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This question is from RxPG TargetPG 2005 Book
Question 274.
A 30-year-old man has 6/5 vision each eye, unaided. His cycloplegic retinoscopy is +1.0 D sph at 1 metre distance. His complaints are blurring of newsprint at 30 cm, that clears up in about two minutes. The most probable diagnosis is:
1. Hypermetropia.
2. Presbyopia.
3. Accommodative inertia.
4. Cycloplegia.
Answer
3. Accommodative inertia.
Reference:
Optometric clinical practice guidelines (American Optometric Association).
Quality:
Thinker
QTDF:
??
Status:
New
Discussion:
Accommodative inertia, also called as accommodative infacility, can be defined as slow or difficult accommodative response to dioptric change—Unstimulus.
Explanation:
Cycloplegia hypermetropia or presbyopia do not “clear up in two minutes.”
Comments:
Accommodative inertia typically occurs when the accommodative system is capable of but slow in making a change. In other words there is a considerable lag between the stimulus and response (starting trouble).
Tips:
‘Plus’ lens can be prescribed initially, but vision therapy is highly effective in correcting accommodative inertia.
Interested reader can refer “Am J Optom Physiol Opt 1984;61:177-83
Relation of symptoms to accommodative infacility of school aged children—Hennessey D, Iosue RA, Rouse MV.
Wednesday, January 16, 2008
Wednesday, January 09, 2008
The shape of structural proteins Fibrous
049. The structural proteins are involved in maintaining the shape of a cell or in the formation of matrices in the body. The shape of these proteins is:
1. Globular
2. Fibrous
3. Stretch of beads
4. Planar
Answer
2. Fibrous
Reference:
Harper 26th Edition Page 38
Lippincott 3rd Edition Page 43
Chaterjee 6th Edition Page 79
Quality
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Status
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Discussion
When the axial ratio of length: width of a protein molecule is more than 10, it is called a fibrous protein. Examples are alpha keratin from hair and collagen
When axial ratio of length: width of a protein molecule is less than 10, it is called a globular protein. Examples are Myoglobin, hemoglobin, Ribonuclease etc
Explanation
Collagen is the most abundant of fibrous proteins that constitute more than 25% of the protein mass in the human body. Other prominent fibrous proteins include keratin and myosin. These proteins represent a primary source of structural strength for cells (ie the cytoskeleton) and tissues.
Comments
There can be some confusion as to whether the shape of the collagen in “planar” due to the pleated structure we often talk about. But many books (including Gray’s Anatomy) just give the shape as fibrous and there is no mention of planar structure of structural proteins in standard books
Tips
In the early 1990’s, premier cell biologist Olga Marko began investigating the use of technology for stimulating a patient’s own cells to produce collagen. Research of this nature was then not yet regulated by the FDA. Through her research, Ms. Marko developed a process of extracting a patient’s own collagen-producing cells (dermal fibroblasts), growing and expanding those cells in a controlled environment, and then re-introducing the fibroblasts by injection into the skin of the patient’s face. Once injected, it was believed that the fibroblasts produced collagen which might prove to be beneficial in the repair of dermal defects. This research lead to the development of the Isolagen Process (ACS - Autologous Cellular System). At this time, the ACS process could be legally marketed.
The comparison of the amino acid sequence of Cytochrome C from different species
048. The comparison of the amino acid sequence of Cytochrome C from different species shows many variations. Most of these variations are found:
1. Randomly
2. Only in helical regions
3. Only in strand regions
4. Mainly in loop regions
Answer
??
Reference:
Dayhoff Atlas of Protein Structure and Function Matrix
Bioinformatics for Beginners, Mani and Vijayaraj, 1st Edition Page 165
“Creative Evolution?!” by John H Campbell Page 10
Quality
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Status
Repeat, but different stems
QTDF
No Idea
Discussion
After waddling through intricacies of cytochrome structure and finding nothing of much use in Harper, Lippincott, Chaterjee or Vasudevan, I was forced to take a sojourn to the myriad world of cyberspace and grasped the following point.
Explanation
Proteins are made up of sequences of amino acids. Amino acids are like letters, and proteins are like words. Just as there are 26 different letters in the modern English alphabet, there are about 20 different amino acids. A protein is constructed from a sequence of its amino acids, just like a word is constructed from a sequence of letters. There are a lot more amino acids in a protein than there are letters in a word, however.
