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STUDY MATERIAL FOR THE COURSE
BICM -101, BIOCHEMISTRY (2+1)
Department of Biochemistry
College of Agriculture
Rajendranagar
Hyderabad
NAME - AMIT NAGAR
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Study Material for BICM-101 Biochemistry Course, Study notes of Biochemistry
Study material for the BICM-101 Biochemistry course offered by the Department of Biochemistry at the College of Agriculture in Hyderabad. It includes a list of contributors who prepared the study material and a brief overview of the history of DNA research. The document also provides information on the structure and function of plant cells and their organelles, including the cell wall, cytoplasm, nucleus, mitochondria, chloroplasts, ribosomes, endoplasmic reticulum, golgi complex, lysosomes, and plastids.
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STUDY MATERIAL FOR THE COURSE
BICM -101, BIOCHEMISTRY (2+1)
Department of Biochemistry College of Agriculture Rajendranagar Hyderabad
Contributors for the preparation of study material
Editor Dr(Mrs) S.Sumathi Professor & University Head Department of Biochemistry College of Agriculture Rajendranagar Hyderabad
S.No Name of the teacher No of lectures prepared
1
2
3
4
Mrs J.Aruna Kumari
Dr(Mrs) Nirmala Jyothi
Mr. Raghavendra
Dr. Sarkar
In 20th^ century, the growth was very fast in the field of biochemistry. Full
structures of many compounds were formulated for eg: ATP structure by Fiske
and Subbarow. The first metabolic pathway elucidated was the glycolytic
pathway during the first half of the 20th^ century by Embden and Meyerhof. Otto
Warburg, Cori and Parnas also made very important contributions relating to
glycolytic pathway. Krebs established the citric acid and urea cycles during
1930-40. In 1940, Lipmann described the central role of ATP in biological
systems.
The biochemistry of nucleic acids entered into a phase of exponential
growth after the establishment of the structure of DNA in 1953 by Watson and
Crick followed by the discovery of DNA polymerase by Kornberg in 1956. From
1960 onwards, biochemistry plunged into an interdisciplinary phase sharing much
in common with biology and molecular genetics.
Frederick Sanger’s contributions in the sequencing of protein in 1953 and
nucleic acid in 1977 were responsible for further developments in the field of
protein and nucleic acid research.
Some important scientists and their contribution to biochemistry you study 1828 Wohler Synthesized the first organic compound, urea from
inorganic components
1854-
1864
Louis Pasteur Proved that fermentation is caused by microorganisms
1877 Kuhne Proposed the term ‘Enzyme’
1894 Emil Fischer Demonstrated the specificity of enzymes and the
lock and key relationship between enzyme and substrate
1897 Buckner Discovered alcoholic fermentation in cell-free yeast
extract
1902 Emil Fischer Demonstrated that proteins are polypeptides
1903 Neuberg First used the term ‘biochemistry’
1913 Michaelis and
Menten
Developed kinetic theory of enzyme action
1926 Sumner First crystallized an enzyme, urease and proved it to
be a protein
1933 Embden
Meyerhof and Parnas
Demonstrated crucial intermediates in the chemical pathway of glycolysis and fermentation
1937 Krebs Discovered citric acid cycle
1940 Lipmann Role of ATP in biological systems
1950 Pauling and
Corey
Proposed the α-helix structure for keratins
Chargaff Discovered the base composition of DNA
1953 Sanger and
Thompson
Determined the complete amino acid sequence of insulin
1953 Watson and
Crick
Proposed the double-helical model for DNA structure
1958 Meselson and
Stahl
Confirmed the Watson-Crick model of semi conservative replication of DNA
1961 Jacob &
Monod
Proposed the operon hypothesis and postulated the function of messenger RNA
1999 Ingo potrykus (^) Golden rice- rich in β-carotene
PLANT CELL
The word cell was coined by Robert Hooke with the help of compound microscope. Cell is the basic unit of life. A plant cell has three distinct regions a. Cell wall b. Protoplasm c. Vacuole Cell wall and vacuole are considered as non-living substances. The protoplasm which is living has two components
- Cytoplasm
- Nucleus The cytoplasm contains several organelles such as mitochondria, chloroplast, ribosomes, endoplasmic reticulum, golgi complex, lysosomes, plastids etc.
