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Elements of Systemic Bacteriology – I
1. Discuss the bonds involved maintenance of secondary structur of proteins .
In molecular biology protein structure describes the various levels of organisation of protein molecules.
Proteins are an important class of biological macromolecules present in all organisms. Proteins
are polymers of amino acids. Classified by their physical size, proteins are nanoparticles (definition: 1–
100 nm). Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20
possible L-α-amino acids, also referred to as residues. For chains under 40 residues the term peptide is
frequently used instead of protein. To be able to perform their biological function, proteins fold into one or
more specific spatial conformations, driven by a number of non-covalent interactions such as hydrogen
bonding, ionic interactions, Van Der Waals forces, and hydrophobicpacking. To understand the functions
of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This
is the topic of the scientific field of structural biology, which employs techniques such as X-ray
crystallography, NMR spectroscopy, and dual polarisation interferometry to determine the structure of
proteins.
Protein structures range in size from tens to several thousand residues [1] Very large aggregates can be
formed from protein subunits: for example, many thousand actin molecules assemble into amicrofilament.
A protein may undergo reversible structural changes in performing its biological function. The alternative
structures of the same protein are referred to as different conformations, and transitions between them
are called conformational changes.
Primary structure
Main article: Protein primary structure
The primary structure refers to amino acid sequence of the polypeptide chain. The primary structure is
held together by covalent or peptide bonds, which are made during the process of protein biosynthesis or
translation. The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus)
and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Counting
of residues always starts at the N-terminal end (NH2-group), which is the end where the amino group is
not involved in a peptide bond. The primary structure of a protein is determined by the gene
corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which
is read by the ribosome in a process called translation. The sequence of a protein is unique to that
protein, and defines the structure and function of the protein. The sequence of a protein can be
determined by methods such as Edman degradation or tandem mass spectrometry. Often however, it is
read directly from the sequence of the gene using the genetic code. Post-translational modifications such
as disulfide formation, phosphorylations and glycosylations are usually also considered a part of the
primary structure, and cannot be read from the gene.
[edit]Amino
acid residues
Main article: Amino acid
Main article: Proteinogenic amino acid
Each α-amino acid consists of a backbone part that is present in all the amino acid types, and a side
chain that is unique to each type of residue. An exception from this rule is proline. Because the carbon
atom is bound to four different groups it is chiral, however only one of the isomers occur in biological
proteins. Glycine however, is not chiral since its side chain is a hydrogen atom. A simple mnemonic for
correct L-form is "CORN": when the Cα atom is viewed with the H in front, the residues read "CO-R-N" in
a clockwise direction.
2. Discuss acid base properties of amino acids.
Amino acids ( /əˈmiːnoʊ/, /əˈmaɪnoʊ/, or /ˈæmɪnoʊ/) are molecules containing an amine group,
a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an
amino acid are carbon, hydrogen, oxygen, and nitrogen. They are particularly important in biochemistry,
where the term usually refers to alpha-amino acids.
An alpha-amino acid has the generic formula H2NCHRCOOH, where R is an organic substituent;[1] the
amino group is attached to the carbon atom immediately adjacent to the carboxylate group (the α–
carbon). Other types of amino acid exist when the amino group is attached to a different carbon atom; for
example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the
amino group attaches is separated from the carboxylate group by two other carbon atoms. The various
alpha-amino acids differ in which side-chain (R-group) is attached to their alpha carbon, and can vary in
size from just onehydrogen atom in glycine to a large heterocyclic group in tryptophan.
Amino acids serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids
can be linked together in varying sequences to form a vast variety of proteins. [2] Twenty amino acids are
naturally incorporated into polypeptides and are called proteinogenic or standard amino acids. These 20
are encoded by the universal genetic code. Nine standard amino acids are called "essential" for humans
because they cannot be created from other compounds by the human body, and so must be taken in as
food.
In the structure shown at the top of the page, R represents a side-chain specific to each amino acid.
The carbon atom next to the carboxyl group is called the α–carbon and amino acids with a side-chain
bonded to this carbon are referred to as alpha amino acids. These are the most common form found in
nature. In the alpha amino acids, the α–carbon is a chiral carbon atom, with the exception of glycine.[9] In
amino acids that have a carbon chain attached to the α–carbon (such as lysine, shown to the right) the
carbons are labeled in order as α, β, γ, δ, and so on.[10] In some amino acids, the amine group is attached
to the β or γ-carbon, and these are therefore referred to as beta orgamma amino acids.
