Molecules to metabolism

Nature of science:

Falsification of theories—the artificial synthesis of urea helped to falsify vitalism. (1.9)

Understandings:

  • Molecular biology explains living processes in terms of the chemical substances involved.
  • Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.
  • Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
  • Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.
  • Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.
  • Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Applications and skills:

  • Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
  • Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.
  • Skill: Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
  • Proteins or parts of polypeptides should be recognized from molecular diagrams showing amino acids linked by peptide bonds.
molecular diagrams showing amino acids linked by peptide bonds

Water Molecule

  • composed of one oxygen atom and two hydrogen atoms.
  • Each hydrogen atom is covalently bonded to the oxygen via a shared pair of electrons.
  • Oxygen also has two unshared pairs of electrons
  • Water is a "polar" molecule, meaning that there is an uneven distribution of electron density.
  • Water has a partial negative charge (δ-) near the oxygen atom due the unshared pairs of electrons, and partial positive charges (δ+) near the hydrogen atoms.
  • An electrostatic attraction between the partial positive charge near the hydrogen atoms and the partial negative charge near the oxygen results in the formation of a hydrogen bond as shown in the illustration.

The ability of ions and other molecules to dissolve in water is due to polarity. For example, in the illustration above sodium chloride is shown in its crystalline form and dissolved in water.

Properties of water

Thermal

Cohesive(when

molecules of same type are attracted towards each other)

Solvent

• Excellent solvent of polar molecules…”likes dissolves like concept”…..dissolves carbohydrates,DNA, RNA

• cellular fluids are primarily water ..called aqueous solutions …for example cytoplasm nucleoplasm, stroma, blood plasma

• Medium of transport ..dissolved minerals in xylem ,phloem ;glucose amino acids ,HCO3 - in blood

• high specific heat

• High heat of vaporization

Other properties

Transparent to sunlight Ice floats on water

Adhesive properties: the dipolarity of water molecules make them adhere to surface that are polar example: adhesive forces between water and cellulose cell walls in the leaf causes water to be drawn out of xylem vessels keeping the cell wall moist.

Properties of Water

https://www.youtube.com/watch?v=ASLUY2U1M-8

How polarity makes water behave strangely -

All organic molecules contain carbon except carbon dioxide

type of organic molecule

subtypes

Examples

Carbohydrates

Monosaccharides

Glucose, fructose, galactose

 

Disaccharides

Maltose, lactose, sucrose

 

Polysaccharides

Starch , glycogen, cellulose

Proteins

 

Enzymes, antibodies

Lipids

 

Phospholipids , triglycerides

Nucleic acids

 

DNA, RNA

Carbohydrates: all contain carbon, oxygen and hydrogen atoms common formula C x( H2O)y where x =y or variable numbers

Monosaccharides (mono means single)

Ø Are simple sugars

Ø Have a general formula (CH2O)n

Ø value of n is any number from 3-7

Ø According to the value of n they are grouped as

trioses where n=3 tetroses where n=4 pentoses where n=5 hexoses where n=6 heptoses where n=7

Examples of triose: early product of photosynthesis pentose :ribose and deoxyribose

hexose : glucose, fructose and

galactose

 

Disaccharides

Made up of 2 monosaccharides

Examples

• 2 Glucose molecules make up Maltose (malt sugar)

• A glucose and a fructose make up Sucrose (table sugar)

• A glucose and a galactose make up Lactose (milk sugar)

 

Glucose(C6H12O6)

The structure of glucose

  • It has ring structure
  • Has 2 isomers e. same chemical formula but different structural formula: alpha glucose and beta glucose
  • α glucose molecules combine to make starch whereas β glucose molecules combine to form cellulose
The function of simple sugars in living organisms

Glucose is the major source of energy. Each gram of glucose yields about 16kJ of energy when fully broken down during respiration

Glucose is soluble and dissolved in blood plasma is transported around the body

Lactose is the main sugar in milk

In plants sugar is transported as sucrose in phloem

Maltose is produced in many germinating seeds by the breakdown of amylose ( a kind of starch)

Ribose and deoxyribose are constituents of genetic material in RNA and DNArespectively

Formation of disaccharide by condensation

Condensation reaction involves removal of a water molecule

The linkage formed between monosaccharide residues due to this is called glycosidic bond/linkage

The condensation reaction is brought about by an enzyme

Disaccharide can be broken down into constituent monosaccharides by hydrolysis. This is the reverse of condensation where the splitting of glycosidic bond occurs, catalysed by an enzyme

The water molecule comes out from the OH group of C1 and C4.In Beta glucose the OH of C1 is on the top.

