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BCHN 213 1-1 M 2020

Assessment 2 - SU9 + SU10

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Part 1 of 2 - 17.0 / 25.0 Points

Question 1 of 194.0 Points

Name 4 non-covalent interactions that are responsible for stabilizing the secondary structures of
proteins.

1. Hydrophobic interactions
2. Ionic interactions
3. Van de waal interactions
4. Hydrogen Bonds

Model Short Answer: hydrogen

bonds,
ionic bonds,
van der Waals interactions,
hydrophobic bonds.

Question 2 of 195.0 Points

What is the Ramachandran diagram, what does it indicate and for what can you use it?
The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino
acids) contained in a peptide. The torsional angles of each residue in a peptide define the geometry
of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the
two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the
residues and the peptide. Many of the angle combinations, and therefore the conformations of
residues, are not possible because of steric hindrance. By making a Ramachandran diagram protein
structural scientists can determine which torsional angles are permitted and can obtain insight into
the structure of peptides, and they can predict if the % of aa is more than 88 % in allowed region the
protein model is good for in silico studies and also It tells about allowed and dis allowed regions of
the aa that reflects the stability of protein structure.

Model Short Answer:

-The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues
(amino acids) contained in a peptide.
-By making a Ramachandran plot, protein structural scientists can determine which torsional
angles are permitted and can obtain insight into the structure of peptides
-Ramachandran Plot is a way to visualize dihedral angles ψ against φ of amino acid residues in
protein structure
Ramachandran plot provides an easy way to view the distribution of torsion angles of a protein
structure
It also provides an overview of allowed and disallowed regions of torsion angle values, serving
as an important factor in the assessment of the quality of protein three-dimensional structures.

A Ramachandran plot can be used in two somewhat different ways. One is to show in theory
which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a
protein

Question 3 of 198.0 Points

Define collagen in terms of structure and function and its formation

Collagen is a rigid, inextensible fibrous protein that is a principal constituent of connective tissue
in animals, including tendons, cartilage, bones, teeth, skin, and blood vessels. The high tensile
strength of collagen fibers in these structures makes possible the various animal activities such
as running and jumping that put severe stresses on joints and skeleton. Broken bones and tendon
and cartilage injuries to knees, elbows, and other joints involve tears or hyperextensions of the
collagen matrix in these tissues.The basic structural unit of collagen is tropocollagen, which has
a molecular weight of 285,000 and consists of three intertwined polypeptide chains, each about
1000 amino acids in length. Tropocollagen molecules are about 300 nm long and only about 1.4
nm in diameter. Several kinds of collagen have been identified. Type I collagen, which is the
most common, consists of two identical
peptide chains designated alpha1(I) and one different chain designated alpha 2(I).type I collagen
predominates in bones, tendons, and skin. Type II collagen, found in cartilage, and type III
collagen, found in blood vessels, consist of three identical polypeptide chains. Collagen is
secreted by various cells, but mainly by connective tissue cells.

Model Short Answer:

Defination
Collagen is a protein that consists of three chains of polypeptides and many units of
hydroxyproline, proline and glycine residues.

Structure
The collagen molecular structure is that of a helix of three chains of polypeptides that are bonded
together and linked by covalent bonds both within and between chains. The helix is made of two
alpha 1 chains and one alpha 2 chain linked together, and every third residue is usually the amino
acid glycine. There are several different types of collagen that have been identified in the human
body, and of these type 1 collagen is the most numerous and abundant.

Functions:
Collagen is the main fibrous protein found in the connective tissues of the human body. It is also
found in the dermis of the skin and in ligaments and tendons that are found at joints of the body.
It is a tough material that is strong and allows for a certain degree of elasticity before breaking; it
is this high tensile strength of collagen that makes it so well suited as a connective tissue fiber.

Formation:
Cells called fibroblasts, that are abundant in connective tissues, produce the collagen fibers.
Generally, collagen is formed by the lysine and proline parts joining together along with various
other components such as hydroxyl groups and sugar molecules. A limited quantity of collagen
can also be synthesized outside of the cell by enzymatic action on procollagen fibrous material.

Question 4 of 198.0 Points

Distinguish between alpha helix and beta sheet

1. alpha helix
a. CO & NH of the mainchain are hydrogen bonded together, allowing the mainchain to be burie
b. all alpha carbons are H bonded and in line with each other
c. R groups are on the outside & backbone on the inside
d. always right handed (clockwise
e. all H bonds are in the same direction as the chain
f. all carbonyl groups are in one direction and all N-H
2. Beta sheet
a. all C=H groups are not in the same direction
b, all N-H groups are not in the same direction
c. cannot exist as a single Beta strand; must be 2 or more
d. in proteins, 4-5 strands make up a beta sheet; it is possible to be made of more than 10
e. Arrow in pictures always points to the CO group
f. can be antiparallel, parallel, or mixed

Model Short Answer: Alpha helix

-Helix stabilized by H bonding between C=O and N-H (4 residues in chain)
-All H bonds in the same direction as the chain
-All carbonyl groups are in one direction and all N-H are in the opposite direction
-Helix from if phi = -60° and psi between -45° and -50°

Beta sheet
-All H bonds perpendicular in direction of chain
-All C=O groups are not in the same direction as with α-helix
-All N-H groups are not in the same direction as α-helix

Feedback:
Part 2 of 2 - Multiple choice 14.0 / 15.0 Points

Question 5 of 191.0 Points

Which of the following does not affect the stability of an α-helix?

 A. Electrostatic repulsion

 B. Bulkiness

 C. Interaction between R groups spaced three residues apart

 D. Occurrence of alanine and glycine residues

Answer Key:D

Feedback:The occurrence of Proline and Glycine residues affect the stability of an α-helix.

Question 6 of 191.0 Points

Which of the following is not true about secondary protein structure?

 A. The hydrophilic/hydrophobic character of amino acid residues is important to

secondary structure

 B. The ability of peptide bonds to form intramolecular hydrogen bonds is important to

secondary structure

 C. The alpha helix, beta pleated sheet and beta turns are examples of protein secondary
structure

 D. The steric influence of amino acid residues is important to secondary structure

Answer Key:A

Feedback:The hydrophilic/hydrophobic character of amino acid residues is important to protein tertiary

structure rather than to secondary structure. In secondary structure, it is the steric size of the residues
that is important and residues are positioned to minimize interactions between each other and the
peptide chain.

Question 7 of 191.0 Points

β-pleated sheets are the examples of

 A. Primary structure

 B. Secondary structure

 C. Tertiary structure

 D. Quaternary structure

Answer Key:B

Feedback: Secondary structure of proteins is of two forms α-helix and β-pleated structures.

Question 8 of 191.0 Points

A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the same chain is?

 A. Primary structure

 B. α-helix

 C. β-pleated sheets

 D. Tertiary structure

Answer Key:B

Feedback: A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the same
chain is α helix.

Question 9 of 191.0 Points

A structure that has hydrogen bonds between polypeptide chains arranged side by side is?

 A. Primary structure

 B. α-helix

 C. β-pleated sheets
  D. Tertiary structure

Answer Key:C

Feedback:A structure that has hydrogen bonds between polypeptide chains arranged side by side is β-
pleated sheets.