Cytochrome C is about one hundred amino acids long. Imagine a word that is one hundred letters long. You could change one or two of the letters to a similar letter (you could replace a C with a K, for instance) and it would not change the pronunciation of the word noticeably. In the same way, you could change a few of the amino acids in cytochrome C with similar amino acids without affecting the function of the protein very much.
It happens that the cytochrome C in humans is slightly different from the cytochrome C in bacteria, but it still functions the same way. As a matter of fact, there are slight differences in the amino acid sequences of cytochrome C in most living creatures.
Cytochrome C in bacteria is 64% different from horses and pigeons, 65% different from tuna and silkmoths, 66% different from wheat, and 69% different from yeast
Comments
Till we see a exact word in a UG text (like that for Ubiquitin where it is clearly given), we are not sure of the answer
Tips
In AIPG 2004,we had the following question
Cytochrome C of the bacteria has 50% identity of amino acid sequence with that of human. Which of the following is the most conserved parameter in these two proteins?
1. Quaternary structure.
2. Tertiary structure.
3. Amino acid sequence.
4. Loop and turn segments.
Valine can be a homologous substitution for isoleucine in a protein sequence
047. Which one of the following can be a homologous substitution for isoleucine in a protein sequence?
1. Methionine
2. Aspartic acid
3. Valine
4. Arginine
Answer
3. Valine
Reference:
Harper 26th Edition Page 15
Quality
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Status
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Discussion
Homologous substitutions are those which don’t affect the function. Valine is an amino acid with aliphatic side chain and isoleucine also has aliphatic side chain
Explanation
1. Methionine is a sulphur containing aminoacid and will not be a homologous substitution for isoleucine
2. Aspartic acid has a acidic side chain and will not be a homologous substitution for isoleucine
3. Valine has aliphatic side chain and will be a homologous substitution for isoleucine
4. Arginine has a basic side chain and will not be a homologous substitution for isoleucine
Comments
Some time back we used to have questions directly from the Classification of Amino Acids such as “The basic amino acid is” All of the following has aliphatic side chains except” Now questions gyrating around the same topic are asked in an indirect way.
Tips
Hemoglobinopathies as well as classification of proteins are important topics. For an overview about the Hemoglobinopathies, refer to Q.No 30 in RxPG AIPG 2003 book
Quaternary structure - folded structures associate to form homo – or hetero-dimers
046. Proteins are linear polymers of amino acids. They fold into compact structures. Sometimes, these folded structures associate to form homo – or hetero-dimers. Which one of the following refers to this associated form?
1. Denatured state
2. Molecular aggregation
3. Precipitation
4. Quaternary structure
Answer
4. Quaternary structure
Reference:
Harper 26th Edition Page 34
Lippincott 3rd Edition Page 20
Chaterjee 6th Edition Page 86
Quality
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Status
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QTDF
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Discussion
When a protein consists of two or more peptide chains held together by non covalent cross links it is referred to as the quaternary structure The quaternary structure complex is often called as the oligomer and each constituent peptide as monomer or subunit. The noncovalent association of a molecule of beta-2 microglobulin with the heavy chain of each class I histocompatibility molecule is an example
Explanation
1. Denaturation is Destruction of the natural three-dimensional structure of large biological molecules (proteins or DNA), eg through heat. In the case of DNA in particular, denaturation means the dissolution of the double strand into single strands
2. Molecular aggregation
3. Precipitation is the formation of a solid in a solution during a chemical reaction. This can occur when an insoluble substance is formed in the solution due to a reaction or when the solution has been supersaturated by a compound. In most situations, the solid forms ("falls") out of the solute phase, and sinks to the bottom of the solution (though it will float if it is less dense than the solvent, or form a suspension).
4. Quaternary structure are Complexes of 2 or more polypeptide chains held together by noncovalent forces but in precise ratios and with a precise 3-D configuration.
Comments
Ä The primary structure of a protein is its linear sequence of amino acids and the location of any disulfide (-S-S-) bridges.
Ä Secondary Structure : Most proteins contain one or more stretches of amino acids that take on a characteristic structure in 3-D space. The most common of these are the alpha helix and the beta conformation.
o Alpha Helix
§ The R groups of the amino acids all extend to the outside.
