Cell Chemistry

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Cell chemistry
Cells: The basic units from which living organism are made, consisting of an aqueous solution of organic
molecules enclosed by a membrane. All cells arise from existing cells, usually by a process of division.
The Atom: Smallest unit of any element.
Molecules:
when two or more atoms join together, they form a Molecule.
Macromolecules: Very large molecules that make most of the structure of the body made of smaller
pieces called monomers that can be assembled to form a variety of structures. A large chain of
monomers is called a polymer.
Carbohydrates
1. Monomer: monosaccharide (sugar) 2. Polymer: polysaccharide (starch)
3. Structure: rings of carbon with oxygen and hydrogen attached; CH2O
4. Uses: energy, plant structure 5. Examples: sucrose, cellulose
Lipids
1. Monomer: fatty acid 2. Polymer: lipid or fat
3. Structure: 3 long chains of carbon hydrogen on a glycerol molecule
4. Uses: energy, structure, warmth 5. Examples: fat, oil, cholesterol
Proteins
1. Monomer: amino acid (20) 2. Polymer: protein or polypeptide
3. Structure central carbon atom with hydrogen, amine, carboxyl, & R groups
4. Uses: structure, emergency energy 5. Examples: skin, insulin, enzymes
Nucleic acids
1. Monomer: nucleotide (5) 2. Polymer: nucleic acid
3. Structure: 5-carbon sugar attachedto nitrogen base and phosphate group
4. Uses: stores genetic code 5. Examples: DNA and RNA

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Complex macromolecules Many macromolecules contain covalent or noncovalent associations of more
than one of the major classes of large biomolecules. Nucleoproteins comprise both nucleic acid and
protein. Ribosomes are large cytoplasmic ribonucleoprotein complexes which are the sites of protein
synthesis .Ribosome comprise a RNA molecules and proteins. Chromatin is a deoxyribonucleoprotein
complex made up of DNA and basic proteins called histones .These form a repeating unit called a
nucleosome. Viruses are another example of nucleoprotein complexes.
Proteins& Nucleic acids
Proteins are polymers of amino acids linked together by peptide bonds, and the nucleic acids, DNA
and RNA are polymers of nucleotides which themselves consist of a nitrogenous base, a pentose sugar
and phosphoric acid. They are both (Proteins& Nucleic acids) essential components of stores and
expresses genetic information. Nucleic acids are involved in the storage and processing of genetic
information, but the expression of this information requires proteins. Proteins have many additional
structural and functional roles.
Proteins
-Proteins are chains of amino acid monomers
-There are 20 different amino acids (All amino acids have the same general structure but the side chain
(R group) of each is different.
-A protein’s amino acid sequence determines its three-dimensional structure (conformation) and a
protein’s structure determines the function of that protein.
Protein Structure
* The shape of proteins is determined by four levels of structure
1-Primary structure: the linear sequence of amino acids which are linked by peptide bonds between
carboxyl and amino groups. The resulting polypeptide sequence has an N- terminus and a C- terminus.
2-Secondary structure: Polypeptides can fold into a number of regular structures which is stabilized by
hydrogen bonds (e.g., the helix or β sheet).
3-Tertiary structure: the overall, three-dimensional arrangement of the polypeptide chain or different
sections of secondary structure and connecting regions fold into a well-defined tertiary structure, with
hydrophilic amino acids mostly on the surface and hydrophobic ones in the interior. The structure is
stabilized by noncovalent interactions and sometimes disulfide bonds.
4-Quaternary structure: the association of two or more polypeptides into a multi-subunit complex,
Hemoglobin has two α and two β chains.

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Protein Function
Proteins have a wide variety of functions:
o Enzymes catalyze most biochemical reactions. Binding of substrate depends on specific interactions.
o Transport and storage, hemoglobin transports oxygen in the blood and ferritin stores iron in the liver.
o Collagen and keratin are important structural proteins.Actin and myosin (contractile muscle fibers).
o Casein and ovalbumin are nutritional proteins providing amino acids for growth.
o The immune system depends on antibody proteins to combat infection.
o Regulatory proteins such as transcription factors bind to and modulate the functions of other
molecules, for example DNA.
Protein analysis
-Protein purification: Proteins are purified from crude cellular extracts by a combination of methods
that separate according to different properties. Gel filtration chromatography separates by size. Ion-
exchange chromatography, isoelectric focusing and electrophoresis take advantage of the different ionic
charges on proteins. Hydrophobic interaction chromatography exploits differences in hydrophobicity.
Affinity chromatography depends on the specific affinity between enzymes or receptors and ligands
such as substrates or inhibitors.
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-Protein sequencing: After breaking a polypeptide down into smaller peptides using specific proteases
or chemicals, the peptides are sequenced from the N -terminus by sequential Edman degradation in an
automated sequencer.
-Mass determination and mass spectrometry Approximate molecular masses can be obtained by gel
filtration chromatography and gel electrophoresis in the presence of sodium dodecyl sulfate (SDS).
Mass spectrometry techniques give accurate masses for proteins of less than 100 kDa. Mass
spectrometry also detects post-translational modifications.
-Antibodies Antibodies are proteins produced by the immune system .Their high binding affinities and
specificities for the protein antigens make them useful laboratory tools for the detection, purification and
analysis of proteins.
-X-ray crystallography and NMR: Many proteins can be crystallized and their three-dimensional
structures determined by X-ray diffraction. The structures of small proteins in solution can also be
determined by nuclear magnetic resonance (NMR),

