biological molecule

Question 1

cohesion and adhesion

Answer 1

• COHESION: is the attraction among water molecules
  ADHESION: is the attraction among water molecules and polar surface

Question 2

Biochemistry

Answer 2

• Biochemistry is a branch of biology which deals with the study of chemical
  components and the chemical processes in living organisms.
• All living organisms are made of organic and inorganic compounds.
• Inorganic substances in living organisms are water, carbon dioxide, acids, bases, and
  salts etc.

Question 3

Some Basics Of Biochemistry

Answer 3

• Living organisms contain macromolecules formed from a small number of simple
  molecules.
• These simple molecules suggest that all life had a common origin.
• The characteristics of an organism are determined by the information contained in its
  DN.
• The DNA contains information that the cell can use to make proteins. Many proteins
  are enzymes, which control the physical and chemical activities of an organism.
• The chemical activities that go on inside an organism can organism can be given the
  general term metabolism.
• Metabolic reactions can be divided into two general categories: anabolic and
  catabolic. Anabolic reactions build up large molecules from smaller ones. While:
  catabolic reactions do the reverse, breaking down larger molecules.
• Anabolic reactions usually involve condensation reactions ill which building-block
  molecules are joined together and a water molecule is released.
• Catabolic reactions, such as those that occur during digestion, usually involve
  hydrolysis reactions in which larger molecules are split as they react with water.
• In photosynthesis, plants use the energy from sunlight to build up organic molecules
  such as sugars from simple ones such as carbon dioxide and water.
• All organisms need a supply of energy, which they obtain via respiration. In respiration
  organic molecules are oxidized into simpler molecules, usually carbon dioxide and
  water. The resulting energy is used to fuel many energy-requiring processes within the
  organism.

Question 4

Water Importance

Answer 4

§ Water is the medium of life.
§ It is the most abundant compound in all organisms. It
varies from 65 to 89 percent in different organisms.
§ Human tissues contain about 20 per cent water in bone
cells and 85 per cent in brain cells.
§ Almost all reactions of a cell occur in the presence of
water. It also takes part in many biochemical reactions
such as hydrolysis of macromolecules.
§ It is also used as a raw material in photosynthesis.
* Ionic substances when dissolved in water, dissociate into
positive and negative ions.
* Non-ionic substances having charged groups in their
molecules are dispersed in water.
* When in solution, ions and molecules move randomly and are in a more favorable state
to react with other molecules and ions. It is because of this property of water that almost
all reactions in cells occur in aqueous media. In cells all chemical reactions are catalyze by
enzymes which work in aqueous environment.
* Non-polar organic molecules, such as fats, are insoluble in water and help to maintain
membranes, which make compartments in the cell.
* Water has great ability of absorbing heat with minimum of change in its own temperature.
* The specific heat capacity of water – the number of calories required to raise the
temperature of 1g of water from 15 to 16°C is 1.0. This is because much of the energy is
used to break hydrogen bonds. Water thus works as temperature stabilizer for organisms
in the environment. Protects living material against sudden thermal changes.
* Water absorbs much heat as it changes from liquid to gas. “Heat of vaporization is
expressed as calories absorbed per gram vaporized.” The specific heat of vaporization of
water is 574 Kcal/kg, which plays an important role in the regulation of heat produced by
oxidation.
* It also provides cooling effect to plants when water is transpired.

Question 5

imp points 1

Answer 5

To animals when water is perspired. Evaporation of only two ml out of one liter of water,
lowers the temperature of the remaining 998 ml by 1°C.
H2O H+ + OH-
* The water molecules ionize to form H+ and OH- ions:
* This reaction is reversible but an equilibrium is maintained. At 25°C the concentration
of each of H+ and OH- ions in pure water is about 10-7 mole/litre.
* The H+ and OH- ions affect, and take part in many of the reactions that occur in cells
* Water is effective lubricant that provides protection against damage resulting from
friction.
* Tears protect the surface of eye from the rubbing of eyelids.
* Water also forms a fluid cushion around organs that helps to protect them from
trauma.