Question 10 of 191.0 Points

Which of the following are known as helix breakers?

 A. Proline and glycine

 B. Isoleucine and leucine

 C. Valine

 D. Threonine

Answer Key:A

Feedback:Proline and glycine are known as helix breakers as they disrupt the regularity of the alpha
helical backbone conformation.

Question 11 of 191.0 Points

NMR is an abbreviated form of Nuclear Magnetic Resonance

 A. NMR is an abbreviated form of Nuclear Magnetic Resonance

 B. The intramolecular magnetic field around an atom in a molecule changes the

resonance frequency giving structural information about the atom

 C. The intermolecular magnetic field around an atom in a molecule changes the

resonance frequency giving structural information about the atom

 D. It is a technique that exploits magnetic properties of atomic nuclei

Answer Key:C
Feedback:The intramolecular magnetic field around an atom in a molecule changes the resonance
frequency giving structural information about the atom.

Question 12 of 191.0 Points

Which of the statements is false about multiple sequence alignment?

 A. Both protein and nucleic acid secondary structures can be used

 B. More useful in RNA

 C. These alignments can be made more accurate by the inclusion of secondary structure
information

 D. A significant increase in accuracy

Answer Key:B

Feedback:Less useful in RNA. This is because base pairing is highly conserved than sequence.

Question 13 of 191.0 Points

Secondary structure is defined by

 A. Hydrogen bonding

 B. Vander Waals forces

 C. Covalent bonding

 D. Ionic bonding

Answer Key:A

Feedback:Hydrogen bonding is present between the amine hydrogen and carbonyl oxygen atoms in the
peptide backbone.

Question 14 of 191.0 Points

Which of the following is a false statement?

 A. α-Keratin is α helical
  B. Collagen is α helical

 C. Hemoglobin has a quaternary structure

 D. α-Keratin is β pleated structure

Answer Key:D

Feedback: Fibrous structural protein, α-Keratin is α helical.

Question 15 of 191.0 Points

Which of the following bonds are not involved in tertiary type of protein structure?

 A. Disulfide bond

 B. Hydrogen bonding

 C. Salt bridges

 D. Hydrophilic interactions

Answer Key:D

Feedback:Hydrophobic interactions are present in tertiary type of protein structure.

Question 16 of 191.0 Points

Which of the following does not possess a quaternary structure?

 A. Myoglobin

 B. Lactate dehydrogenase

 C. Immunoglobin M

 D. Creatine Phospho Kinase

Answer Key:A
Feedback:Myoglobin is a monomer, so it does not possess a quaternary structure.

Question 17 of 191.0 Points

Which of the following is abundantly found in collagen

 A. Glycine

 B. Serine

 C. Alanine

 D. Tryptophan

Answer Key:A

Feedback:Each three amino acids of the collagen peptide chain is a glycine. It is thus an abundant amino
acid that is important for collagen structure.

Question 18 of 191.0 Points

Which of the following is first determined as oligomer?

 A. Myoglobin

 B. Collagen

 C. Keratin

 D. Hemoglobin

Answer Key:D

Feedback: Hemoglobin contains four polypeptide chains and four heme prosthetic groups in which iron
atoms are present in Fe+2 state.

Question 19 of 191.0 Points

Which of the following is false about fibrous protein?

 A. It is in rod or wire like shape

 B. Keratin and collagen are the best examples

  C. Hemoglobin is the best example

 D. It provides structural support for cells and tissues

Answer Key:C

Feedback:Hemoglobin is the best example of globular protein.

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BCHN 213 1-1 M 2020
BCHN213 Tutorial
 Return to Assessment List
Part 1 of 4 - Multiple choice 8.0 / 10.0 Points
Chose one correct answer

Question 1 of 200.5 Points

The correct sequence for homologous recombination steps is: A. ligation B. branch migration and strand
exchange C. nicking D. EW or NS cleavage, resolution and re-ligation E. strand invasion

 A. D, C, B, A, E

 B. C, E, A, B, D

 C. B, C, E, A, D

 D. C, A, B, E, D

 E. C, B, E, D, A

Answer Key:B

Question 2 of 200.5 Points

What type of bonding is responsible for maintaining the shape of the tRNA molecule as shown in the
accompanying figure?

 A.
ionic bonding between phosphates

 B.
hydrogen bonding between base pairs

 C.
 peptide bonding between amino acids

 D.
van der Waals interactions between hydrogen atoms

Answer Key:B

Question 3 of 200.5 Points

The cell cycle is regulated by:

 A. Enzymes

 B. Cyclins

 C. Hormones

 D. Sugars

Answer Key:B

Question 4 of 200.5 Points

Regulatory proteins bind to _____.

 A. to the operator region of DNA

 B. the promoter region of DNA

 C. the -10 and -35 region of DNA

 D. RNA polymerase

Answer Key:A

Question 5 of 200.5 Points

Which reagent in a DNA sequencing procedure leads to production of DNA fragments that are used for
sequencing?
  A. DNA ligase

 B. Deoxynucleotide triphosphates

 C. DNA endonuclease

 D. Ribonucleotide triphosphates

 E. Dideoxynucleotide triphosphates

Answer Key:E

Question 6 of 200.5 Points

In a sample of double-stranded DNA containing 32% cytosine, the percentage of adenine would be:

 A. 0%

 B. 68%

 C. 18%

 D. 32%

Answer Key:C

Question 7 of 200.5 Points

If a weak acid is 25% deprotonated at pH 4, what would the pKa be?

 A. 3.52

 B. cannot determine from given information

 C. 4.48

 D. 4.60

 E. 3.40
Answer Key:C

Question 8 of 200.5 Points

To position a gene in an expression vector downstream from a promoter (i.e., perform directional
cloning), it is best to:

 A. use the largest plasmid available

 B. restrict each end of the DNA fragment (gene) with a different restriction endonuclease
and do likewise for the plasmid

 C. treat the gene with DNase I

 D. use a vector with two sites for the same restriction endonuclease

 E. restrict both the gene and the plasmid with one restriction endonuclease and then
screen all colonies for those that express the gene

Answer Key:B

Question 9 of 200.5 Points

The hyperchromic shift that occurs when dsDNA is ____ is due to a(n) ____ in absorption at ____ nm.

 A. methylated; increase; 220

 B. methylated; decrease; 260

 C. melted; decrease; 280

 D. denatured; decrease; 260

 E. denatured; increase; 260

Answer Key:E

Question 10 of 200.5 Points

Naturally occurring, self-replicating, extra-chromosomal DNA molecules found in bacteria that carry
genes specifying novel metabolic capacity advantageous to the bacterium are called:
  A. probes

 B. plasmids

 C. cruciform

 D. toroidal DNA

 E. all of the above

Answer Key:B

Question 11 of 200.5 Points

Replication in prokaryotes differs from replication in eukaryotes for which of the following reason

 A. Prokaryotic chromosomes have histones, whereas eukaryotic chromosomes do not

 B. The rate of elongation during DNA replication is slower in prokaryotes than in

eukaryotes

 C. Prokaryotic chromosomes have a single origin of replication, whereas eukaryotic

chromosomes have many

 D. Prokaryotes produce Okazaki fragments during DNA replication, but eukaryotes do

not

Answer Key:C

Question 12 of 200.5 Points

In DNA replication, the new strand is synthesized in a _______________ direction and the template
strand is read by the polymerase in a _______________ direction.