§ The helix makes a complete turn every 3.6 amino acids.
§ The helix is right-handed; it twists in a clockwise direction.
§ The carbonyl group (-C=O) of each peptide bond extends parallel to the axis of the helix and points directly at the -N-H group of the peptide bond 4 amino acids below it in the helix. A hydrogen bond forms between them [-N-H·····O=C-] .
o Beta Conformation
§ consists of pairs of chains lying side-by-side and
§ stabilized by hydrogen bonds between the carbonyl oxygen atom on one chain and the -NH group on the adjacent chain.
§ The chains are often "anti-parallel"; the N-terminal to C-terminal direction of one being the reverse of the other.
Ä Tertiary structure refers to the three-dimensional structure of the entire polypeptide chain.
Tips
The number of sub units may vary
Ä 2 subunits (dimmer) – CPK
Ä 4 subunits (tetramer) – Hemoglobin and lactate dehydrogenase
Ä 24 subunits – Apoferritin
Ä 72 subunits – Aspartate transcarboxylase
More than 300 variants of human hemoglobin gene
045. There are more than 300 variants of human hemoglobin gene. Among these only a few are fatal. Hence, the most important factor to be conserved in a protein for its function is the:
1. Amino acid sequence
2. Ligand binding residues
3. Structure
4. Environment
Answer
2. Ligand binding residues
Reference:
Ä Harper 26th Edition Page 46 http://globin.cse.psu.edu/
Ä Genome Research 15:978-986, 2005 , Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
Ä MBE Advance Access originally published online on
Lippincott 3rd Edition Page
Chaterjee 6th Edition Page
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Discussion
Missense mutations that impair protein function may result in disease. For diseases caused by such deleterious mutations, a simple but plausible model presents itself: The type of disease is dependent on when and where the protein's function is required in the organism. Given the type of disease, its severity is likely determined by at least three parameters: (1) the degree to which the function of the protein is impaired by the missense mutation; (2) variants of other genes that modulate the effect of the major locus, also referred to as genetic background; and (3) the environment.
Explanation
In the article 3rd cited, there is clear proof that ligand binding residues are conserved in a protein for its function. The key findings of the study are given here
Ä The significance of these findings was investigated further by observing the structural distribution of the 40 H positions identified in mammalian paralogous comparisons. These positions appeared evenly dispersed all over the structure, both at internal and external locations. Within the pool of H positions there were some likely to hold high functional significance, as they presented strong constraints in one subunit and much higher variability in the other. Consistently, the function of such residues was critical to only one chain. This was the case of six positions lying at inter-subunit contact surfaces.
o For example, leucine alpha 40 presented no substitutions over the whole mammalian tree, whereas its ß39 homolog was much more variable. This site is crucial in the alpha chain as it interacts with histidine ß146 at the sliding interface. Instead, we found no functional indication for residue ß39.
o Similarly, position ß60 displayed a remarkably conserved valine over the whole mammalian tree, whereas its alpha homolog switched to variable amino acids on different branches. A valine to glutamate mutation at this site is reported to lead to a highly unstable ß globin responsible for a severe form of thalassemia (Podda et al. 1991), whereas the alpha 55 homolog does not appear to be involved in any essential interaction.
Ä As an alternative, we focused on those residues showing highly constrained states in two sequence groups, but different in each group, and we named them CBD (for "constant but different"). As opposed to heterotachous positions, CBD sites were markedly overrepresented in paralogous ({alpha}/ß) comparisons, as opposed to orthologous ones ({alpha}/{alpha}, ß/ß), identifying them as likely signatures of functional specialization between the two subunits. When superimposed onto the three-dimensional structure of hemoglobin, CBD positions consistently appeared to cluster preferentially on inter-subunit surfaces, two contact areas crucial to function in vertebrate tetrameric hemoglobin.