Question 6

Carbohydrates

Answer 6

• Carbohydrates are polyhydroxy aldehydes or ketones, or complex substances which
  on hydrolysis produce polyhydroxy aldehyde or ketone subunits.
• Three major groups of Carbohydrates are: Monosaccharides, Oligosaccharides &
  Polysaccharides.
• General formula for Carbohydrates is Cx(H2Q)y. General formula for monosaccharides
  is (CH2O)n. General formula of oligosaccharides is Cx(H2O)y – General formula of
  polysaccharides is Cx(H2O)y –.
• Monosaccharides: These are generally Trioses, Tetroses, Pentoses. Hexoses &
  Heptoses. Examples of trioses are dihydroxy acetone and glyceraldehyde’s. These are
  also intermediates in respiration and photosynthesis. Examples of Hexose”, Glucose,
  Galactose, Fructose etc.
• Oligosaccharides: These have 2 – 10 Monosaccharides. If two Monosaccharides then
  it is a Disaccharide. Examples of Disaccharides are: Maltose, Lactose and Sucrose etc.
• Polysaccharides: These have more than ten Monosaccharides. Examples are
  Cellulose. Starches and Glycogen etc. Most abundant polysaccharide is Cellulose.
• Polysaccharides are usually branched.
• Cellulose present in wood, cotton and paper.
• Starches present in cereals and root tubers etc.
• In biology the most important hexose is glucose. Our blood normally contains 10.08 %
  glucose.
• For the synthesis of 10 g of glucose 717.6 Kcal of solar energy is used.
  *Glucose is aldose sugar. Fructose is ketose sugar. Fructose is sweeter as compared to glucose.

Question 7

Monosaccharide

Answer 7

Types: Glucose, fructose, Galactose
sources: fruits and Vegetable
Function: Provide energy converted to glycogen
for storage

Question 8

Disaccharide (double/complete sugar)

Answer 8

Types: Sucrose, Maltose, Lactose
sources: Sugar cane,Beat root, Milk
Function: Excess is stored as fat

Question 9

Polysaccharide

Answer 9

Types: Starch,Cellulose,Glycogen
sources: Rice, Cereal, Bread
Function: Used in synthesis of many complex molecules

Question 10

Starch

Answer 10

• Starch is compact, insoluble and IS a mixture of two compounds, amylase and
  amlyopectin.
• Amylose is an un-branched polymer in which glucose monomers are joined by α-1 4-
  glycosidic linkages. They are soluble in hot-water.
• Amylopectin molecule α-1, 4-glycosidic linkages and α-1, 6-glycosidic linkages. This
  allows branching. They arc “Insoluble in hot or cold water.

Question 11

Glycogen

Answer 11

• In humans, glycogen is the main storage carbohydrate. Its structure is similar to
  amylopectin, but it is even more frequently branched.
• In humans, glycogen is stored in large amounts in the liver and the muscles. During
  prolonged exercise, when the immediate supply of glucose is used up, the body
  restores its supplies by breaking down glycogen.
• If an average person goes without food, his or her glycogen stores last for about a day.
  When glycogen runs out, the body turns to using its lipid store. This is why eating less
  while taking more exercise is the quicker way to lose weight.
• One of the major changes associated with improving fitness is an increase in the
  amount of the enzyme glycogen synthetase in the muscles. This allows glycogen to be
  built up faster after it has been used.

Question 12

Cellulose

Answer 12

• Cellulose is a structural polysaccharide. It gives strength and rigidity to plant cell walls.
• Individual cellulose molecules are long un-branched chains containing many β-1, 4-
  glycosidic linkage. The molecules are straight, side by side and are called microfibrils.
• Cellulose is probably the most abundant structural chemical on Earth but few animals
  can digest it because they do not make the necessary enzyme, cellulose. Herbivorous
  animals, whose diet contains large amounts of cellulose, can deal with it because they
  have cellulose-producing microorganisms in their digestive system.