 A. 5' to 3'; 3' to 5'

 B. 3' to 5'; 3' to 5'

 C. 3' to 5'; 5' to 3'

 D. 5' to 3'; 5' to 3'

Answer Key:A

Question 13 of 200.5 Points

Thermodynamic parameters (entropy, enthalpy, free energy, and internal energy) are given for an
unknown enzyme. Explain which results would be expected for the breaking of hydrogen bonds and the
exposure of hydrophobic groups from the interior during the unfolding process of a protein

 A. The reaction is spontaneous

 B. Enthalpy change, ΔH, is negative

 C. Enthalpy change, ΔH, is positive

 D. Entropy change, ΔS, is positive

 E. Entropy change, ΔS, is zero

Answer Key:D

Question 14 of 200.5 Points

What would be the 9-residue primer used to amplify: 5'-ATCGACGTTACGCTACATAGCATAAGGCTT-3'

 A. 5'-TAGCTGCAA-3'

 B. 5'-AAGCCUUAU-3'

 C. 5'-TGCGATGTA-3'

 D. 5'-AAGCCTTAT-3'

 E. 5'-UAGCUGCAA-3'

Answer Key:D

Question 15 of 200.5 Points

Choose the correct site of inhibition associated with the protein synthesis inhibitor, tetracycline
  A. 30S

 B. 40S

 C. 50S

 D. 70S

 E. 80S

Answer Key:A

Question 16 of 200.5 Points

The natural conformation of DNA in solution as well as in vivo is:

 A. Antiparallele DNS α-heliks / An antiparallel DNA α-helix

 B. Parallele DNS dubbel heliks / A parallel DNA double helix

 C. B-DNA

 D. Z-DNA

 E. A-DNA

Answer Key:C

Question 17 of 200.5 Points

Which are the four most common elements in the human body?

 A. H, O, C, N

 B. O, Si, Ca, N

 C. H, O, Fe, C

 D. O, C, Fe, N

 E. H, Ca, O, Na
Answer Key:A

Question 18 of 200.5 Points

1.The therapeutic rationale for using AZT for treatment of AIDS is based on the fact that:

 A. AZT is incorporated into DNA, but forms a base-pair mismatch.

 B. AZT is incorporated into DNA, but inhibits the movement of DNA polymerase during
replication

 C. AZT is incorporated into DNA, but blocks the elongation of viral DNA by reverse
transcriptase

 D. AZT is incorporated into viral RNA, causing nonsense mutations in the viral genome.

 E. AZT is incorporated into viral RNA, yielding mutant proteins that cannot support
virus assembly.

Answer Key:C

Question 19 of 200.5 Points

Rank the following bonds in order of increasing bond strength a) b) c) d) e)

 A. electrostatic, hydrogen bond, van der Waals, covalent

 B. covalent, van der Waals, electrostatic, hydrogen bond

 C. van der Waals, electrostatic, hydrogen bond, covalent

 D. van der Waals, hydrogen bond, electrostatic, covalent

 E. electrostatic, van der Waals, hydrogen bond, covalent

Answer Key:C

Question 20 of 200.5 Points

Which of the following sequences of DNA would form a duplex with a complementary sequence to yield
the highest melting point?

 A. AGAGAGAGA

 B. ATATATATA

 C. GCGCGCGCG

 D. AGTAGTAGT

 E. AAAAAAAAA

Answer Key:C
Part 2 of 4 - True or false 8.0 / 10.0 Points

Question 1 of 101.0 Points

tRNA dra aminosure na ribosome vir gebruik in proteïensintese / tRNA carries amino acids to ribosomes
for use in protein synthesis

True

False

Answer Key:True

Question 2 of 101.0 Points

If one strand of a DNA molecule has the base sequence ATTGCAT, its complementary strand will have
the sequence TAACGTA

True

False

Answer Key:True

Question 3 of 101.0 Points

Tumor suppressor protein are normal genes that slow down cell division/repair DNA mistakes, /tell cells
when to die – suppresses the growth of cancer cells

True

False

Answer Key:True

Question 4 of 101.0 Points

Genetic transformation refers to uptake and expression of exogenous DNA

True
False

Answer Key:True

Question 5 of 101.0 Points

Chromosomes are tightly wound DNA/packaged form of RNA

True

False

Answer Key:False

Question 6 of 101.0 Points

Hydrogen bonds interactions are destroyed when DNA is denatured

True

False

Answer Key:True

Question 7 of 101.0 Points

H2A, H2B, H3, H4 histones that make up Histone core

True

False

Answer Key:True

Question 8 of 101.0 Points

During DNA replication sequence of nucleotide in one strand are –copied to– new daughter strand and
Each original strand serves as template for biosynthesis that yields two daughters DNA duplexes from
parental

True

False

Answer Key:True

Question 9 of 101.0 Points

A promoter is a DNA sequence at the 5' end of the transcription initiation site that acts as a binding site
for RNA polymerase during the initiation of transcription.

True

False

Answer Key:True

Question 10 of 101.0 Points

S phase or Interphase is the phase of the cell cycle where DNA replication process takes place

True

False

Answer Key:True
Part 3 of 4 - Define 5.0 / 10.0 Points

Question 1 of 101.0 Points

Define or differentiate between Mitosis and Cytokinesis

Both Mitosis and Cytokinesis are a part of cell division

Mitosis is a process by which the duplicated genome in a cell is separated into halves that are
identical in nature. Cytokinesis is the process where the cytoplasm of the cell divides to form two
‘daughter’ cells

in simple mitosis is the division of the nucleus, while cytokinesis is the division of the cytoplasm

Model Short Answer:

•Mitosis happens when Nuclear division, daughter nuclei are clone copies of the original
•Cytokines is the Cell division of the cytoplasm and its contents
Comment:Copied from Google

Question 2 of 101.0 Points

Define Gene therapy

is the process of replacing defective genes with healthy ones, adding new genes to help the body
fight or treat diseases.

Model Short Answer: Gene therapy is the transplantation/insertion of normal genes into cells in place of
missing or defective ones in order to correct genetic disorders.

Question 3 of 101.0 Points

Define Hyperchromic shift

is a change of spectral band position in the absorption, reflectance, transmittance, or emission spectrum
of a molecule to a shorter wavelength

Model Short Answer: An increase absorption of ultraviolet light by a solution of DNA as these molecules
are denatured (subjected to heat, alkaline conditions, etc)
Question 4 of 101.0 Points

Define genetic recombination

is the exchange of genetic material between different organisms which leads to production of offspring
with combinations of traits that differ from those found in either parent

Model Short Answer: genetic recombination is a natural process of rearranging genetic information to
form new associations
or
Exchange or incorporation of 1 DNA sequence with/ into another

Question 5 of 101.0 Points

Define genetic code

The genetic code is a set of rules defining how the four-letter code of DNA is translated into the 20-letter
code of amino acids, which are the building blocks of proteins. The genetic code is a set of three-letter
combinations of nucleotides called codons, each of which corresponds to a specific amino acid or stop
signal.

