anabolism
these reactions involve carbon oxidation and produce energy for the cell
catabolism
The food we eat consists of many types of compounds, three of which are:
carbohydrates, lipids, and proteins
To convert carbohydrates, proteins, lipids, and other compounds to energy, the body uses a different pathway for each type of compound. All of these diverse pathways converge to what?
common catabolic pathway
The site for most of the catabolic redox reactions
mitochondria (Fig. 33.4 pf. 969)
In what form to the diverse catabolic pathways drop their products into the funnel of the common catabolic pathway?
C2 (acetyl CoA)
True or False: The spinning wheel of the citric acid cycle further builds up the entering molecules.
False- the citric acid cycle breaks these molecules down further.
In the citric acid cycle, the carbon atoms are released in the form of ________, and the hydrogen atoms and electrons are picked up by special compounds such as _______ and _________.
CO2, NAD+ and FAD
In the citric acid cycle, NAD+ and FAD are reduced to _________ and _______.
NADH and FADH2
After NAD+ and FAD have been reduced to NADH and FADH2, they cascade down into the stem of the funnel, where the electrons are transported inside the walls of the stem and the ______ ______ are expelled to the outside.
H+ ions
In their drive to get back on the inside of the cycle, the H+ inos form what energy carrier?
ATP
Once H+ are back inside, they combine with the oxygen that picked up the electrons and produce:
H2O
The common catabolic pathway is a series of _______ ________ through which foodstuffs are __________ to yield energy in the form of _______.
chemical reactions
oxidized
ATP
The common catabolic pathway consists of what two parts?
1. The citric acid cycle (krebs cycle)
2. Oxidative phosphorylation
The citric acid cycle is also known as what?
The Krebs cycle
What two parts make up the oxidative phosphorylation pathway?
1. electron transport chain
2. phosphorylation
What are the three categories of compounds of the common metabolic pathway?
1. agents for transfer of electrons in biological oxidation-reduction reactions.
2. agents for storage of energy and transfer of phosphate groups.
3. Agents for transfer of acetyl groups.
What two coenzymes are agents for transfer of electrons in biological oxidation-reduction reactions?
NAD+ and FAD
NAD+ and FAD are the ____ ____ and ______ transporting molecules.
H+ ion and electron
In NAD+, the operative part/reactive component of the coenzyme is the _________ ____ i.e, when NAD+ is reduced, this part gets reduced.
Nicotinamide ring
The reduced form of NAD+ is:
NADH
In FAD, the operative part is the _______ ______ portion.
flavin ring
the reduced form of FAD is:
FADH2 (see pg. 971)
What are the three agents for strage of energy and transfer of phosphate groups?
AMP (adenosine monophosphate)
ADP (adensoine diphosphate)
ATP (adenosine triphosphate)
What is the difference btwn AMP, ADP, and ATP?
the number of phosphate groups
In AMP, ADP, ATP, the first phosphate is attached to the ribose by what kind of bond?
phosphoric ester
In ADP, ATP, each phosphate is attached to the next by what kind of bond?
phosphoric anhydride bond
What kind of bond contains more chemical energy than a phosphoric ester linkage? Why?
a phosphoric anhydride bond b/c it has more oxygen.
In NAD+, the operative part/reactive component of the coenzyme is the _________ ____ i.e, when NAD+ is reduced, this part gets reduced.
Nicotinamide ring
The reduced form of NAD+ is:
NADH
Why, when ATP and ADP are hydrolyzed to yield phosphate ion, do they release more energy per phosphate group than does AMP?
b/c they are bonded together by phosphoric anhydride bonds, which contain more chemical energy than phosphoric ester linkages.
In FAD, the operative part is the _______ ______ portion.
flavin ring
the reduced form of FAD is:
FADH2 (see pg. 971)
What are the three agents for strage of energy and transfer of phosphate groups?
AMP (adenosine monophosphate)
ADP (adensoine diphosphate)
ATP (adenosine triphosphate)
What is the difference btwn AMP, ADP, and ATP?
the number of phosphate groups
In AMP, ADP, ATP, the first phosphate is attached to the ribose by what kind of bond?
phosphoric ester
In ADP, ATP, each phosphate is attached to the next by what kind of bond?
phosphoric anhydride bond
What kind of bond contains more chemical energy than a phosphoric ester linkage? Why?
a phosphoric anhydride bond b/c it has more oxygen.
Why, when ATP and ADP are hydrolyzed to yield phosphate ion, do they release more energy per phosphate group than does AMP?
b/c they are bonded together by phosphoric anhydride bonds, which contain more chemical energy than phosphoric ester linkages.