Question 13

Lipids

Answer 13

§ Lipids are heterogeneous group
of compounds that include fats
and oils.
§ As they are non-polar molecules,
most lipids are insoluble in
water but soluble in nonpolar
solvents such as alcohol and
ether. Important exceptions are
phospholipids, which have polar
heads,
§ Lipids contain the elements
carbon, hydrogen, oxygen and sometimes phosphorus and nitrogen.
§ They are intermediate-sized molecules that do not achieve the giant sizes of the
polysaccharides, proteins and nucleic acids.

Question 14

Lipid Structure And Function

Answer 14

• The triglycerides, which act mainly as energy stores in animals and plants, are a large
  important group of lipids.
• Triglycerides consist of one molecule of glycerol and three fatty acids.
• The glycerol molecule is common to all triglycerides and so the properties of different
  triglycerides depend on the nature of the fatty acids. Monounsaturated fatty acids
  possess one C=C bond and polyunsaturated contain more than one.

Question 15

Phospholipids

Answer 15

• Phospholipids are derivatives of phosphatidic acid. The phosphatidic acid is composed
  of glycerol, fatty acids and phosphoric acid.
• Phosphatidylcholine is one of the common phospholipids.
• Phospholipids have a similar structure to triglycerides but one of the fatty acids is
  replaced by polar phosphoric acid.
• This gives the molecule a polar head and a non-polar tail. When placed in water,
  phospholipids arrange themselves with their hydrophobic (water-hating) tails pointing
  inwards and their hydrophilic (water-loving) heads pointing outwards. This is very
  important because it results in double layers called bilayers. Phospholipid bilayers
  form the basis of all biological membranes.

Question 16

Cholesterol

Answer 16

• This lipid is a normal component of every cell in our body. As well as eating food that
  contains cholesterol, we can also synthesis cholesterol in the liver.
• The more there is in the diet the less the liver needs to make.
• Vegetarians who eat no animal products are easily able to make all the cholesterol
  they need.

Question 17

Steroid Hormones

Answer 17

• Steroid hormones have a similar structure to the cholesterol from which they are
  made.
• They include testosterone, progesterone and the estrogens.

Question 18

Waxes

Answer 18

• Waxes are lipids that are often used to waterproof surface, so preventing water loss.
• The cuticle of a leaf and the protective covering on an insect’s body are both waxes.
• Waxes are mixtures of long chain alkanes (C25 to C35 odd numbers), alcohols, ketones
  and esters of long chain fatty acids.
• They have no nutritional value because they cannot be digested by lipases (lipid
  digesting enzymes).

Question 19

Summary of Lipids

Answer 19

1. Lipids are a heterogeneous group of compounds related to fatty acids.
2. Lipids are classified as acylglycerols, waxes, phospholipids, sphingolipids, glycolipid
   and terpenoid lipids (including carotenoids and steroids).
3. Acylglycerols are esters of fatty acids and alcohol.
4. An ester is produced as a result of a reaction of an alcohol with an acid and a water
   molecule is released.
5. Fatty acids having no double bond are called saturated fatty acids while the fatty acid
   having double bonds between carbon atoms are called unsaturated fatty acids.
6. Palmitic acid (C16) is much more soluble in the organic solvent than butyric acid (C4)·
7. Fats and oils are lighter than water and have a specific gravity of about 0.8.
8. Higher fat contents of food cause slower movements of feces through the bowels.
   Bacteria in food convert the undigested fats into cancer causing compounds.
9. Terpenoids is a large group of compounds which are made up of simple repeating
   isoprenoid units (C5H8).