Model Short Answer: Genetic code is a set of rules by which information encoded in genetic material
(DNA or RNA sequences) is translated into proteins (amino acid sequences)

Question 6 of 101.0 Points

Define Gene

a gene is a specific sequence of nucleotides in DNA or RNA that is located usually on a chromosome and
that is the functional unit of inheritance

Model Short Answer: Genes are segment or section of DNA

Question 7 of 101.0 Points

Define Spliceosome

A dynamic complex of RNA and protein subunits that removes introns from precursor mRNA.

Model Short Answer: Spliceosome s the nuclear complex responsible for removing intron sequences and
ligation of exon sequences 5' 3' to generate a mRNA.
Question 8 of 101.0 Points

What is an operon?

An operon is a cluster of functionally-related genes that are controlled by a shared operator

Model Short Answer: An operon is two or more genes that are regulated by the same control region

Question 9 of 101.0 Points

What is a codon

is a triplet of adjacent nucleotides in the messenger RNA chain that codes for a specific amino acid in the
synthesis of a protein molecule

Model Short Answer: A series of 3 nucleotides in the mRNA

Question 10 of 101.0 Points

Define or differentiate Transposons and transitions

1. Transposons is a DNA sequence that can change its position within a genome, sometimes
creating or reversing mutations and altering the cells genetic identity and genome size.

2. Transitions is A mutation in which a purine/pyrimidine base pair is replaced with a base pair
in the same purine/pyrimidine relationship eg. GC with AT

Model Short Answer:

Transposons mobile/moveable segment of DNA while transition: 1 purine (or pyrimidine)

change for another
Part 4 of 4 - Differentiate 16.5 / 20.0 Points

Question 1 of 76.0 Points

Identify the molecule and label A-E and function of each

it is a tertiary structure of tRna

A. D loop
B. Anticodon loop
C. Variable loop
D. TC loop
E. Acceptor stem

Model Short Answer: Trna/transfer RNA/transport RNA

A= D loop - binds to 50S ribosomal subunit

B= Anticodon - Binds mRNA codon
C= variable loop
D= TC loop - Binds to charging enzyme
E= acceptor stem - accepts amino acid /amino acid binding

Question 2 of 72.0 Points

List 2 differences between DNA replication, transcription and translation

1. DNA replication
is the process of making new copies of DNA
occurs in the S phase of cell cycle

2. Transcription
is the process by which DNA is copied (transcribed) to RNA
Occurs in the G1 and G2 phases of cell cycle

3. Translation
is a process by which the genetic code contained within an mRNA molecule is decoded to
produce the specific sequence of amino acids
occurs in the cytoplasm

Model Short Answer:

Replication Transcription Translation

1.bidirectional synthesis of two unidirectional synthesis of only Polypeptide/protein is

strands of nucleic acid a single strand of nucleic acid synthesised

2.Primer is required initiation does not require a Recognition of 5’ end of mRNA√

primer

3.D√NA polymerase RNA polymerase Amino-acyl t transferase

4.replication begins at origin of Begins at promoter region Ribosome encounter AUG (start
replication codon)

5. nucleus Nucleus Cytoplasm (eukaryotic model)

Question 3 of 72.0 Points

What is the difference between a genomic library and a cDNA library?

A) A genomic library contains coding and noncoding sequences, whereas a cDNA library
contains only coding sequences

B) A genomic library can be made using a restriction enzyme only, whereas a cDNA library
requires plasmids and DNA ligase.

Model Short Answer: The key difference between these two libraries is that genomic library contains
DNA fragments that express the whole genome of an organism
while
cDNA library, mRNA is taken from specific cells of an organism, and then cDNA is made from that mRNA
in a reaction which is catalyzed by an enzyme, RT.
Question 4 of 72.0 Points

Describe 2 possible problems/risks associated with gene therapy

1. Possibility of causing a tumor. If the new genes get inserted in the wrong spot in DNA, there is
a chance that the insertion might lead to tumor formation
2. Unwanted immune system reaction. a body's immune system may see the newly introduced
viruses as intruders and attack them. This may cause inflammation and, in severe cases, organ
failure

Model Short Answer:

• Unwanted immune system reaction. Your body's immune system may see the newly introduced
viruses as intruders and attack them. This may cause inflammation and, in severe cases, organ
failure.
• Transferred genes could be “overexpressed,” producing so much of the missing protein as to be
harmful; that the viral vector could cause inflammation or an immune reaction;
• Targeting the wrong cells. Because viruses can affect more than one type of cells, it's possible
that the altered viruses may infect additional cells — not just the targeted cells containing
mutated genes. If this happens, healthy cells may be damaged, causing other illness or diseases,
such as cancer.
• Another danger is that the new gene might be inserted in the wrong location in the DNA,
possibly causing cancer or other harmful mutations to the DNA.
• Uunintentionally be introduced into the patient’s reproductive cells. If this happens, it could
produce changes that may be passed on if a patient has children after treatment.
• Infection caused by the virus. It's possible that once introduced into the body, the viruses may
recover their original ability to cause disease.
• Possibility of causing a tumor. If the new genes get inserted in the wrong spot in your DNA,
there is a chance that the insertion might lead to tumor formation.

Question 5 of 74.0 Points

Distinguish eukaryotic and prokaryotic in terms of transcription and translation

1. Prokaryotic transcription and translation are simultaneous processes

2. eukaryotic transcription and translation are discontinuous processes
3. Prokaryotic mRNAs occur in the cytoplasm while in eukaryotic occur in the nucleus

Model Short Answer: Prokaryotes:

• no nucleus and nuclear membrane;
• no post-transcriptional processing of primary transcript;
• as mRNA becomes available during transcription, translation commences;
• allows protection of labile mRNA and quick adjustment to varying growth conditions.
Eukaryotes:
• nucleus with a nuclear membrane present;
• post-transcriptional processing of primary transcript in nucleus;
• mature mRNA transported to cytoplasm ready for translation
• protein made as needed. Slower process

Question 6 of 72.0 Points

Describe one structural feature/characteristic which makes histones well-suited for attracting and
assisting with the packaging of DNA.

1.T hey contain a large proportion of the basic (positively charged) amino acids lysine, arginine,
and histidine which makes it easier for them to assist in packaging and attraction of DNA

Model Short Answer: Rich in positively charges amino acid residues and will attract the negatively
charged DNA. Increased binding affinity of the DNA to histones-> coiling-> compacting the long nucleic
acid

Question 7 of 72.0 Points

Tabulate 2 similarities between DNA replication and the process of transcription and translation

1. Replication and transcription involves a parental DNA strand that is the foundation on which
the products are built on
2 Replication and transcription both have initiation step which involve the breakage of the
parental DNA strand.
3. Replication and transcription both have specific proteins that keep the polymerase molecule
attached to the parental DNA strand. There are elongation factors for transcription and sliding
clamp for replication.

Model Short Answer: 1. Involves a parental DNA strand that is the foundation on which the products are
built on
2.Synthesizes/codes for molecules in the 5′-to-3′ direction. 5’ end of mRNA codes for the N terminal of
protein
3. All occurs in cytoplasm (prokaryotic model)
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 Question 2 of 124.0 Points

 Describe in detail why the atoms surrounding the peptide bond are planar, forming the
so-called amide plane.