Cell nucleus : It is oval or spherical in shape and is generally larger in active cells than in resting cells. A nucleus consists of three main parts viz. nuclear envelope, nucleolus and chromatin. The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope. The space between the outer and inner membrane is known as nuclear pores which provide direct connection between nucleus and cytoplasm. Nucleolus is a spherical, colloidal body found in the nucleus and is the place where almost all DNA replication and RNA synthesis occur. Chromatin is the basic unit of chromosome and contains genes which play important role in the inheritance of characters to offspring from parents.
Functions of cell nucleus :
- It regulates growth and reproduction of cells.
- The nuclear envelope allows the nucleus to control its contents, and separate them from the rest of the cytoplasm where necessary.
- The DNA replication, transcription and post transcriptional modification occur in the nucleus.
Chloroplast : Chloroplasts are organelles found in plant cells and other eukaryotic organisms that perform photosynthesis because of the presence of green pigment, chlorphyll. They are flattened discs usually 2-10 micrometers in diameter and 1 micrometer thick. The chloroplast is surrounded by double layered membrane. The space between these two layers is called intermembrane space. Stroma is the aqueous fluid found inside the chloroplast. The stroma contains the machinery required for carbon fixation, circular DNA, ribosomes etc. within the stroma the stacks of thylakoids are arranged as stacks called grana. A thylakoid has a flattened disc shape and has a lumen or thylakoid space. The light reactions occur on the thylakoid membrane.
Functions of chloroplast :
- The important processes of photosynthesis i.e, light and dark reactions occur within the chloroplast.
- The granum is the site of NADP reduction forming NADPH+H +^ and photophosphorylation i.e., formation of ATP in presence of light. Thus, light reaction of photosynthesis takes place in the granum region.
- The stroma is the main site for the dark reaction of photosynthesis.
- The chloroplast has its own genetic system and is self replicating. Thus, associated with cytoplasmic inheritance.
Mitochondria : Mitochondria are rod shaped cytoplasmic organelles, which are main sites of cellular respiration. Hence, they are referred to as power house of the cell. Each mitochondrion is enclosed by two concentric unit membranes comprising of an outer membrane and an inner membrane. The space between the two membranes is called perimitochondrial space. The inner membrane has a series of infoldings known as cristae. The inner space enclosed by cristae is filled by a relatively dense material known as matrix. The matrix is generally homogeneous, but may rarely show finely filamentous or fibrous structures. The matrix contains several copies of round or circular DNA molecules. Functions of mitochondria:
- ATP, the readily available form of energy is produced in mitochondria.
- Krebs cycle takes place in the matrix of mitochondria
- The enzymes of electron transport chain are found in the inner membrane or cristae of mitochondria.
- Heme synthesis occurs in mitochondria.
- Controls the cytoplasmic Ca+2 concentration
Ribosomes : Chemically, ribosomes are ribonucloprotein complexes. Ribosomes are of two types. Ribosomes of prokaryotes have sedimentation coefficient of 70 S and consist of two sub units of unequal sizes 50S and 30 S subunits. Ribosomes of eukaryotes have 80 S sedimentation coefficient (40S & 60 S). The two or more ribosomes become connected by a single m RNA and then may be called polyribosome The major function of the smaller subunit of ribosome is to provide proper site for binding of mRNA and its translation. The larger subunit of ribosome supports translation and translocation processes coupled with polypeptide synthesis.
Functions of Ribosomes :
- They provide the platform for protein synthesis
- They have the machinery for protein synthesis.
Golgi complex: Golgi bodies is an assemblage of flat lying cisternae one above the other in close parallel array. Each golgi complex has 3 to 12 interconnected cisternae which are composed of lipoproteins.
Functions of Golgi complex:
- It helps in Packaging of proteins for exporting them.
- It plays a role in sorting of proteins for incorporation into organelles.