Amino acids are usually classified by the properties of their side-chain into four groups. The side-chain
can make an amino acid a weak acid or a weak base, and a hydrophile if the side-chain is polar or
a hydrophobe if it is nonpolar.[9] The chemical structures of the 22 standard amino acids, along with their
chemical properties, are described more fully in the article on these proteinogenic amino acids.
The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side-chains
that are non-linear; these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid
whose side-group links to the α-amino group and, thus, is also the only proteinogenic amino acid
containing a secondary amine at this position.[9] In chemical terms, proline is, therefore, an imino acid,
since it lacks a primary amino group,[11] although it is still classed as an amino acid in the current
biochemical nomenclature,[12] and may also be called an "N-alkylated alpha-amino acid".[13]
3. Explain Ramachandran's plot.
A Ramachandran plot (also known as a Ramachandran diagram or a [φ,ψ] plot), originally
developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan,[1] is a way to
visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure.
The figure at left illustrates the definition of the φ and ψ backbone dihedral angles [2] (called φ and φ' by
Ramachandran). The ω angle at the peptide bond is normally 180°, since the partial-double-bond
character keeps the peptide planar.[3] The figure at top right shows the allowed φ,ψ backbone
conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius
in solid outline, reduced radius in dashed, and relaxed tau (N-Calpha-C) angle in dotted
lines.[4] Becausedihedral angle values are circular and 0° is the same as 360°, the edges of the
Ramachandran plot "wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values
along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.
Amino-acid preferences
One might expect that larger side chains would result in more restrictions and consequently a smaller
allowable region in the Ramachandran plot. In practice this does not appear to be the case; only the
methylene group at Cβ has a large influence. Glycine has only a hydrogen atom for its side chain, with a
much smaller van der Waals radius than the CH3, CH2, or CH group that starts all other amino acids.
Hence it is least restricted, and this is apparent in the Ramachandran plot for glycine (see Gly plot at left)
for which the allowable area is considerably larger. In contrast, the Ramachandran plot for proline, with its
5-membered-ring side chain connecting Cα to backbone N, shows only a very limited number of possible
combinations of ψ and φ (see Pro plot at left).
[edit]More
recent updates
The first Ramachandran plot was calculated just after the first protein structure at atomic resolution was
determined (myoglobin, in 1960[5]), although the conclusions were based on small-molecule
crystallography of short peptides. Now, many decades later, there are tens of thousands of highresolution protein structures determined by X-ray crystallography and deposited in the Protein Data Bank
(PDB). Many studies have taken advantage of this data to produce more detailed and accurate φ,ψ plots
(e.g., Morris et al. 1992;[6] Kleywegt & Jones 1996;[7] Hooft et al. 1997;[8] Hovmöller et al. 2002;[9] Lovell et
al. 2003[10]). The three figures at left show the datapoints from a large set of high-resolution structures and
contours for favored and for allowed conformational regions for the general case (all amino acids except
Gly, Pro, and pre-Pro), for Gly, and for Pro.[10] The most common regions are labeled: α for α helix, Lα for
lefthanded helix, β for β-sheet, and ppII for polyproline II.
4. Discuss ionic product of water and the concept of PH.
In chemistry, pH is a measure of the acidity or basicity of an aqueous solution.[1] Pure water is said to
be neutral, with a pH close to 7.0 at 25 °C (77 °F). Solutions with a pH less than 7 are said to
be acidic and solutions with a pH greater than 7 are basic or alkaline. pH measurements are important
inmedicine, biology, chemistry, agriculture, forestry, food science, environmental
science, oceanography, civil engineering and many other applications.