 A pure double bond between C and O would permit a free rotation around C-N bond,
the other extreme would prohibit C-N bond rotation but would place too great a charge
on O and N, the true electron density is intermediate, the barrier to C - N bond rotation
of about 88kj/mol is enough to keep the amide group planar. The planarity of the
peptide bond means that there are only two degrees of freedom per residue for the
peptide chain. The peptide bond has double bond character because the electrons from
the carbonyl oxygen are delocalized into the C-N bond, as with any double bond the two
bonded atoms , plus the four atoms attached to these two are co-planar , thus the alpha
carbon, the carbonyl carbon , the carbonyl oxygen , the amino nitrogen , and the
hydrogen it bears and the next alpha carbon in the chain are all in the same plane. due
to the bond character , the six atoms of the peptide bond groups are always planar.
 What does “diastereomer” and enantiomer” mean?

 Diastereomers they are pairs of isomers that have opposite conformation at one
or more of the chiral centers but that are not mirror images of each other.
 Enantiomers they are chiral molecules that are mirror images of each other

 Question 5 of 1210.0 Points

 Name 4 steps that you can use to isolate a protein from a liver homogenate. Also, briefly
discuss each method/step so that the basic principle of each step is clear.
  1. Affinity chromatography --> is a method of separating biochemical mixture
based on a highly specific interaction between antigen and antibody, enzyme and
substrate, receptor and ligand, or protein and nucleic acid.
 2. Salt precipitation --> It can be a very powerful tool to purify proteins by
precipitation. Ammonium sulfate is usually the salt of choice since it is cheap,
very soluble in water, and can become much more hydrated (interacts with more
water molecules) than almost any other ionic solvent.
 3. Molecular sieves --> also known as molecular sieve chromatography, is a
chromatographic method in which molecules in solution are separated by their
size, and in some cases molecular weight.
 4. Ion exchange chromatography --> is a chromatographic separation method
essentially based on the net charge of the protein and is generally used to follow
deamidation and succinimide formation. normally there are two types of IEX,
cation exchange and anion exchange chromatography. At buffer pH values
above this IP, the protein is negatively charged (anionic); at pH values below
that, the protein is positively charged (cationic

 Question 6 of 124.0 Points

 Acid hydrolyses of proteins is often used to determine the amino acid composition of a
protein. Briefly describe the limitations / disadvantages of the method.

 1. The hydrolysis of protein can destroy Tryptophan as it is not quantifiable under

acidic conditions
 2. The Serine and threonine are destroyed slowly and are generated in low yield.
 3. Peptide bonding of hydrophobic (e.g. valine, isoleucine) are slowly hydrolyzed.
 4. NH2 groups on asparagine and glutamine side chains are acidic labile meaning
they are not stable.


BCHN 213 1-1 M 2020

Assessment 1 - SU7 + SU8

 Return to Assessment List
Part 1 of 1 - 36.0 / 50.0 Points

Question 1 of 1210.0 Points

Describe in detail why amino acids protonate and deprotonate as the pH of the solution changes. In your
answer, refer to the general structure of amino acids, pKa- values, what this means and what role it
plays in protonation and deprotonation of amino acids.

Amino acids they can be protonated and deprotonated this is because when the amino is in the
solution that is acidic meaning the pH of the solution is 1, the total amino acid is in the cationic
form , which makes it to have a net charge of positive 1, as the pH of the solution increases to pH
7, the COOH group losses the hydrogen, becoming deprotonated and the structure becomes the
zwitterion(neutral form) having a net charge of 0, however the amine group remains the same as
the NH , as the pH solution increases futher to pH 13, the NH also losses the hydrogen becoming
3 3

deprotonated remaining as the NH , the total net charge of the structure changes to negative 1
2

meaning it is in the Anionic form. therefore the pKa of the carboxylic groups is always lower
than that of the amonium group so as the pH increases it will always be deprotanated before the
amonium group.

Question 2 of 124.0 Points

Describe in detail why the atoms surrounding the peptide bond are planar, forming the so-called amide
plane.

A pure double bond between C and O would permit a free rotation around C-N bond, the other
extreme would prohibit C-N bond rotation but would place too great a charge on O and N, the
true electron density is intermediate, the barrier to C - N bond rotation of about 88kj/mol is
enough to keep the amide group planar. The planarity of the peptide bond means that there are
only two degrees of freedom per residue for the peptide chain. The peptide bond has double bond
character because the electrons from the carbonyl oxygen are delocalized into the C-N bond, as
with any double bond the two bonded atoms , plus the four atoms attached to these two are co-
planar , thus the alpha carbon, the carbonyl carbon , the carbonyl oxygen , the amino nitrogen ,
and the hydrogen it bears and the next alpha carbon in the chain are all in the same plane. due to
the bond character , the six atoms of the peptide bond groups are always planar.

Question 3 of 123.0 Points

Briefly describe why a carbon atom can give rise to isomers.

Carbons have an incomplete outermost electron shell, with an atomic number of 6( six electrons
and six protons) the first two electrons fill the inner shell leaving four in the second shell
therefore carbon can form four covalent bonds with other atoms, as the four atoms are filled this
can give rise to isomers because it has multiple bond formation , and this enables it to form many
multiple chains

Question 4 of 122.0 Points

What does “diastereomer” and enantiomer” mean?

Diastereomers they are pairs of isomers that have opposite conformation at one or
more of the chiral centers but that are not mirror images of each other.
Enantiomers they are chiral molecules that are mirror images of each other

Question 5 of 1210.0 Points

Name 4 steps that you can use to isolate a protein from a liver homogenate. Also, briefly discuss each
method/step so that the basic principle of each step is clear.

1. Affinity chromatography --> is a method of separating biochemical mixture based on a

highly specific interaction between antigen and antibody, enzyme and substrate,
receptor and ligand, or protein and nucleic acid.
2. Salt precipitation --> It can be a very powerful tool to purify proteins by precipitation.
Ammonium sulfate is usually the salt of choice since it is cheap, very soluble in water,
and can become much more hydrated (interacts with more water molecules) than
almost any other ionic solvent.
3. Molecular sieves --> also known as molecular sieve chromatography, is a
chromatographic method in which molecules in solution are separated by their size, and
in some cases molecular weight.
4. Ion exchange chromatography --> is a chromatographic separation method
essentially based on the net charge of the protein and is generally used to follow
deamidation and succinimide formation. normally there are two types of IEX, cation
exchange and anion exchange chromatography. At buffer pH values above this IP, the
protein is negatively charged (anionic); at pH values below that, the protein is positively
charged (cationic

Question 6 of 124.0 Points

Acid hydrolyses of proteins is often used to determine the amino acid composition of a protein. Briefly
describe the limitations / disadvantages of the method.

1. The hydrolysis of protein can destroy Tryptophan as it is not quantifiable under acidic
conditions
2. The Serine and threonine are destroyed slowly and are generated in low yield.
3. Peptide bonding of hydrophobic (e.g. valine, isoleucine) are slowly hydrolyzed.
4. NH2 groups on asparagine and glutamine side chains are acidic labile meaning they
are not stable.

Question 7 of 124.0 Points

Briefly describe the usage of Edman degradation to determine the primary structure of a protein.