Question 20

Proteins

Answer 20

1. Proteins are polymers of amino acids. the compounds containing carbon, nitrogen,
   oxygen and hydrogen.
2. Proteins are the most abundant organic compounds in cells. They are over 50 of total
   dry weight of the cell.
3. About 170 types of amino acids are present in the cells and tissues of these about 25
   types are involved in the formation of proteins. However, most of the proteins are
   made of 20 types of amino acids.
4. The linkage between C of carboxyl group of one amino acid and N of amino group of
   next amino acid is called peptide bond.
5. Glycylalanine has two amino acids and is called dipeptide.
6. Each protein has specific properties which are due to: Number of amino acids. Kinds
   of amino acids specific sequence of amino acids and the shape of protein molecule.
7. Sanger was the first scientist who determined the sequence of amino acids in a protein
   molecule.
8. Insulin is composed of 51 amino acids in two chains. One with 21 amino acids and the
   other with 30 amino acids. Both the chains are linked by disulphide bonds.
   Hemoglobin is composed of four chains two alpha and two beta chains. Each alpha
   chain contains 141 amino acids which each beta chain contains 146 amino acids.
9. There are over 10.000 proteins in the human body. These are formed by the specific
   arrangements of 20 types of amino acids.
10. The sequence of amino acids is determined by the order of nucleotides in the DNA.
11. In the sickle cell hemoglobin only one amino acid (Glutamic acid) in each beta chain
    out of the 574 amino acids does not occupy the normal place in the proteins.
    Actually, glutamic acid is replaced by valine. Therefore, hemoglobin fails to carry
    sufficient oxygen. The result is the death of the patient.
12. Secondary structure of proteins is the coiling of primary polypeptide chains.
13. α helix is very uniform geometric structure with 3.6 amino acids in each turn of the
    helix
14. Tertiary protein structure is formed when a polypeptide chain bends and folds upon
    itself forming a globular shape.
15. Quaternary proteins are polymers of several tertiary structures.
16. All enzymes are proteins (e.g. amylase, lipase, pepsin etc). Enzymes control the cell
    metabolism.
17. Some hormones are proteins (e.g. insulin). Hormones regulate metabolic processes.
18. Antibodies (Immunoglobulins) are proteins which protect the body from pathogens.
19. Blood clotting proteins (like fibrinogens) prevent the loss of blood from the body after
    injury.
20. Movement of organs and organisms are caused by proteins (e.g. actin and mysosin et.
    are involved).
21. Movement of chromosomes during anaphase of cell division, are caused by proteins
    (tubuis are involved).
22. The term protein is for the finished, functional molecule.
23. Some proteins consist of one polypeptide, others consist of two or more than two
    hemoglobin for example, contains four polypeptides.
24. Amino acids join together in long chains to form proteins by means of peptide bond.
    This is an example of a condensation reaction.

Question 21

Primary Structure

Answer 21

• The primary structure of proteins depends upon the number, kind (types) and sequent
  of amino acids in a protein molecule.
• Real proteins usually consist of a lot more than five amino acids. The hormone
  insulin for example for example the relatively small protein has 51 amino acids.
• The code for the primary structure of any protein is contained in the gene. This code
  determines the order in which amino acids are assembled. This order then dictates
  the way they will twist and turn to produce the three-dimensional shape that allows
  the protein to carry out its specific function.

Question 22

Secondary Structure

Answer 22

§ The first level of three-dimensional twisting
is described as the secondary structure of
the protein.
§ When combinations of amino acids join
together in a chain they fold into particular
shapes and patterns (such as spirals).
§ These shapes form because the amino
acids twist around to achieve the most
stable arrangement of hydrogen bonds.
The main types of secondary structure in
proteins are:
§ The α-helix, a spiral, is the most common
type of secondary structure. The hydrogen
bonds stabilize the α-helix.
§ The β-pleated sheet, a flat structure that
consists of two or more amino acid chains
running parallel to each other, linked by
hydrogen bonds.
§ The secondary structure of a protein
depends on its amino acid sequence; some
amino acids produce α-helices. Others
usually make β-pleated sheets.

Question 23

Tertiary Structure

Answer 23

• The tertiary structure of a protein is its overall three-dimensional shape and is produce
  as a result of the following:
• The sequence of amino acids that produces a-helices &β-sheets bends at particular
  places.
• The hydrophobic nature of many amino acid side chains. Globular proteins are
  surrounded by water and so the hydrophobic side chains tend to point inwards.
• Tertiary structure is maintained by ionic bonds, hydrogen bonds and disulfide (-S-S-)
  bonds.
• Functional proteins, such as enzymes and antibodies, must have an exact shape-and
  sometimes the ability to change shape - to fulfill their role in the organism.
• Many structural proteins depend on their tertiary structure for strength. The large
  number of disulphide bridges in keratin, of example, makes body structures such as
  hair and nails very tough.
• If a protein consists of only one polypeptide, the tertiary structure is the final shape
  of the molecule. If, however, the protein has more than one, it has a further,
  quaternary level of structure.

