Exam 3 Long Version Flashcards
Enzyme
the biological chemical reaction catalyst. In the context of this chapter, an enzyme is an example of a bioactive protein
Insulin
A major metabolic hormone that is secreted in response to feed consumption and elevated blood glucose. In the context of this chapter, insulin is an example of a hormone whose structure is a protein
Amino acid
the fundamental “building block” of protein structure. There are 20 common amino acids in feeds and foods, and additional examples in animal tissues. Each amino acid contains an amino group on one side of the molecule and a carboxyl group on the other. Of the 20 different amino acids, there are 20 different “side chains” which are structures bonded to the same centralized carbon atom as the amine and carboxyl groups
Side chain
the structure on an amino acid that distinguishes it from the other 19 amino acids
Peptide
a protein that consists of less than 10 amino acids
Peptide bond
the amide bond that bonds amino acid to the next in a protein. Recall that the peptide bond occurs as a reaction between a carboxyl group and an amine group
Hydrolysis
in the context of this chapter, hydrolysis refers to the breaking of a peptide bond (amide bond) such that a water molecule is introduced into the reaction
Primary structure of a protein
the sequence of amino acids in the protein. Do not confuse sequence with composition.
Sequence is the order in which the amino acids occur from one end of the protein to the other.
Secondary structure of a protein
this refers to the changes in conformation or three dimensional structure that the protein begins to form as the primary structure grows.
Examples of secondary structure include helix and pleated sheets. These difference are determined by the primary structure because it’s the side chains of the amino acids that interact to form different three dimensional configurations
Tertiary structure of a protein
this refers to the final three dimensional structure of the protein after it has been synthesized. In order for tertiary structure to occur and be maintained, amino acid side chains interact with one another in specific locations through different types of bonding: hydrogen bonds, electrostatic interactions between polar residues, and by covalent bonds between Cys residues that form disulfide bonds.
Quaternary structure of a protein
this type of structure refers to two or more complete proteins combining to form a larger protein in which the individual proteins represent subunits of the larger, complete protein. Not all complete and functional proteins have quaternary structure. An example of a protein with quaternary structure is hemoglobin.
Glycine
An amino acid with a hydrogen atom as its side chain
Non-polar side chains
These are side chains of amino acids in which there is no polarity or charge.
Amino acids with non-polar side chains include: (8)
- Alanine (Ala)
- Valine (Val)
- Leucine (Leu)
- isoleucine (Ile)
- Proline (Pro)
- Tryptophan (Trp)
- Phenylalanine (Phe)
- Methionine (Met)
Imino group
Basically, an amino acid molecule contains an amine group. There is an “amino” acid in which the amine group is bonded to the central carbon of the amino acid, as well as to a carbon atom in the side chain such there is no true amino group. Such a nitrogen containing group is a “imino” group, and the amino acid identified with this type of structure is proline (Pro).
Polar side chains
these are amino acid side chains that contain polar groups, either positive or negative polarities (or charges).