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Nucleic acids (DNA and RNA)
Nucleic acids, DNA and RNA are polymers of nucleotides which themselves consist of a nitrogenous
base, a pentose sugar and phosphoric acid. Nucleic acids are involved in the storage and processing of
genetic information.
Bases: The bases of DNA and RNA are aromatic rings (Fig. 1). Adenine (A) and guanine (G) are
purines, bicyclic structures whereas cytosine (C), thymine (T) and uracil (U) are monocyclic
pyrimidines. In RNA, the thymine base is replaced by uracil.
Nucleosides A nucleoside consists of a base covalently bonded to the 1'-position of a pentose sugar
molecule. In RNA the sugar is ribose and the compounds are ribonucleosides, or nucleosides, whereas
in DNA it is 2'-deoxyribose and the nucleosides are named 2'-deoxyribonucleosides, or just
deoxynucleosides. Base + sugar = nucleoside.
Nucleotides: Nucleotides are nucleosides with one or more phosphate groups covalently bound to the
3'-, 5'- or (in ribonucleotides) the 2'-position. If the sugar is deoxyribose, then the compounds are termed
deoxynucleotides (Fig. 3) In the case of the 5'-position, up to three phosphates may be attached, to
form, for example, adenosine 5'-triphosphate, or deoxyguanosine 5'-triphosphate, commonly abbreviated
to ATP and dGTP respectively.In the same way, we have dCTP, UTP and dTTP (equivalent to TTP). 5'-
Mono and -diphosphates are abbreviated as, for example, AMP and dGDP. Nucleoside 5'-triphosphates
(NTPs), or deoxynucleoside 5'-triphosphates (dNTPs) are the building blocks of the polymeric nucleic
acids..The repeat unit of a DNA or RNA chain is hence a nucleotide. Base + sugar +phosphate =
nucleotide

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Phosphodiester bonds: In a DNA or RNA molecule, deoxyribonucleotides or ribonucleotides
respectively are joined into a polymer by the covalent linkage of a phosphate group between the 5'-
hydroxyl of one ribose and the 3'-hydroxyl of the next (Fig. 4).This kind of bond or linkage is called a
phosphodiester bond, since the phosphate is chemically in the form of a diester. A nucleic acid chain can
hence be seen to have a direction. Any nucleic acid chain, of whatever length (unless it is circular, has a
free 5'-end, which may or may not have any attached phosphate groups, and a free 3'-end, which is most
likely to be a free hydroxyl group. At neutral pH, each phosphate group has a single negative charge.
This is why nucleic acids are termed acids; they are the anions of strong acids. Nucleic acids are thus
highly charged polymers.
Properties of nucleic acids
Effect of alkali: High pH denatures DNA and RNA by disrupting specific hydrogen bonding. RNA is
also susceptible to hydrolysis at high pH, by participation of the 2'-OH in intramolecular cleavage of the
phosphodiester backbone.

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Stability of nucleic acids Although it might seem obvious that DNA double strands and RNA structures
are stabilized by hydrogen bonding, this is not the case. H-bonds determine the specificity of the base
pairing, but the stability of a nucleic acid helix is the result of hydrophobic and dipole–dipole
interactions between the stacked base pairs.
Effect of acid: Highly acidic conditions may hydrolyze nucleic acids to their components: bases, sugar
and phosphate. Moderate acid causes the hydrolysis of the purine base glycosylic bonds to yield a
purinic acid. More complex chemistry has been developed to remove particular bases, and is the basis of
chemical DNA sequencing.
Chemical denaturation : Some chemicals, such as urea and formamide, can denature DNA and RNA at
neutral pH by disrupting the hydrophobic forces between the stacked bases.
Viscosity: DNA is very long and thin, and DNA solutions have a high viscosity. Long DNA molecules
are susceptible to cleavage by shearing in solution, this process can be used to generate DNA of a
specific average length.
UV absorption The aromatic bases of nucleic acids absorb light with a max of 260 nm.
Hypochromicity: The extinction coefficient of nucleic acid bases depends on their environment. The
absorbance of isolated nucleotides is greater than that of RNA and single stranded DNA, which is in
turn greater than that of double-stranded DNA. Double-stranded DNA is hypochromic with respect to
single-stranded DNA.
Quantitation of nucleic acids:The absorbance at 260 nm is used to determine the concentration of
nucleic acids. At a concentration of 1 mg/ ml and 1 cm path length, double-stranded DNA has A260 =
20. RNA and single-stranded DNA have A260 = 25. The values for RNA and single-stranded DNA
depend on base composition and secondary structure.
Purity of DNA The A260/A280 ratio of a double-stranded DNA sample can be used to assess its purity.
For pure DNA, the value is 1.8. Values above 1.8 suggest RNA contamination and those below 1.8
suggest protein contamination.
Thermal denaturation: Increased temperature can bring about the denaturation of DNA and RNA.
RNA denatures gradually on heating, but double-stranded DNA ‘melts’ cooperatively to give single
strands at a defined temperature, Tm, which is a function of the G+C content of the DNA. Denaturation
may be detected by the change in A260.
Renaturation DNA: renatures on cooling but will only form fully double-stranded native DNA if the
cooling is sufficiently slow to allow the complementary strands to anneal.