Ä To confirm this prediction, we studied the distribution of CBD sites onto the hemoglobin quaternary structure. When superimposed onto the 3D structure of human adult hemoglobin, the 13 CBD sites identified in mammalian paralogous comparisons were concentrated at non-exposed locations. This concentration was confirmed by the fact that almost all of them (10/13) were indeed reported to occupy contact surfaces, such as central cavity, ligand binding pockets, and inter-subunit contacts. In particular, six CBD sites were directly involved in both {alpha}1ß2 (sliding) and {alpha}1ß1 (packing) interfaces (Perutz 1970; Shionyu, Takahashi, and Go 2001). For example, tyrosine {alpha}41 and its homolog arginine ß40 were identified as a highly constrained CBD couple in mammals. These sites interact with each other at the sliding surface in the oxy state. Another case is that of arginine {alpha}141 and its homolog histidine ß146, both of which presented no substitutions over the whole mammalian tree. These sites are involved in crucial interactions with different residues in the deoxy state. The high proportion of CBD positions at inter-subunit surfaces supports their role as potential indicators of functional divergence, because the refinement of interactions at these interfaces played a fundamental role in the evolution of critical functions such as modulation of oxygen affinity and cooperative binding (Perutz 1970).
Comments
I must confess that I do not find a satisfying evidence from a standard text book for this question, and hence have to go for the journal. But we have already had enough questions asked in AIPG and AIIMS that were not from textbooks, but from research papers just published or in some cases, papers that were not even published (but were researched in AIIMS). Once we had question on B Cell Acute Lymphoblastic Leukemia (ALL) with hypereosinophilia in AIIMS Nov 2004 and also in AIPG Jan 2005. More details are given in RxPG TargetPG Series AIPG 2005. Question 166
Tips
In aggregate, these studies suggest that mutations in evolutionarily conserved sites tend to impair protein function and lead to disease. There is also weak evidence that protein impairment and disease severity are somewhat correlated with the physicochemical difference between the original amino acid and the missense variant.
tRNA has the highest percentage of modified base
044. Which type of RNA has the highest percentage of modified base:
1. mRNA
2. tRNA
3. rRNA
4. snRNA
Answer
3. rRNA
Reference:
Harper 26th Edition Page 356
Chaterjee 6th Edition Page 222 Table 16.3
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Discussion
Ä The tRNAs contain many modifications of the standard bases A,U,G and C, including methyaltion, reduction, deamination and rearranged glycosidic bonds.
Ä Further modification of the tRNA molecules includes nucleotide alkylations and the attachment of the characteristic CpCpAOH terminal at the 3’ end of the molecule by the enzyme nucleotidyl transferase
Explanation
Self Explanatory
Comments
Though it is given in books that tRNA has more number of modified bases than mRNA or rRNA, we have no specific information about bases in the snRNA
Tips
Consider this answer with the proverbial “pinch of salt”
The sigma (s) subunit of prokaryotic RNA Polymerase Specifically recognizes the promoter site
043. The sigma (s) subunit of prokaryotic RNA Polymerase:
1. Binds the antibiotic Rifampicin
2. Is inhibited by a-amanitin
3. Specifically recognizes the promoter site
4. Is part of the core enzyme
Answer
3. Specifically recognizes the promoter site
Reference:
Harper 26th Edition Page 343
Lippincott 3rd Edition Page 415
Chaterjee 6th Edition Page 233
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Discussion
Transcription by prokaryotic RNA Polymerase involves a core enzyme and several auxiliary proteins
1. Core Enzyme : Four of the enzymes subunits, 2 a, 1 b and 1b’ are responsible for the 5’-3’ RNA polymerase activity and are referred to as the core enzyme. However this enzyme lacks specificity, that is, ti cannot recognize the promoter region on the DNA template
2. Holoenzyme : The sigma (s) subunit (Sigma factor) enables RNA polymerase to recognize promoter regions of the DNA. The sigma (s) subunit plus the core enzyme makes up the holoenzyme. Different sigma (s) factors recognize different groups of genes
3. Termination factor : Some regions on the DNA that signal the termination of transcription are recognized by the RNA polymerase itself. Others are recognized by specific termination factors, an example of which is the rho (r) factor of E.coli
Explanation
1. Rifampicin and Streptovaricin bind with the beta subunit of RNA Polymerase to block the initiation of trascription
2. RNA Polymerase II (of eukaryotic RNA synthesis) is inhibited by a-amanitin
3. With the assistance of sigma (s) factor, the core enzyme recognizes a promoter
4. The (s) factor is not a part of the core enzyme
Comments
Ä Action of Drugs :
o Actinomycin D forms a complex with double stranded DNA and prevents the movement of core enzyme and as a result inhibit the process of chain elongation
o Streptoglydigin bnds with the beta subunit of prokaryotic polymerase and this inhibits elongation
o Heparin binds to the beta’ subunit
Ä Eukaryotic Gene Transcription
o Nuclear RNA polymerases
§ RNA Polymerase I: synthesizes the precursor of the large ribosomal RNAs(28S, 18S and 5.8S) in the nucleolus. Please note that mRNA and tRNA are synthesized in the nucleoplasm.