Edman degradation is a powerful method for stepwise release and sequential

identification of amino acids from the N-terminus of the polypeptide. The amino acid
sequence of the entire protein can be re constructed once the sequences of overlapping
sets of peptide fragments are known. In this method, the amino-terminal residue is
labeled and cleaved from the peptide without disrupting the peptide bonds between
other amino acid residues, after each round the amino acid is identified by comparing it
to standards.

 Question 8 of 122.0 Points

 What makes up protein structure?

 Protein structure is a polymer composed of amino acids, amino acids linked together by
peptide bonds that form a polypeptide chain, one or more polypeptide chains twisted
into a 3-D shape form a protein, proteins have complex shapes that include various
loops and curves

Model Short Answer: A protein’s primary structure refers to the amino acid sequence in the polypeptide
chain. Peptide bonds that are made during the protein biosynthesis process hold the primary structure
together
  Question 9 of 124.0 Points

 What are the 4 stages of protein structure?

 1. Primary (1°) structure—the protein’s amino acid sequence

2. Secondary (2°) structure—regular elements of structure (helices, sheets) within the protein
created by hydrogen bonds
3. Tertiary (3°) structure—the folding of the polypeptide chain in three-dimensional space
4. Quaternary (4°) structure—the subunit organization of multimeric proteins

Model Short Answer: primary, secondary, tertiary and quaternary

 Question 10 of 122.0 Points

 What is the process of protein folding?

 Protein folding is the process in which a polypeptide folds into specific , stable ,
functional three dimensional structure. it is the process by which a protein
structure assumes its 3D functional shape or conformation

Model Short Answer: The folding of proteins is the mechanism through which a protein structure
assumes its functional shape or conformation. Both molecules of protein are heterogeneous
unbranched amino acid chains. They may perform their biological function by coiling and folding in a
particular three-dimensional shape.

 Question 11 of 122.0 Points

 How proteins are formed?

 Proteins actually start off as DNA. One strand of our double stranded DNA (chromatin)
is copied by enzymes and taken to the ribosomes. At the ribosomes 3 bases of the
strand of what is now called RNA code for one of 20 different Amino Acids (the building
 blocks of protein). When the strand is fully coded then you have a protein . Proteins are
formed during translation

Model Short Answer: Amino acids form a polypeptide, another word for protein when bound by a
sequence of peptide bonds. The polypeptide then folds into a particular conformation based on the
interactions (strained lines) between its side chains of amino

Question 12 of 12

3.0

3.0 Points

Is DNA a protein? Support your answer

No, DNA is not a protein. Because DNA contains the genetic information of all living organisms

and proteins are large molecules made up of 20 small molecules called amino acids, proteins

perform all of an organism’s vital functions

 Model Short Answer: DNA is often associated with proteins in the nucleus called histones, but

DNA itself is not a protein. No. DNA is a nucleic acid consisting of phosphate and sugar groups

based on purine and pyrimidine, while proteins are large molecules made up of one or more

long amino acid chains.

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BCHN 213 1-1 M 2020

Assessment 2 - SU9 + SU10

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Part 1 of 2 - 17.0 / 25.0 Points

Question 1 of 194.0 Points

Name 4 non-covalent interactions that are responsible for stabilizing the secondary structures of
proteins.

1. Hydrophobic interactions
2. Ionic interactions
3. Van de waal interactions
4. Hydrogen Bonds

Model Short Answer: hydrogen

bonds,
ionic bonds,
van der Waals interactions,
hydrophobic bonds.

Question 2 of 195.0 Points

What is the Ramachandran diagram, what does it indicate and for what can you use it?
The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino
acids) contained in a peptide. The torsional angles of each residue in a peptide define the geometry
of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the
two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the
residues and the peptide. Many of the angle combinations, and therefore the conformations of
residues, are not possible because of steric hindrance. By making a Ramachandran diagram protein
structural scientists can determine which torsional angles are permitted and can obtain insight into
the structure of peptides, and they can predict if the % of aa is more than 88 % in allowed region the
protein model is good for in silico studies and also It tells about allowed and dis allowed regions of
the aa that reflects the stability of protein structure.

Model Short Answer:

-The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues
(amino acids) contained in a peptide.
-By making a Ramachandran plot, protein structural scientists can determine which torsional
angles are permitted and can obtain insight into the structure of peptides
-Ramachandran Plot is a way to visualize dihedral angles ψ against φ of amino acid residues in
protein structure
Ramachandran plot provides an easy way to view the distribution of torsion angles of a protein
structure
It also provides an overview of allowed and disallowed regions of torsion angle values, serving
as an important factor in the assessment of the quality of protein three-dimensional structures.

A Ramachandran plot can be used in two somewhat different ways. One is to show in theory
which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a
protein

Question 3 of 198.0 Points

Define collagen in terms of structure and function and its formation

Collagen is a rigid, inextensible fibrous protein that is a principal constituent of connective tissue
in animals, including tendons, cartilage, bones, teeth, skin, and blood vessels. The high tensile
strength of collagen fibers in these structures makes possible the various animal activities such
as running and jumping that put severe stresses on joints and skeleton. Broken bones and tendon
and cartilage injuries to knees, elbows, and other joints involve tears or hyperextensions of the
collagen matrix in these tissues.The basic structural unit of collagen is tropocollagen, which has
a molecular weight of 285,000 and consists of three intertwined polypeptide chains, each about
1000 amino acids in length. Tropocollagen molecules are about 300 nm long and only about 1.4
nm in diameter. Several kinds of collagen have been identified. Type I collagen, which is the
most common, consists of two identical
peptide chains designated alpha1(I) and one different chain designated alpha 2(I).type I collagen
predominates in bones, tendons, and skin. Type II collagen, found in cartilage, and type III
collagen, found in blood vessels, consist of three identical polypeptide chains. Collagen is
secreted by various cells, but mainly by connective tissue cells.

Model Short Answer:

Defination
Collagen is a protein that consists of three chains of polypeptides and many units of
hydroxyproline, proline and glycine residues.

Structure
The collagen molecular structure is that of a helix of three chains of polypeptides that are bonded
together and linked by covalent bonds both within and between chains. The helix is made of two
alpha 1 chains and one alpha 2 chain linked together, and every third residue is usually the amino
acid glycine. There are several different types of collagen that have been identified in the human
body, and of these type 1 collagen is the most numerous and abundant.

Functions:
Collagen is the main fibrous protein found in the connective tissues of the human body. It is also
found in the dermis of the skin and in ligaments and tendons that are found at joints of the body.
It is a tough material that is strong and allows for a certain degree of elasticity before breaking; it
is this high tensile strength of collagen that makes it so well suited as a connective tissue fiber.

Formation:
Cells called fibroblasts, that are abundant in connective tissues, produce the collagen fibers.
Generally, collagen is formed by the lysine and proline parts joining together along with various
other components such as hydroxyl groups and sugar molecules. A limited quantity of collagen
can also be synthesized outside of the cell by enzymatic action on procollagen fibrous material.