Amino acids with polar side chains include: (4)
three amino acids contain hydroxyl groups:
- Serine (ser)
- Threonine (thr)
- Tyrosine (tyr)
and one amino acid contains a thiol group
- Cystein (cys)
Polar acid side chains (2)
- Glutamic acid (glu)
- Aspartic acid (asp)
Polar basic side chains (5)
three amino acids have amino groups on their side chains
- Glutamine (gln)
- Aspargine (asn)
- Lysine (lys)
one has an imino group on its side chain
- Histidine (his)
and one has a combination of amino and imino groups on its side chain
- Arginine (arg)
genetic code
the code for all proteins that is determined by the sequence of nucleic acids in the animal’s DNA
Transcribe
to copy from one form to another. In the context of this chapter, transcribing or transcription refers to reading the genetic code of the DNA and re-writing it chemically in a form that can then be directly used for making the protein designated by the genetic code
Nucleotide sequence
the sequence of the four nucleotides in DNA: adenine, guanine, thymine and guanine
Messenger RNA
the chemical copy of the genetic code of a small section of the DNA. When the genetic code section is transcribed, the result is the messenger RNA (mRNA). The “messege” is therefore written chemically in a form that can move to a location in the cell where a protein can be synthesized; this form is mRNA
Ribosome
a organelle in the cell outside of the nucleus where proteins are synthesized in a manner consistent with the genetic code as chemically written as the mRNA
Translation
the process in which the message of the genetic code that occurs (was transcribed) as mRNA is converted to a protein. For this process, an amino acid that occurs in conjunction with a sequence of three nucleotides will be used to build the new protein. In this way, the genetic code is translated into amino acid sequence specific for a give protein as indicated by the genetic code
Codon
A sequence of three nucleotides in the mRNA. For every amino acid there will be a specific sequence of three nucleotides. Therefore, the order that the nucleotides occur will determine the order of the amino acids that are added to the growing protein. In this way, the cell takes the genetic code, transcibes it into large groups of codons that ultimately determine which amino acids which will be used and in what order (sequence).
Post-translation modification
any changes to the structure of a protein after the initial translation of the gentic code to amino acid sequence has occurred. This is common for most proteins and involves number elaborate reaction steps
Sickle cell anemia
a genetic disease in which the primary structure of the protein subunits (quaternary structure) of hemoglovin is altered. In this dcondition, a glutamic acid (carboxylic acid side chain) is replaced with a valine (non-polar side chain). The resulting tertiary and quaternary structures cause the proteins to clump and take on a sickle shape. This also reduce the ability of the hemoglobin to bind oxygen; hence the anemia that also characterizes the condition.
Bioactive Molecule
any molecule in the animal’s cell or circulation that causes or induces a biochemical reaction. The best example of a bioactive molecule is an enzyme. Other examples include hormones, hemoglobin, myoglobin, and contractile proteins (muscle).
Essential Amino Acids
Any amino acid that cannot be made at all or in sufficient quantities to meet the requirements of the animal
- Arg- Arganine
- His- Histadine
- Ile- Isoleucine
- Leu- Leucine
- Lys- Lysine
- Met- Methanomine
- Phe- Phenoalanine
- Thr- Threonine
- Trp- Tryptophan
- Val- Valine
Non-essential amino acid
Amino acids that can be synthesized by the animal and thus do not need to be in the diet
Indispensable Amino acid
these are the same amino acids listed for essential amino acids. In non-ruminant animals, the essential and indispensabe amino acids are the same. In a ruminant, ruminal microbes convert dietary proteins to microbial proteins, which contain the essential amino acids, and do so regardless of the dietary amino acid composition. Thus, ruminant animals do not need to consume the essential amino acids; however, the essential amino acids are not made by the animal itself. Therefore, they remain indespensable to the animal.
enzymes
Specialized proteins of the cell that serve as the true reaction catalyst. Virtually all reactions have a specific enzymes. Enymes are at the root of metabolism and often it is an enzyme thatis the cause or result of disease
activation energy
the reaction energy required to initiate a biochemical reaction to the point that conversion to product(s) begins
transition state
the progression through the biochemical reaction where product formation occurs
substrates
the materials that are involved in the initial part of the biochemical reaction. Substrates are the same as reactants of a chemical reaction
Products
the end result of the biochemical reaction. the materials that occur from the reaction; materials could represent a single product of synthesis or multiple products of a degradation reaction, for example, hydrolysis
enzyme-substrate complex
often abbreviated as the ES complex, it represents the initial substance that develops when a substrate and the enzyme combine at the first part of the biochemical reaction
active site
the part of the enzyme’s three dimensional structure where the actual biochemical reaction takes place. The active site is where the substrate initially interacts with the enzyme to form the ES complex
Lock and Key Model
the theoretical mechanism of an enzyme and substrate interaction in which the substrate “fits” into the active site of the of the enzyme specifically based on the three dimensional structures of the substrate and the active site
Induced fit model
the theoretical mechanism of an enzyme and substrate interaction in which the first substrate that encounters enzyme causes a change in the enzyme’s three dimensional conformation so that subsequent interaction with more substrate occurs rapidly
Enzyme Specificity
different enzymes are synthesized to catalzye specific reactions. Usually, two different types of enzymes will not catalyze the same reaction.