§ RNA Polymerase II: synthesizes the precursor of messenger RNA that are subsequently translated to produce proteins. Polymerase II also synthesizes certain small nuclear RNAs (snRNA) and is used by some viruses to produce viral RNA
§ RNA Polymerase III: produces small RNAs including small tRNAs, the small 5S ribosomal RNA and some snRNA
o Mitochondrial RNA Polymerases
§ Mitochondria contain a single RNA polymerase that resembles bacterial RNA polymerase more closely that it does the eukaryotic enzyme
Tips
Do you know that the following medical terminologies originated from Greek Alphabets
Ä Delta (D d) like
o Deltoid(Muscle),
o Delta Peptide (Sleep Inducing Peptide)
o Delta Rhythm (EEG),
o Delta Virus (Hepatitis D Virus),
Ä Lambda (L l) like
o Lambdoid (Suture Defect),
o Lambda Phage (Bacteriophage)
o Lambda Sign (Small Ascending Aorta)
Ä Sigma (S s) like
o Sigmoid (
o Sigma Factor (86 kD-binds RNA Polymerase.)
Ä Upsilon (u Y) like
o Hyoid (Bone)
Ä Chiazo (c C) like
o Chiasma(in Chromosomes)
o Optic Chiasma
regulated by calcium or calmodulin, except Hexokinase
042. All of the following enzymes are regulated by calcium or calmodulin, except:
1. Adenylate cyclase
2. Glycogen synthase
3. Guanylyl cyclase
4. Hexokinase
Answer
4. Hexokinase
Reference:
Harper 26th Edition Page 458
Lippincott 3rd Edition Page 130
Ganong 22nd Edition page 43
Chaterjee 6th Edition Page 271
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Discussion
Enzymes and proteins regulated by Calcium and Calmodulin are (Harper)
1. Adenylyl cyclase
2. Ca2+-depended protein kinases
3. Ca2+- Mg2+ ATPase
4. Ca2+-phospholipid-dependent protein kinase
5. Cyclic nucleotide phosphodiesterase
6. Some cytoskeletal proteins
7. Some ion channels (eg L-type Calcium channels)
8. Nitric Oxide synthase
9. Phosphorylase kinase
10. Phosphoprotein phosphatase 2B
11. Some receptors (eg NMDA-type glutamate receptors)
Explanation
1. Several of the isoforms of the adenyl cyclase are stimulated by Calmodulin (Ganong)
2. Active Glycogen synthase (GS-a) is converted to inactive Glycogen synthase (GS-b) by phosphorylation, which is modulated by cAMP dependent protein kinase (Chaterjee)
3. Guanylyl cyclase is activated by Atriopeptins and Nitric Oxide, nitroprusside, nitroglycerin, sodium nitrate and sodium azide.(Harper). Nitric Oxide Synthase is activated by Calcium or Calmodulin. Hence we can assume that Calcium or Calmodulin regulate Guanylyl cyclase
4. Hexokinase is inhibited by Glucocorticoids and GH and Glucose-6-Phosphate. Insulin does not have effect on hexokinase
Comments
Cyclic AMP was the first intracellular signal identified in mammalian cells
Tips
Guanylate cyclase (EC 4.6.1.2, also known as guanylyl cyclase or GC) is a lyase, an enzyme that catalyzes the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate. There are soluble and membrane-bound forms of guanylyl cyclases. Soluble GC (sGC) is activated by nitric oxide, most notably involved in vasodilation. Membrane-bound forms are receptors: GC-A & GC-B for natriuretic factors such as atrial natriuretic factor (ANF), and GC-C for guanylin.
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