Chapter 3 - Biochemistry

chichi's version from 2017-02-25 21:24

Section 1

Question Answer
The chirality of an amino acid results from the fact that its alpha-carbonis bounded to four different chemical groups
Two amino acids of the standard 20 contain sulfur atomsmethionine and cysteine
all of the amino acids that are foud in proteins, except for proline contain anamino group
How cysteine is formed from cysteines?Oxidation of cysteine molecules to create disulfide bonds
Amino acids are ampholytes because they can function as either _______acid or base
The formation of peptide bond between two amino acids is an example of a condensation reaction: True or False?True
The peptide alanylglutamylglycylalanylleucine has five peptide bonds: True or False?False. It has 4 peptide bonds 5 amino acids
At the isoelectric pH of a tetrapeptide, the total net charge is zero: True or False?True

Section 2

Question Answer
Proteins with different functions usually differ significantly in their amino acid composition: True or False?True
What is the prosthetic group of a conjugated protein?A part of the protein that is NOT composed of amino acids
Prostheitc groups in the class of proteins known as glycoproteins are composed of carbohydrates
Only one of the common amino acids has no free alpha-amino group. Name this amino acidL-Proline has no free alpha-amino group, but rather has an imino group
Briefly describe the five major grouping of amino acidsNonpolar aliphatic - Alanine; Polar - Serine; Aromatic - Tyrosine; Positive Charged - Lysine; Negative Charged - Glutamic Acid
Why do amino acids, when dissolved in water become zwitterions?Near ph 7.0, the carboxylic acid group (-COOH) will dissociate to acetate ion and H+. The amino group will attract a proton to become a positively charged NH3+ group
What is the pI, and how it determined amino acids that have non ionizable R groups?The pI is the isoelectric pH. At this pH, the molecule has no net charge. With nonionizable R groups, pI is the arithmetric mean of molecules's two pKa values.
What is the uniquely important acid-base characteristic of the histidine R group?Only, the imidazole ring of the histidine R groups has a pKa (6.0) near physiological pH, sugessting that histidine may provide buffering power in intracelluar and intercellular fluids.

Section 3

Question Answer
Define primary structure of a proteinThe primary structure of a protein is its unique sequence of aminoacids and any disulfide bridges present in the native structure, that is, its covalent bond structure
Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a gel filtration column?The gel filtration column matrix contains pores of selected sizes. Since large molecules can not enter into the pores of the matrix and they will migrate faster through the column. Smaller molecules will enter into the pores and will elute from the column after the large molecules
An octapeptide composed of four repeating glycylalanyl units has:one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue
At the isoelectric pH of a tetrapeptide:the total net charge is zero
Which of the following is correct with respect to the amino acid composition of proteins?Proteins with different functions usually differ significantly in their amino acid composition
The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino aids in a protein of known molecular weight. Why?The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms.
In a conjugated protein, a prosthetic group is:a part of the protein that is not composed of amino acids
Prosthetic groups in the class of proteins known a glycoproteins are composed of:carbohydrates
Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns?secondary structure
Which of the following describes the overall three-dimensional folding of a polypeptide?Quarternary structure
For the study of a protein in detail, an effort is usually made to first:purify the protein
By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:separate proteins exclusively on the basis of molecular weight
To determine the isoelectric point of a protein, first establish that a gel:exhibits a stable pH gradient when ampholytes becomes distributed in an electric field
The first step in 2D gel electrophoresis generates a series of proteins bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step:proteins with similar isoelectric points become further separated according to their molecular weights
The term specific activity differs from the term activity in that specific activity:is the activity (enzyme units) in a milligram of protein
The functional differences, as well as differences in 3D structures, between two different enzymes from E. coli result directly from their different:amino acid sequences