glycosidic bond
in the context of this chapter, a glycosidic bond is an ether bond connecting two glucose molecules. There are two types of glycosidic bonds, alpha and beta
denatured protein
a protein that has lost its tertiary structure, mainly through disruption of hydrogen bonds and altered electrostatic interactions
Hydrolase
a class of enzyme that catalyzes a hydrolysis reaction
Isomerase
a class of enzyme that catalyzes a change in the structure of a molecule without changing its fomula
Ligase
a class of enzyme that catalyzes formation of obnds between carbon or other atoms
Lyase
a class of enzyme that catalyzes breaking of bonds between carbon atoms, as well as other atoms such as S and N
Oxidoreductase
a class of enzyme that catalyzes reactions involving oxidation and reduction
dehydrogenase
a class of enzyme that catalyzes oxidation and reduction reactions; this is an example of an oxidoreductase. However, there are numerous reactions involving different specific dehydrogenase enzymes
Transferase
a class of enzyme that catalyzes the transfer of certain functional groups from one molecule to another
First order catalysis
a type of catalysis in which the rate of the reaction is directly proportional to the concentration of substrate when the concentration of enzyme is held constant
allosteric enzyme catalysis
a type of enzyme catalysis in which the first substrates bind slowly and then the subsequent substrate bind rapidly and in proportion to the concentration of substrate
Sigmoidal Plot
a graph in which the curve is “S” shaped
Hyperbola
a graph in which the curve is a straight line through the origin
Competitive inhibition
inhibition of an enzyme catalyzed reaction in which the inhibitor material has a shape similar to the real substrate and inhibits by binding to the active site. With half and half substrate and competitive inhibitor, the two will compete for binding to the active site of the enzyme and result in about half the rate of product formation comparaed to the reaction with no inhibitor
Vmax
abbreviation for the maximum velocity of the enzyme catalyzed reaction. As the concentration of substrate increases, the reaction rate increases until the concentration of substrate has saturated all of the enzyme active sites, at which point, the reaction velocity slows down to a slope of the line of essentially zero
Km
abbreviation for a term called the “Michaeles Constant”. A Km is a value representing the concentration of substrate that supports a reaction velocity of one half the maximum velocity for that enzyme (Km= concentration for 1/2 Vmax)
Non-competitive inhibition
reaction inhibition in which the inhibitor binds to a location on the enzyme that is different from the substrate binding site (active site). The ability to bind substrate is not reduced, but the reaction velocity is decreased (Km is the same, but the Vmax is decreased)
Allosteric regulation
regulation of enzymes that have multiple binding sites for substrates and for regulatory substances
Positive effector
a regulatory substance that affects an allosteric enzyme by increasing reaction velocity
Negative effector
a regulatory substance that affects an allosteric enzyme by decreasing reaction velocity
Feedback Regulation
inhibition of an enzyme by a substance that is synthesized by a sequence of enzyme catalyzed reactions and in which the enzyme inhibited is the first one in the sequence. Usually, the substance synthesized is utilized so it does not accumulate; however, when need for the substance is decreased, it will accumulate. Thus, inhibition of the first enzyme in the sequence will slow down production of substance until more is needed by the cell.
Covalent Modification
regulation of an enzyme’s activity by bonding of a molecule to the enzyme via a covalent bond. The best example is the bonding of a phosphate to an enzyme through a phosphate ester created from the reaction of the phosphate and an alcohol on a serine of the enzyme protein. Some enzymes are more active and some are less active when this happens.
Phosphorylation
enzyme catalyzed addition of a phosphate molecule to another molecule, for example, addition of a phosphate to serine of an enzyme