Question 4 of 198.0 Points

Distinguish between alpha helix and beta sheet

1. alpha helix
a. CO & NH of the mainchain are hydrogen bonded together, allowing the mainchain to be burie
b. all alpha carbons are H bonded and in line with each other
c. R groups are on the outside & backbone on the inside
d. always right handed (clockwise
e. all H bonds are in the same direction as the chain
f. all carbonyl groups are in one direction and all N-H
2. Beta sheet
a. all C=H groups are not in the same direction
b, all N-H groups are not in the same direction
c. cannot exist as a single Beta strand; must be 2 or more
d. in proteins, 4-5 strands make up a beta sheet; it is possible to be made of more than 10
e. Arrow in pictures always points to the CO group
f. can be antiparallel, parallel, or mixed

Model Short Answer: Alpha helix

-Helix stabilized by H bonding between C=O and N-H (4 residues in chain)
-All H bonds in the same direction as the chain
-All carbonyl groups are in one direction and all N-H are in the opposite direction
-Helix from if phi = -60° and psi between -45° and -50°

Beta sheet
-All H bonds perpendicular in direction of chain
-All C=O groups are not in the same direction as with α-helix
-All N-H groups are not in the same direction as α-helix

Feedback:
Part 2 of 2 - Multiple choice 14.0 / 15.0 Points

Question 5 of 191.0 Points

Which of the following does not affect the stability of an α-helix?

 A. Electrostatic repulsion

 B. Bulkiness

 C. Interaction between R groups spaced three residues apart

 D. Occurrence of alanine and glycine residues

Answer Key:D

Feedback:The occurrence of Proline and Glycine residues affect the stability of an α-helix.

Question 6 of 191.0 Points

Which of the following is not true about secondary protein structure?

 A. The hydrophilic/hydrophobic character of amino acid residues is important to

secondary structure

 B. The ability of peptide bonds to form intramolecular hydrogen bonds is important to

secondary structure

 C. The alpha helix, beta pleated sheet and beta turns are examples of protein secondary
structure

 D. The steric influence of amino acid residues is important to secondary structure

Answer Key:A

Feedback:The hydrophilic/hydrophobic character of amino acid residues is important to protein tertiary

structure rather than to secondary structure. In secondary structure, it is the steric size of the residues
that is important and residues are positioned to minimize interactions between each other and the
peptide chain.

Question 7 of 191.0 Points

β-pleated sheets are the examples of

 A. Primary structure

 B. Secondary structure

 C. Tertiary structure

 D. Quaternary structure

Answer Key:B

Feedback: Secondary structure of proteins is of two forms α-helix and β-pleated structures.

Question 8 of 191.0 Points

A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the same chain is?

 A. Primary structure

 B. α-helix

 C. β-pleated sheets

 D. Tertiary structure

Answer Key:B

Feedback: A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the same
chain is α helix.

Question 9 of 191.0 Points

A structure that has hydrogen bonds between polypeptide chains arranged side by side is?

 A. Primary structure

 B. α-helix

 C. β-pleated sheets
  D. Tertiary structure

Answer Key:C

Feedback:A structure that has hydrogen bonds between polypeptide chains arranged side by side is β-
pleated sheets.

Question 10 of 191.0 Points

Which of the following are known as helix breakers?

 A. Proline and glycine

 B. Isoleucine and leucine

 C. Valine

 D. Threonine

Answer Key:A

Feedback:Proline and glycine are known as helix breakers as they disrupt the regularity of the alpha
helical backbone conformation.

Question 11 of 191.0 Points

NMR is an abbreviated form of Nuclear Magnetic Resonance

 A. NMR is an abbreviated form of Nuclear Magnetic Resonance

 B. The intramolecular magnetic field around an atom in a molecule changes the

resonance frequency giving structural information about the atom

 C. The intermolecular magnetic field around an atom in a molecule changes the

resonance frequency giving structural information about the atom

 D. It is a technique that exploits magnetic properties of atomic nuclei

Answer Key:C
Feedback:The intramolecular magnetic field around an atom in a molecule changes the resonance
frequency giving structural information about the atom.

Question 12 of 191.0 Points

Which of the statements is false about multiple sequence alignment?

 A. Both protein and nucleic acid secondary structures can be used

 B. More useful in RNA

 C. These alignments can be made more accurate by the inclusion of secondary structure
information

 D. A significant increase in accuracy

Answer Key:B

Feedback:Less useful in RNA. This is because base pairing is highly conserved than sequence.

Question 13 of 191.0 Points

Secondary structure is defined by

 A. Hydrogen bonding

 B. Vander Waals forces

 C. Covalent bonding

 D. Ionic bonding

Answer Key:A

Feedback:Hydrogen bonding is present between the amine hydrogen and carbonyl oxygen atoms in the
peptide backbone.

Question 14 of 191.0 Points

Which of the following is a false statement?

 A. α-Keratin is α helical
  B. Collagen is α helical

 C. Hemoglobin has a quaternary structure

 D. α-Keratin is β pleated structure

Answer Key:D

Feedback: Fibrous structural protein, α-Keratin is α helical.

Question 15 of 191.0 Points

Which of the following bonds are not involved in tertiary type of protein structure?

 A. Disulfide bond

 B. Hydrogen bonding

 C. Salt bridges

 D. Hydrophilic interactions

Answer Key:D

Feedback:Hydrophobic interactions are present in tertiary type of protein structure.

Question 16 of 191.0 Points

Which of the following does not possess a quaternary structure?

 A. Myoglobin

 B. Lactate dehydrogenase

 C. Immunoglobin M

 D. Creatine Phospho Kinase

Answer Key:A
Feedback:Myoglobin is a monomer, so it does not possess a quaternary structure.

Question 17 of 191.0 Points

Which of the following is abundantly found in collagen

 A. Glycine

 B. Serine

 C. Alanine

 D. Tryptophan

Answer Key:A

Feedback:Each three amino acids of the collagen peptide chain is a glycine. It is thus an abundant amino
acid that is important for collagen structure.

Question 18 of 191.0 Points

Which of the following is first determined as oligomer?

 A. Myoglobin

 B. Collagen

 C. Keratin

 D. Hemoglobin

Answer Key:D

Feedback: Hemoglobin contains four polypeptide chains and four heme prosthetic groups in which iron
atoms are present in Fe+2 state.

Question 19 of 191.0 Points

Which of the following is false about fibrous protein?

 A. It is in rod or wire like shape

 B. Keratin and collagen are the best examples

  C. Hemoglobin is the best example

 D. It provides structural support for cells and tissues

Answer Key:C

Feedback:Hemoglobin is the best example of globular protein.

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Assessment 3 - SU11 + SU12

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Part 1 of 1 - 30.5 / 35.0 Points

Question 1 of 63.0 Points

Describe the structural changes that occur when O2 binds to myoglobin.