- It is involved in the formation of the cell wall of plant cells
Endoplasmic reticulum: Endoplasmic reticulum arises from the outer membrane of the nucleus forming an intermediate meshed network. It is of two types. The granular or rough endoplasmic reticulum in which the outer surface of endoplasmic reticulum is studded with ribosome and agranular or smooth endoplasmic reticulum in which the ribosomes are not attached.
Functions of Endoplasmic reticulum :
- Rough endoplasmic reticulum is associated with the synthesis of proteins.
- Smooth endoplasmic reticulum is associated with synthesis of lipids and glycogen.
- It acts as an inter-cellular transport system for various substances.
- It contains many enzymes which perform various synthetic and metabolic activities.
Vacuole: It is a membrane bound organelle found in plant cell and occupies most of the area in the plant cell. A vacuole is surrounded by a membrane called tonoplast. It is an enclosed compartment filled with water containing inorganic and organic molecules including enzymes in solution.
Functions of vacuole:
- Isolating materials that might be harmful or a threat to the cell.
- Stores waste products.
- Maintains internal hydrostatic pressure or turgor within the cell
- Maintains an acidic internal pH
- Exports unwanted substances from the cell
- Allows plants to support structures such as leaves and flowers due to the pressure of the central vacuole.
- Most plants stores chemicals in the vacuole that react with chemicals in the cytosol.
- In seeds, stored proteins needed for germination are kept in protein bodies which are modified vacuole.
Microbodies : Microbodies are ubiquitous organelles found in the majority of
eukaryotic plant cells. They are mostly spherical and have a diameter ranging
- Defines cell’s position within the plant
- Cell- cell and cell- nucleus communication
- Defense against pathogens
- Recognises symbiotic nitrogen fixing bacteria
- Recognises self
Cell wall is made up of three layers. They are a) Middle lamella: This is the first layer formed during cell division. It makes up the outer wall of the cell. It is shared by adjacent cells. It is composed mainly of pectic compounds and proteins
b) Primary wall: Primary wall deposited by cells before and during active growth. Plant cells are surrounded by a polysaccharide rich primary wall. The primary walls of different plant cells differ greatly in appearance. Young cells have a very thin cell wall. Composition of primary wall Primary walls are composed predominantly of polysaccharides together with lesser amounts of structural glycoproteins, phenolic esters, enzymes, and calcium and boron minerals
Functions of primary wall:
- It gives structural and mechanical support
- It maintains and determines cell shape
- It resists internal turgor pressure of cell
- Controls rate and direction of growth
- Ultimately responsible for plant architecture and form
- Regulate diffusion of material through the apoplast
- Protects against pathogens
- Protects against dehydration and other environmental factors
- Source of biologically active signaling molecules
- Plays a major role in cell – cell interaction
- Participates in early recognition of symbiotic nitrogen fixing bacteria.
c) Secondary cell wall: Secondary cell wall is formed after cell enlargement is completed. Some cells deposit additional layers inside the primary wall. This occurs after growth stops or when the cells begin to differentiate (specializes). The secondary wall is mainly for support and is comprised primarily of cellulose, hemicellulose and lignin. It often can distinguish distinct layers, S1, S2 and S3 - which differ in the orientation, or direction, of the cellulose microfibrils. It is extremely rigid and provides compression strength.
Composition of secondary cell wall The secondary cell walls are much thicker than the primary walls and consist of 40-45% cellulose, 15 – 35 % hemicellulose, 15 – 30 % lignin and negligible amounts of pectic polysaccharides.
Functions of secondary cell wall:
- It plays major role in providing mechanical support.
- It facilitates the transport of water and nutrients.
- It allows extensive upright growth
Formation of cell wall
A cell plate formed between the two daughter cells originates from microtubles, which act as the base for the construction of the new cell wall. The microtubules may direct the cell- wall forming materials to the cell plate which grows from the centre towards periphery of the cell and soon becomes the pectin rich middle
lamella. Above the middle lamella the primary wall formation takes place. The protoplasts of the cells of the primary wall secrete the secondary wall materials, when the cells have stopped enlarging. The protoplast then totally diminishes and only the wall remains. The rings, spirals or network in a mature stem cross section are due to secondary wall deposition.