In a solution pH approximates but is not equal to p[H], the negative logarithm (base 10) of the molar
concentration of dissolved hydronium ions (H3O+); a low pH indicates a high concentration of hydronium
ions, while a high pH indicates a low concentration. This negative of the logarithm matches the number of
places behind the decimal point, so, for example, 0.1 molar hydrochloric acid should be near pH 1 and
0.0001 molar HCl should be near pH 4 (the base 10 logarithms of 0.1 and 0.0001 being −1, and −4,
respectively). Pure (de-ionized) water is neutral, and can be considered either a very weak acid or a very
weak base, giving it a pH of 7 (at 25 °C (77 °F)), or 0.0000001 M H+.[2] The pH has no upper or lower limit
and can be lower than 0 or higher than 14,[3]although with water, it is limited by the acidity and basicity of
water. For an aqueous solution to have a higher pH, a base must be dissolved in it, which binds away
many of these rare hydrogen ions. Hydrogen ions in water can be written simply as H + or
as hydronium (H3O+) or higher species (e.g., H9O4+) to account for solvation, but all describe the same
entity. Most of the Earth's freshwater bodies surface are slightly acidic due to the abundance and
absorption of carbon dioxide;[4] in fact, for millennia in the past, most fresh water bodies have had a
slightly acidic pH.
However, pH is not precisely p[H], but takes into account an activity factor. This represents the tendency
of hydrogen ions to interact with other components of the solution, which affects among other things the
electrical potential read using a pH meter. As a result, pH can be affected by the ionic strength of a
solution—for example, the pH of a 0.05 M potassium hydrogen phthalate solution can vary by as much as
0.5 pH units as a function of added potassium chloride, even though the added salt is neither acidic nor
basic.[5]
Hydrogen ion activity coefficients cannot be measured directly by any thermodynamically sound method,
so they are based on theoretical calculations. Therefore, the pH scale is defined in practice
as traceable to a set of standard solutions whose pH is established by international agreement. [6] Primary
pH standard values are determined by the Harned cell, a hydrogen gas electrode, using the Bates–
Guggenheim Convention.
5. Write a note on Beer-Lambert's law and it's applications.
6. Describe the structure of tRNA.
Transfer RNA (tRNA) is an adaptor molecule composed of RNA, typically 73 to 93 nucleotides in
length, that is used in biology to bridge the four-lettergenetic code (ACGU) in messenger RNA (mRNA)
with the twenty-letter code of amino acids in proteins.[1] The role of tRNA as an adaptor is best
understood by considering its three-dimensional structure. One end of the tRNA carries the genetic
code in a three-nucleotide sequence called theanticodon. The anticodon forms three base pairs with
a codon in mRNA during protein biosynthesis. The mRNA encodes a protein as a series of contiguous
codons, each of which is recognized by a particular tRNA. On the other end of its three-dimensional
structure, each tRNA is covalently attached to the amino acid that corresponds to the anticodon
sequence. This covalent attachment to the tRNA 3’ end is catalyzed by enzymes calledaminoacyl-tRNA
synthetases. Each type of tRNA molecule can be attached to only one type of amino acid, but, because
the genetic code contains multiple codons that specify the same amino acid, tRNA molecules bearing
different anticodons may also carry the same amino acid.
During protein synthesis, tRNAs are delivered to the ribosome by proteins called elongation factors (EFTu in bacteria, eEF-1 in eukaryotes), which aid in decoding the mRNA codon sequence. Once delivered,
a tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the
amino acid attached to the 3’ end of the newly-delivered tRNA, a reaction catalyzed by the ribosome.
nticodon
An anticodon[5] is a unit made up of three nucleotides that correspond to the three bases of the codon on
the mRNA. Each tRNA contains a specific anticodon triplet sequence that can base-pair to one or more
codons for an amino acid. For example, the codon for lysine is AAA; the anticodon of a lysine tRNA might
be UUU. Some anticodons can pair with more than one codon due to a phenomenon known as wobble
base pairing. Frequently, the first nucleotide of the anticodon is one of two not found on
mRNA: inosine and pseudouridine, which can hydrogen bond to more than one base in the corresponding
codon position. In the genetic code, it is common for a single amino acid to be specified by all four thirdposition possibilities, or at least by both Pyrimidines and Purines; for example, the amino acid glycine is
coded for by the codon sequences GGU, GGC, GGA, and GGG.
To provide a one-to-one correspondence between tRNA molecules and codons that specify amino acids,
61 types of tRNA molecules would be required per cell. However, many cells contain fewer than 61 types
of tRNAs because the wobble base is capable of binding to several, though not necessarily all, of the
codons that specify a particular amino acid. A minimum of 31 tRNA are required to translate,
unambiguously, all 61 sense codons of the standard genetic code.[6][7]
7. Describe the A and z forms of DNA. Elucidate the differences between A, B and z forms.
8. Describe the structure and functions of polysaccharides.Add a note on the differences
between starch and glycogen.