Polysaccharides

  • A molecule with many monosaccharide units is called a Polysaccharide
  • This process is called polymerisation
  • They are relatively insoluble in water
  • Its property depends on the number and types of monomer it contains
  • Polysaccharides can combine with lipid forming glycolipid or with protein called glycoprotein (on plasma membrane acting as labels of cells and taking part in immune response)
  • Types and Function:

Starch

It is a compact molecule making it ideal for a storage product. In flowering plants they are present in plastids.

Glycogen

Much more branched as it has many more 1-6 glycosidic bonds

Storage by hydrolysis more rapidly than starch.

compound particularly abundant in liver and muscle cells.

Breaks down

Cellulose

Tough ,completely permeable. Major constituent of plant cell wall. Cannot be hydrolysed easily. Humans do not have cellulase to digest cellulose. Gut microorganisms of cow produce the enzyme.

Types of glycosidic bond:1-4 or 1-6carbon links

STARCH is comprised of alpha glucose units.

Starch is of two types : amylose(1-4 glycosidic bonds) and amylopectin (both 1-4 and 1-6 glycosidic bonds).

The long chains are coiled into helix.

Because of its structure starch is compact and ideal for storage. In flowering plants starch granules are present in plastids.

CELLULOSE is made up of beta subunits

(1-4 glycosidic bonds).

Orientation of glucose units alternates which makes the polymer straight. The OH in C1 and C4 point in opposite directions. To allow condensation each unit has to be positioned at 180 degrees to the previous one.

CELLULOSE

Groups of cellulose molecules are arranged in parallel with hydrogen bonds forming crosslinks. Cellulose is found in the form of microfibrils that make up the main structural molecules of the plant cell wall.

Glycogen was discovered by Claude Bernard in 1857,

  • Glucoses are linked together linearly by α(1→4) glycosidic bonds from one glucose to the next. Branches are linked to the chains from which they are branching off by α(1→6) glycosidic bonds.

Polysaccharides

Proteins

  • The amino group is attached by a covalent bond to a central carbon called the alpha carbon
  • The R group is different for each of the 20 amino acids.
  • The simplest amino acid is glycine, where the R group is a single hydrogen atom
  • Some R groups are non-polar and hydrophobic while others are polar and hydrophilic.
  • Amino acids are amphoteric e. they have both acidic (derived from carboxyl group)and basic properties (from amino group)when they dissociate in water
  • The ability to donate or receive protons causes amino acid solutions to behave as buffers i.e. tends to resist changes in pH

R GROUP

Peptide bonds: joining amino acids together

  • 2 amino acids combine to form a dipeptide by a condensation reaction between the carboxyl group of one and the amino group of the other.
  • The resulting bond is called peptide bond.
  • Condensation needs energy which comes from ATP.
  • Addition of further amino acids form a polypeptide chain •The polypeptide chain is folded into unique 3D shape.

Hydrolysis is the reverse of condensation

A protein is a large polypeptide, or several polypeptides joined together, and having a specific shape and function. Proteins have many important biological functions.

Types of protein

Function

Enzymes

Biological catalysts that control biochemical reactions :example amylase that catalyses the digestion of starch. Digestion of food and synthesis of important molecules occur in living cells only in the presence of enzymes

Structural proteins

Form the part of the body of an organism. For example the silk of spiders ; collagen in tendons and ligaments; keratin the major component of hair

Signal proteins

Carry messages around the body: insulin , a hormone involved in controlling glucose level in the blood

Contractile proteins

Actin and myosin are muscle proteins that help the muscle to contract thereby bringing about movements

Storage proteins

Albumen , the protein store that forms the egg white

Defensive proteins

Blood antibodies that fight infections

Transport proteins

Hemoglobin , carrying oxygen in blood

Proteins perform a huge variety of functions in wide range of environments

  • Thermophilic bacteria living in hot volcanic springs where proteins work at temp in excess of 80⁰C
  • This is because the heat-resistant enzymes that these bacteria have evolved to survive in such hot conditions are proving to have a number of useful applications.