In deoxymyoglobin, the ferrous ion has but five ligands, and it lies 0.055 nm above the
plane of the heme, in the direction of His F8. The iron porphyrin complex is therefore
dome-shaped. in When O2 binds, the iron atom is pulled back toward the porphyrin
plane and is now displaced from it by only 0.026 nm, and no effect on effectivity of Mb

Question 2 of 68.0 Points

Explain the allosteric regulation of hemoglobin by O2, by referring to the structural changes in
hemoglobin induced during binding

Haemoglobin has a quaternary structure, Haemoglobin is an O2 - transport protein, Hemoglobin

shows cooperative binding of O2 and allosteric regulation by H2, CO2, and 2,3-
bisphosphoglycerate. The allosteric properties of Hb can be traced to the movement of the F
helix upon O2 binding to Hb heme groups and the effects of F-helix movement on interactions
between the protein’s subunits that alter the intrinsic affinity of the other subunits for O2. The
allosteric transitions in Hb partially conform to the MWC model in that a concerted
conformational change from a T-state, low-affinity conformation to an R-state, high-affinity form
takes place after 2 O2 are bound (by the 2 Hb -subunits). However, Hb also behaves somewhat
according to the KNF model of allostery in that oxygen binding leads to sequential changes in
the conformation and O2 affinity of hemoglobin subunits. Sickle-cell anemia is a molecular
disease traceable to a tendency for Hb S to polymerize as a consequence of having a E6V
amino acid substitution

Question 3 of 64.0 Points

Explain the allosteric regulation of hemoglobin by BPG, by referring to the structural changes in
hemoglobin induced during binding.

The binding of 2,3-bisphosphoglycerate (BPG) to Hb promotes the release of O2, BPG

binding stoichiometry because the tetrameric Hb molecule has but one binding site for
BPG. This site is situated within the central cavity formed by the association of the four
subunits. The strongly negative BPG molecule Is electrostatically bound via interactions
with the positively charged functional groups of each Lys B82, His B2, His B143, and the
NH3+ -terminal group of each B-chain. These positively charged residues are arranged to
form an electrostatic pocket complementary to the conformation and charge distribution
of BPG (In effect, BPG crosslinks the two B-subunits. The ionic bonds between BPG and
 the two B-chains aid in stabilizing the conformation of Hb in its deoxy form, thereby
favoring the dissociation of oxygen. In oxyhemoglobin, this central cavity is too small for
BPG to fit. Or, to put it another way, the conformational changes in the Hb molecule that
accompany O2 binding perturb the BPG-binding site so that BPG can no longer be
accommodated. Thus, BPG and O2 are mutually exclusive allosteric effectors for Hb,
even though their binding sites are physically distinct

Question 4 of 66.0 Points

Describe the clonal selection theory in detail

Clonal selection theory is the idea that lymphocytes have antigen-specific binding receptors
before they encounter with an antigen, and are selected to proliferate because they have the
specific antigen receptor needed during an adaptive immune response. Clonal selection is an
theory that attempts to explain why lymphocytes are able to respond to so many different
types of antigens. T and B cells are able to respond to nearly all of the world’s vast variety of
antigens upon presentation. Clonal selection assumes that lymphocytes are selected during
antigen presentation because they already have receptors for that antigen.

In clonal selection, an antigen is presented to many circulating naive B and (via MHC) T cells,
and the lymphocytes that match the antigen are selected to form both memory and effector
clones of themselves. This mass production is termed “clonal expansion,” in which daughter
cells proliferate into several generations of clones of the original parent cells. The theoretical
basis of clonal selection is the assumption that lymphocytes bearing an antigen receptor for an
antigen exist long before antigen presentation occurs, explained by the idea of random
mutations (VDJ recombination) that occur during lymphocyte maturation. During antigen
presentation, pre-existing lymphocytes that bear that antigen receptor are merely selected
because they can bind with that antigen. It is also assumed that most lymphocytes never
encounter the antigen for which they bear a receptor.

Question 5 of 64.0 Points

Name and describe in brief the process by which immunological diversity is generated

immunological diversity is also called antibody diversity.

The antibody diversity found in IgG molecules are a prime example of proteins produced via
gene rearrangements. IgG L-chain genes are created by combining three separate genes, and
H-chain genes by combining four. V–J and V–D–J joining in L- and H-chain gene assembly is
mediated by RAG proteins.

Antibody diversity comes from several stages of Ig (Immunoglobulin) development, including

both pre-immune repertoire, in which antibodies are developed for sampling the system for
foreign bodies, and the post-immune repertoire, in which antibodies against foreign antigens
are selected for and matured. In the pre-immune repertoire, there are four major sources of
antibody diversity. The first source of pre-immune diversity is the recombination of VH, DH, and
JH chains to build a functional VH chain, and VL and VJ (λ or κ) chains to build a functional light
chain. To build a functional VH gene, there is a random assortment in which one of 39
functional VH genes is coupled with one of 27 functional D genes and 6 JH chains. Second,
within the VDJ joining process, the junctional diversity created in the recombination process
adds infinitely more diversity in 4 different ways. 1. The D genes can be translated in any one of
three open reading frames in either direction to yield a total of six possible peptide fragments.
2. During the rearrangement process, a hairpin is formed that when resolved can result in the
addition or deletion of N nucleotides resulting in added diversity. 3. About the VDJ joining
mechanism, N nucleotides can be added or deleted as part of the VDJ joining process. In some
cases, the coding sequences for several amino acid residues can be lost during the
recombination process. 4. N nucleotides can be added or replaced by the activities of TdT
(Terminal deoxynucleotidyl Transferase), particularly on either side of the D segment within the
VDJ junctions, which make up CDR-H3 in the functional V-region. It has been estimated that
these N changes can result in up to >107 different variations of CDR-H3, including CDR lengths
ranging from just a few amino acid residues to over 25. Combined together, the somatic
rearrangements, the combinatorial diversity within chains, the inherent mutagenesis that
occurs in the assembly process, and the combination of heavy and light chains result in a
potential pre-immune diversity of >1016 different antibodies. After exposure of cell-bound IgM
to antigen, the antibody genes undergo an affinity maturation process, generating new diversity
from which antibodies with higher affinity to the targeted antigen epitope are selected,
resulting in more effective binding and elimination of the antigen from circulation during the
secondary immune response.

Question 6 of 6

10.0

10.0 Points

Describe the structure of IgG in detail by referring to the different levels of protein structure

IgG is a type of antibody which is the most common and abundant in blood circulation and

approximately 80% of total serum antibodies in human body. This antibody is secreted by

plasma B cells and have 2 antigen binding sites. IgG antibodies are large monomeric molecules

of about 150 kDa with a tetrameric quaternary structure. An IgG antibody comprises of heavy

and light chains. It possesses the basic monomeric “H2L2” structure consisting of: Its H-chain
 type is gamma (γ heavy chains) about 50 kDa in weight and each H chain is paired with an L

chain of about 25 kDa. The two heavy chains are linked to each other and to a light chain each

by disulfide bonds. The immunoglobulin structure represents the confluence of all the details of

protein structure for all proteins, the primary structure determines other aspects of structure.

There are numerous elements of secondary structure, including B sheets and tight turns. The

tertiary structure consists of 12 distinct domains, and the protein adopts a hetero tetrameric

quaternary structure. Both intra subunit and inter subunit disulphide linkages act to stabilize

the discrete domains and to stabilize the tetramer itself. The amino acid sequences of both light

and heavy immunoglobulin chains are not constant! Instead, the primary structure of these

chains is highly variable in the N-terminal regions (first 108 residues). Heterogeneity of the

amino acid sequence leads to variations in the conformation of these variable regions. This

variation accounts for antibody diversity and the ability of antibodies to recognize and bind a

virtually limitless range of antigens. This full potential of antibody: antigen recognition enables

organisms to mount immunological responses to almost any antigen that might challenge the

organism.