Section 4

Question Answer
One method used to prevent disulfide bond interference with protein sequencing procedures is:reducing disulfide bridges and preventing their reformation by further modifying the -SH group
A nonpeptide was determined to have the following amino acid composition: (Lys)2, (Gly)2, (Phe)2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4- dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2-4-dinitrophenylhistidine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys)2, Phe, and Gly. The native sequence was determined to be:His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly
Even when a gen is available and its sequence of nucleotides is known, chemical studies of the protein are still required to determine:the location of disulfide bonds
The term "proteome" has been used to describe:the complement of proteins encoded by an organism's DNA
A major advance in the application of mass spectrometry to macromocleules came with the development of techniques to overcome which of the following problems?Mass spectrometric analysis involved molecules in the gas phase.
The term "residue" is applied to amino acids in a polypeptide because they lost a _________ when they formed a peptide bond.water
The anti-oxidant tripeptide___________functions by reducing potentially dangerous oxidizing agents; in the process two tripeptides are oxidized, forming a new disulfide bondglutathione
Histamine is formed from histidine by a ________ reactiondecarboxylatoin
__________ is a neurotransmitter formed from tyrosine by hydroxylation and decarboxylation reactionsdopamine
Proline differs from the other 19 amino acids in proteins in that it has a __________ amino groupsecondary
The two amino acids with amide-containing side chains are asparagine and____________glutamine
The two amino acids containing sulfur are _________ and -methionine.cysteine

Section 5

Question Answer
Which of the following aminog acids has a charged polar side chain at pH7?Glu
Which of the following amino acids has a sulfur atom in its side chain?Met
Which of the following amino acids has an uncharged polar side chain at pH7?Thr

Section 6

Question Answer
One of the reasons primary structure is important for a protein is that this determines the ______the molecule adopts in aqueous solution3D shape
If the gene for a protein has been clones, it may be possible to obtain large quantites of the protein by ________ in bacteria.high level expression
To help prevent denaturation of proteins in solution, take steps to avoid _________ and adsorption to surfaces.foaming
Molecules that contain a ___________ are capable of absorbing lightchromophore
If antiibodies to the protein being assayed are available, an _____________ can be developed.enzyme-linked immunosorbent assay
_________ chromatography is a method of fractionating a protein mimxutre according to the different polarities of the proteinshydrophobic
In order for DEAE to act as an anion exchanger, it must have a ____________.postive charge
In ________ chromatography, a protein mixture must be applied to the column at a low pH so that the proteins will have a net positive charge and bind to the columncation exchange
In SDS-PAGE electrophoresis, disulfide-linked protein subunits are separated by first reacting them with_______.2-mercapteoethanol
Either dansyl chloride or Edman's reagent can be used to identify the________ of a proteinnegative charge

Section 7

Question Answer
It takes a minimum of about _____ amino acids residues for a polypeptide to fold into a stable structure.40
The different polypeptide chains in a protein are known as _______.subunits
The two amino acids that absorb the most ligt at 280 nm are ______ and Trp.Tyrosine
The method of __________ separates proteins using a immobilized pH gradient.Isoelectric
In gel filtration chromatography, very large proteins are the first to be eluted from the column because they are ________ from the gel pores.exclueded
If a mixture of lysine and asapartic acid is applied to a cation exchange column at a low pH, the first amino acid to elute would be _____.Aspartic acid
If a mixture of lysine and aspartic acid is applied to an anion exchange column at high pH, the first amino acid to elute would be Lys.Lysine
When a large and a small protein are subjected to SDS-PAGE electrophoresis, the protein with the highest mobility would be the ________ one.small
Repeated cycles of the technique known as _______ can reveal the complete sequence of a polypeptide containing fewer than about 100 residuesEdman Degradation

Section 8

Question Answer
A fast and common method for determining the concentration of protein in aqueous solution is:measuring light absorption at 280 nm.
The "salting in" of proteins can be explained by:salt counter-ions reducing electrostatic attractionos between protein molecules
The field of proteomics involves:cataloging vital information on all the expressed proteins of a particular cell.
Enzymes that hydrolyze the internal peptide bonds (not the peptide bonds of the terminal amino acids) of a protein are:endopeptidases
The positive charge on proteins in electrospary ionziation mass spectrometry is the result of:protonated Arg and Lys residues
In two homologous proteins, which residue is most likely to replace a Gly residue as a conservative substitution?Asp
A frist step in purifying a protein that was intially associated with fatty substances would be:hydrophobic chromatography