Question 24

Quaternary Structure

Answer 24

Quaternary proteins are polymers of several tertiary structures.
In quaternary structure, the highly complex polypeptide tertiary chains are aggregated
held together by:
(i) hydrophobic interactions
(ii) hydrogen bonds and
(iii) ionic bonds

Question 25

Fibrous And Globular Proteins

Answer 25

• The final three-dimensional structure of proteins results in two main classes of protein
• fibrous and globular.
• Fibrous proteins contain polypeptides that bind together to form long fibers or
  sheets. They are physically tough and are insoluble in water.
• Globular proteins are usually individual molecules with complex tertiary and quaternary
  structures. They are spherical, or globular in shape, hence the name. Most are soluble in
  water and they have a biochemical function.

Question 26

Stability of Proteins

Answer 26

§ As the final shape of globular proteins is maintained by relatively weak molecular interactions such
as hydrogen bonds, proteins are very sensitive to temperature increases and other changes in their
environment.
§ As the temperature goes up beyond 40° C, molecular vibration increases and bonds that· are
holding together the tertiary or quaternary structure break, changing the shape of the molecule.
This is known as denaturation.
§ Different proteins are denatured at different temperatures. Some begin to be denatured after
about 40-45o C or even below but many are not totally denatured until 60° C or even higher.
§ It is an oversimplification to say organisms die at temperatures over 44° C because their proteins
become denature. In practice organisms die because of a metabolic imbalance caused when
enzymes work at different rate.
§ Proteins can also be denatured by adverse chemical conditions. Chemicals that affect weak bonds
change the overall structure. Even a slight change in protein shape mean loss of function, some
proteins are particularly sensitive to changes in pH

Question 27

Nucleic Acids

Answer 27

• Nucleic acids are so called because they are slightly acidic and present mainly in the
  nucleus.
• The two types of nucleic acid, DNA and RNA both contain carbon, hydrogen, oxygen,
  nitrogen and phosphorus.
• Nucleic acids are polymers of nucleotides.
• Nucleotides are the building blocks of nucleic acids. A nucleotide consists of three units:
• A sugar (ribose or deoxyribose)
• A phosphate group
• A nitrogen-containing base
• In a typical nucleotide the nitrogenous base is
  attached to position 1 of pentose sugar, while
  phosphoric acid is attached to carbon at position 5 of
  pentose sugar.
• DNA has nucleotides in which the sugar is
  deoxyribose, while RNA contains the sugar ribose.

Question 28

Deoxyribonucleic Acid (DNA)

Answer 28

• A German chemist, Friedrich Miescher, discovered DNA in
  1869. Miescher extracted a, white substance from the
  nuclei of human cells and fish sperm. He called this substance nuclein because it was associated
  with the nucleus. Since nuclein was acidic, it was called as nucleic acid.
• Most of the DNA in a eukaryotic cell is in the nucleus and in very less amount in Mitochondria
  and Chloroplasts.
• The nucleotides in DNA contain the nitrogenous (nitrogen-containing) bases
  which are adenine, guanine, cytosine or thymine.
• Names of four nucleotides of DNA are:
  o d-adenosine monophosphate (d-AMP)
  o d-guanosine monophosphate (d-GMP)
  o d-cytidine monophosphate (d-CMP)
  o d-thymidine monophosphate (d-TMP)
• When DNA replicates (copies itself), it makes new strands by
  adding nucleotides. These are available as free molecules in
  the cytoplasm. Generally, cells can synthesize their own
  nucleotides.
  Genetic Code
  DNA has two remarkable
  characteristics:
• It is a store of genetic
  information.
• It can copy itself
  exactly, time after time.