Chemical changes in cell wall
Chemical changes take place in cell wall by accumulation of various depositions as the cell matures. These chemical changes bring corresponding change in the structure and function of the cell. The various depositions are
Lignification : The deposition of the lignin on cell walls is called lignification. As a result of lignification, the cell walls become hard, thick walled and dead. Usually after of the thickening of the cell wall, the protoplasm of the cell diminishes in size and the cell becomes dead and rigid. Cellulose microfibrils are impregnated in phenoloic polymer called lignin. Lignin displaces water in matrix and form hydrophobic meshwork that bonds tightly to cellulose and prevent wall enlargement. Lignins add up mechanical strength and reduce susceptibility of wall to attack by pathogens
Suberization : The cell wall of cork cells and casparian strips of endodermis get deposited with a layer of suberin by a process known as suberization.
Cutinization : In some cells, in the outer layers of the cell wall, the cellulose gets converted to cutin by a processs of cutinization. This forms a definite, impermeable membrane on the cell wall of cuticle. Cutinization helps in checking evaporation of water. It is found normally on the exposed parts of the plant.
Mucilaginous changes: Sometimes the cellulose is changed to mucilage which has the property of absorbing and retaining water. This forms a viscous, mucilaginous coating on the cell walls and helps to tide ove dry conditions. Many sea weeds yield mucilaginous substances such as agar, alginic acid and carageenen of great commercial value.
Mineralization: The deposition of the minerals on the cell walls by the process of infilteration or by deposition of inorganic salts is known as mineralization. The minerals usually deposited are silica, carbonates and oxalates of calcium. The phenomenon of silica and calcium deposition are known as silicification and calcification respectively.
Role of plant cell wall in live stock, food and paper industry:
- Primary walls are the major textural component of plant-derived foods.
- Plant-derived beverages often contain significant amounts of wall polysaccharides. Some wall polysaccharides bind heavy metals, stimulate the immune system or regulate serum cholesterol.
- Wall polysaccharides are used commercially as gums, gels, and
- stabilizers.
- Cell wall structure and organization is of interest to the plant scientist, the food processing industry and the nutritionist.
- Cellulose plays a major role in paper industry.
- Secondary walls also have a major impact on human life, as they are a major component of wood
- It is a source of nutrition for livestock.
- The cell walls of fruits and vegetables are now recognized as important dietary components and may protect against cancer of colon, coronary heart disease, diabetes, and other ailments.
Layers of cell wall
PROTEINS
Proteins are made up of different amino acids. Amino acids : In amino acids, there are two functional groups: an amino group and a carboxylic group. Both these groups are attached to the α carbon atom only. Amino acids are alpha (α) amino carboxylic acids. The carbon atom is tetrahedral in shape. The various groups attached to it are placed in different positions. Since the valence of the carbon atom is four, four groups can be attached to the carbon atom. Based on the groups attached to the carbon atom it may be of two types.
1. Symmetric carbon atom : When the valence of the carbon is satisfied by more than one similar atoms/ groups then the particular carbon atom is called as symmetric carbon atom. Eg : Glycine
Compounds containing symmetric carbon atoms are optically inactive since they cannot rotate the plane of polarized light.
2. Asymmetric carbon atom : When the valence of the carbon is satisfied by four different groups, then that particular carbon atom is called as asymmetric carbon atom. Eg: Alanine
In amino acids, to α carbon atom, an amino group, a carboxylic group and a hydrogen atom are attached and the fourth group is the R group. This R group varies for each amino acid. All amino acids except glycine have at least one asymmetric carbon atom, hence they are optically active.
Classification of amino acids : Amino acids can be classified in various ways.
1. Based on side chains: Based on the structure of the R groups, all the amino acids are classified as aliphatic, aromatic and heterocyclic amino acids.
Structure of amino acids
Name of the amino acid
letter code
Structure Unique feature
ALIPHATIC R GROUP CONTAINING HYDROPHOBIC AMINO ACIDS
Glycine Gly
symmetric amino acid, optically inactive amino acid
Alanine Ala
Aliphatic hydrophobic neutral.