Ice fish living in the waters of the

Antarctic have proteins designed to function at sub-zero temperature

THE SHAPE OF A PROTEIN IS DETERMINED BY FOUR LEVELS OF STRUCTURE

PRIMARY STRUCTURE

  • sequence of amino acids that make up the polypeptide chain
  • To carryout its function a protein should have correct amino acids arranged in precise order
  • The possibility is immense as

SECONDARY STRUCTURE

  • the folding and coiling of the polypeptide chain
  • A variety of forces between different parts of the molecule and hydrogen bonding cause the chain either to coil into an alpha –helix or to fold into a beta-pleated sheet. Beta-pleated sheets are so called because of the 'pleated' or folds when view form the side.

http://www.youtube.com/watch?v=lijQ3a8yUYQ&feature=related

http://www.youtube.com/watch?v=8-RoBZVbHOU

An α helix is generated when a single polypeptide chain twists around on itself to form a rigid cylinder. A hydrogen bond is made at regular intervals, linking the C=O of one peptide bond to the N–H of another. This gives rise to a regular helix with a complete turn every 3.6 amino acids.

Methionine, Cysteine(Cys, CH2SH)

TERTIARY STRUCTURE OF PROTEIN

Breaking down tertiary structure : DENATURATION of enzymes

ØIf the bonds holding the protein in shape are broken denaturation occurs.

ØThe primary structure is retained but the folds open up

Øthe chain loses its shape

ØDenatured globular protein lose its specific function

A number of tertiary polypeptides joined together.

Haemoglobin is a quaternary structure.

It is composed of four different polypeptide chains.

Each chain forms a tertiary structure called a haem group.

QUARTERNARY STRUCTURE 

Proteins are classified into 2 main groups on basis of tertiary structure

Fibrous

  • Parallel Polypeptide chains cross linked at intervals forming long fibers.
  • Usually insoluble in water
  • Physically tough
  • Eg: Collagen in tendons & bones , Silk of spiders web, keratin of human hair

Globular

  • Polypeptide chains tightly folded to form spherical shapes.
  • Hydrophobic groups are on inside and hydrophilic outside making it water soluble

• Eg : Enzymes, Antibodies, many hormones

COLLAGEN is a fibrous protein

Collagen is distinct from other proteins in that the molecule comprises three polypeptide chains which form a unique triple-helical structure

  • It is tough and inextensible,
  • with great tensile strength
  • main component of cartilage, ligaments and tendons,
  • main protein component of bone and teeth

Polar and non polar amino acids in protein structures.

Those sections of the molecule that contain polar amino acids are hydrophilic and can exist in contact with water.

Polar amino acids allow the positioning of proteins on the external and internal surface of a cell membrane. Both cytoplasm and tissue fluid are water based regions.

The non-polar amino acids allow the same protein to site within the phospholipid bilayer.

The lining of the channel itself will be of polar amino acids to allow the diffusion of charged molecules and ions.

Diversity of amino acids

  • Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo
  • Post-translational modifications to form the mature protein product.
  • PTMs are important components in cell signaling.
  • Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini.
  • Example collagen polypeptide has several prolines , some are removed and replaced with hydroxyproline.

LIPIDS

  • diverse group of compounds • Insoluble in water • Dissolves readily in organic solvents like ethanol • Contains carbon hydrogen and oxygen • Less oxygen than carbohydrates • Fats( triglycerides) and oils are lipids made from fatty acids and glycerol

LIPID

  • Fatty acids have a long hydrocarbon (carbon and hydrogen) chain with a carboxyl (acid) group. The chains usually contain 14 to 18 carbons.
  • Glycerol contains 3 carbons and 3 hydroxyl groups. It reacts with 3 fatty acids to form a triglyceride or fat

Triglycerides

• Are lipids made from glycerol and fatty acids • Liquid triglycerides (at 20⁰C room temp)are called oils

  • Those that are solids at room temperature are called fats. Fatty acid in triglyceride may be saturated (carbon atoms are bonded to their maximum number of other atoms, have only single bonds in the hydrocarbon chain)or

unsaturated

Unsaturated fatty acids

Cis- unsaturated fatty acids are not good at packing together therefore they have lower melting point. Trans fatty acids do not bend at double bond and

have higher melting point. They are produced by hydrogenation of vegetable oil or fish oil and present in margarine and other processed foods.

Role of lipids in living organisms

  • Concentrated source of energy 38kJ/g more than twice of carbohydrate
  • In mammals excess fat is laid for storage in special connective tissue called adipose tissue
  • Heat insulation: fat is a bad conductor of heat
  • Shock absorption: some organs have thick layer of fat around them
  • Buoyancy: many unicellular aquatic organisms produce oil droplet to aid buoyancy
  • Phospholipids: major part of cell membrane including the myelin sheath around nerve fibres .they have one end hydrophobic and other end hydrophilic
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