Question 29

DNA parts

Answer 29

Base pair
* Adenine and guanine are purines (large/double ring) while thymine and cytosine are pyrimidines
(small/single ring).
* Because of the shape of the two types of molecules, each purine always bonds with only one
pyrimidine. So, in DNA, adenine always bonds with thymine, and cytosine with guanine. In RNA,
cytosine bonds with guanine and adenine bonds with uracil:
DNA: A = T RNA: A = U
G = C G = C
* The base pairs are held together by hydrogen bonds. There are two H-bonds between A and T
(or U) and three between C and G.
* A nucleotide has ester bond. A polynucleotide chain has phosphodiester bonds.
* In phosphodiester linkage, one phosphate group is linked to the two sugars by means of a pair of
esters (P-O-C) bonds.
* According to Erwin Chargaff the quantity of A and T are almost equal. Similarly, the quantity of G
and C are almost equal. It means A with T and G with C in DNA double strand.
* British Chemist Rosalind Franklin carried on an X-ray diffraction analysis of DNA in the Lab of
Maurice Wilkins.
* Maurice Wilkins (British biochemist) prepared DNA fibers.
* The diffraction pattern suggested that the DNA molecule had a shape of a helix with a diameter
of2 nm and a complete helical turn every 3.4 nm.
* James Watson and Francis crick proposed structure of the DNA molecule.
* In DNA the sides are formed by alternating sugar-phosphate units, while the base pairs form the
cross-bridges, like the rungs of a ladder. Each base pairing causes a twist in the helix and there is
a complete 360o turn every 10 base pairs.
* DNA & Histones form Eukaryotic chromosomes.
* A gene is a unit of biological inheritance.
* The E. coli genome consists of 4,639,221 base pairs. It codes for about 4288 proteins.
* The first microbe whose genome is completely sequenced is Haemophilus influenza. It was
published in July 28, 1995.

Question 30

Ribonucleic Acid (RNA)

Answer 30

§ RNA is synthesized ‘by DNA in a
process known as transcription.
§ RNA is present in the
Nucleus/nucleolus, ribosomes,
cytosol and in smaller amounts in
other parts of the cell.
§ The RNA molecule has single
strand. It may fold back on itself
to give double helix.
§ ATP is highly unstable nucleotide.
It is used as energy currency by
the cell.
§ All types of RNA’s are synthesized’ from DNA in the nucleus and then are moved out in
the cytoplasm to perform their specific functions.
§ Three of the bases in RNA - adenine guanine and cytosine - are the same as those it
DNA. The fourth is different: RNA contains uracil instead of thymine.
§ RNA molecules are much smaller than DNA molecules.
§ DNA can consist of over 300,000,000 nucleotides. RNA usually consists of a few hundred.
§ RNA is also less stable.
§ DNA molecules are the permanent store for genetic information and last for many years.
In contrast, RNA molecules have a short-term function and are easily replaced.
§ There are three forms of ribonucleic acid (RNA) in the cell:
§ Small lengths of mRNA are assembled in the nucleus using a single gene within the DNA
as a template. When a complete copy of the gene has been produced the mRNA moves
out of the nucleus to the ribosome, where the protein is synthesized according to thecode taken from the DNA. For a protein molecule of 1000 amino acids, the length of
mRNA will be 3,000 nucleotides. The mRNA is about 3to 4 % of the total RNA in the cell.
§ Transfer RNA is found in the cytoplasm and is a carrier molecule, bringing amino acids to
the ribosomes for assembly into a new amino acid chain according to the order specified
on the mRNA code. There is one specific tRNA for each kind of amino acid. So there are
at least 20 kinds of tRNAs in the cell. tRNAs are about 10 to 20% of the total RNA in the
cell. Human cells contain about 45 different kinds of tRNA molecules.
§ Ribosomal RNA makes up part of the ribosome. Ribosomal RNA is up to 80 % of the total
RNA in the cell. In ribosome, rRNA is 40 – 50 %. During translation, rRNA provides the
site where polypeptides arc assembled.