ATP is a very useful compound for?
storage and release
What is the agent for transfer of acetyl groups?
Acetyl CoA (CH3-C=O) transporting molecule
What is the active part of coenzyme A?
mercaptoethylamine
What are the 8 steps in the citric acid cycle?
1. C2 + C4 = C6 or Oxaloacetate + Acetyl CoA = Citrate
2. Isomerization
3. Oxidation + Decarboxylation
4 and 5. Decarboxylation + Formation of GTP
6. Oxidation
7. Hydrolysis
8. Oxidation
What happens in step 1 of the Krebs cycle?
C2 enters + C4 = C6
Oxaloacetate + Acetyl CoA = citrate
What happens in step 2 of the Krebs cycle?
Isomerization- the changing of a tertiary alcohol to a secondary alcohol.
What happens in step 3 of the Krebs cycle?
NAD+ oxidation and removal of CO2. NAD+ is an oxidizing reagent.
What happens in steps 4 and 5 of the Krebs cycle?
C5 becomes C4 by decarboxylation and formation of GTP
What happens in step 6 of the Krebs cycle?
Oxidation- where FAD is the oxidizing reagent that becomes FADH2
What happens in step 7 of the Krebs cycle?
Hydrolysis- water is inserted, breaking the double bond in fumarate.
What happens in step 8 of the Krebs cycle?
Oxidation and the cycle is completed resulting in the final product, oxaloacetate (C4).
One C2 (acetyl CoA) group enters the krebs cycle and ________ are given off.
2 CO2
How does the Krebs cycle produce energy?
1 step in teh cycle produces a high energy molecule of GTP, but most of the energy is produced in the other steps that convert NAD+ to NADH and FAD to FADH2. These reduced coenzymes carry the H+ and electrons that eventually will provide the energy for the synthesis of ATP
What does oxidative phosphorylation mean?
It means that something is being oxidized while something else is being phosphorylated, or a phosphate is being added.
What is the purpose of the Electron transport chain?
1. to synthesize ATP from ADP
2. to regenerate NAD+ and FAD
The food we eat serves what two main purposes?
1. It fulfills our energy needs
2. It provides the raw materials to build the compounds our bodies need.
What is the specific pathway by which energy is extracted from monosaccharides?
Glycolysis
Once monosaccharides are produced, what two things can they be used for?
1. to build new oligo- and polysaccharides
2. to provide energy
simple and complex lipids are hydrolyzed by ________ to _______ and ____ _____ or to ___________, which are absorbed through the intestine.
lipases to glycerol and fatty acids or to monoglycerides.
These two smaller molecules are used to build the complex molecules needed in membranes; they can be oxidized to provide energy; or they can be stored in fat cells
glycerol and fatty acids
Stored fat can later by hydrolyzed to __________ and ____ _____ whenever they are needed as fuel.
glycerol and fatty acids
The specific pathway by which energy is extracted from glycerol is?
glycolysis
The specific pathway used to obtain energy from fatty acids is called ?
beta-oxidation
Proteins are hydrolyzed by what in the stomach?
HCl and digestive enzymes
What digestive enzymes in the stomach and intestines hydrolyze proteins to produce amino acids?
pepsin and trypsin, chymotrpsin, and carboxypeptidases
The specific pathways of carbohydrate, lipids, and protein catabolism converge to the?
common catabolic pathway
an amino acid that can be converted into glucose through gluconeogenesis.
glucogenic amino acids
a metabolic pathway that generates glucose from noncarbohydrate carbon substrates.e.g. lactate, glycerol, and glucogenic amino acids.
gluconeogenesis (GNG)
examples of noncarbohydrate carbon substrates:
lactate, glycerol and glucogenic amino acids
The two main mechanisms humans and many other animals uses to keep blood glucose levels from dropping too low (hypoglycemia).
gluconeogenesis and glycogenolysis
the conversion of glycogen polymers to glucose monomers.
glycogenolysis
amino acids which are converted into ketone bodies
ketogenic amino acids
three water-soluble compounds that are produced as byproducts when fatty acids are broken down for energy in the liver and kidney.
ketone bodies
What are the three ketone bodies?
1. acetone
2. acetoacetic acid
3. beta-hydroxybutyric acid
see pg. 1016
These are used as a source of energy in the heart and brain when the body is low in carbohydrates
ketone bodies
the removal of an amino group from an amino acid and the amino group is converted to ammonia
deamination
The metabolic pathway that converts glucose into pyruvate
glycolysis
The free energy released in this process is used to form the high-energy compounds ATP and the coenzyme NADH
glycolysis