NEGATIVELY CHARGED AMINO ACIDS
Glutamatic acid Glu
Polar, hydrophilic
- ve charged R group containing amino acid
α , γ dicarboxylic acid
Aspartatic acid Asp
Polar, hydrophilic
- ve charged R group containg amino acids. α ,β dicarboxylic acid
ALIPHATIC R GROUP CONTAINING HYDROPHILIC NEUTRAL AMINO ACIDS
Glutamine Gln
Polar hydrophilic neutral
Asparagine Asn
Polar hydrophilic neutral It is a diamide
Cysteine Cys
polar hydrophobic neutral
Methionine Met
Hydrophobic neutral, sulphur containing amino acid.
Serine Ser
Polar hydrophilic neutral
AROMATIC R GROUP CONTAINING AMINO ACIDS
Tryptophan Trp
Aromatic hydrophobic neutral, indole group containing amino acid
Tyrosine Tyr
Aromatic polar hydrophobic phenol group containing amino acid.
Phenylalanin e Phe
Aromatic hydrophobic neutral amino acid
2.Based on their presence or absence in proteins: Amino acids are classified as protein amino acids and non protein amino acids.
a) Protein amino acids: - Amino acids that are used for synthesis of proteins are called protein amino acids. All the above mentioned 20 amino acids are present in proteins.
b) Non protein amino acids: Apart from the 20 amino acids that are present in proteins, several non protein amino acids are also present in nature. These are obtained by slight modification of 20 protein amino acids. Eg:- beta alanine, hydroxy proline, N- acetyl glutamic acid etc
3. Based on requirement to the body as essential and non essential: Animals cannot synthesis all the 20 amino acids that are present in proteins. Some have to be provided to the body through external diet. The amino acids which cannot be synthesized by the body, which have to be supplied through diet are called essential amino acids. On the other hand, some amino acids can be synthesized by the body, and they are called as non essential amino acids.
RUHEMANN’S PURPLE
This ninhydrin reaction is employed in the quantitative determination of amino acids. Proteins and peptides that have free amino group(s) (in the side chain) will also react and give color with ninhydrin
2. Peptide bond formation:- Amino acids are linked together by formation of covalent bonds. The covalent bond is formed between the α-carboxyl group of one amino acid and the α-amino group of the next amino acid. The bond so formed between the carboxyl and the amino groups, after elimination of a water molecule is called as a peptide bond and the compound formed is a peptide.
A peptide is a chain of amino acids linked together by peptide bonds. Proteins on partial hydrolysis yield the polypeptides and oligopeptides. Polypeptides are usually long peptides whereas oligopeptides are short (< 10 amino acids). Proteins are made up of one or more polypeptides with more than 50 amino acids.
Nomenclature of the peptides:- In a peptide, always the first amino acid has its N terminal free. It will not be involved in the formation of a peptide bond, but the carboxyl group of first
amino acid and amino group of second amino acid are involved in the formation of the peptide bond. While naming a peptide, the first amino acid is usually named by adding yl and the second amino acid as it is. Example:
Glycyl alanine
Peptides can be classified based on the structure as linear or cyclic peptides and based on number of amino acids involved in the formation of the peptide.
Based on structure:
- Linear peptide: - When a peptide has its structure in the form of linear structure it is called as linear peptide. Eg: Glutathione and insulin. Number of peptide bonds present in a linear peptide = (n – 1) where n represents the number of amino acids.
a) Glutathione: It is a small molecule made up of three amino acids, which exists in almost every cell of the body. This is called as natural redox tripeptide. There is an unusual peptide bond present between glutamic acid and cysteine and glycine. It is chemically called as gamma glutamyl cysteinyl glycine.
Glutamic acid
Cysteine Glycine
b) Insulin: The peptide hormone insulin is produced by clusters of specialized cells called the beta cells of islets of Langerhans of pancreas. It is synthesized as large precursor molecule pre-proinsulin. Pre-proinsulin undergoes partially hydrolysis and forms proinsulin with the removal signal peptide. Proinsulin is made up of three chains, chain A, B and C. In proinsulin, Chain A and C are connected by chain B which is made up of 30 amino acids. It undergoes a proteolytic cleavage and forms insulin with the removal of chain B. Chain A and chain C are connected by means of two disulphide bonds in insulin molecule.