Biology – Premed 1

Molecules of the Cell

Dr. Veipu

Inorganic vs Organic

Essential nutrients are organic and inorganic

Cellular pool consists of inorganic materials and organic compounds

INORGANIC ---- Salts, mineral ions, water ORGANIC ---- Carbohydrates, Lipids,

Amino acids, Proteins, Nucleotides, Nucleic acids, Hormones, Vitamins

Inorganic Substances Mineral Elements

Occur in living organisms as components of organic and inorganic molecules and ions

In all body fluids there is a balance between the amount of minerals present as ions and in complexes

Major minerals of animal body ---------Calcium, Phosphorus, Sodium, Chlorine, Magnesium and Sulphur

Some minerals occur in small amounts or “Trace amounts” ---- Iron, Copper, Cobalt, Manganese, Fluorine, Zinc, Iodine and Selenium

Inorganic Substances

In plants, minerals required in large amounts are termed “Maconutrients”E.g. Phosphorus, Potassium, Calcium, Magnesium, Sulphur and Iron

Minerals required in trace amounts are termed “Micronutrients”E.g. Manganese, Cobalt, Zinc, Copper

Inorganic Substances• Calcium --- Imparts strength and rigidity to bones and teeth by

deposition within them along with phosphates– Bone dust used as fertilizer due to high calcium and phosphorus

Magensium (Mg) --- Also contributes to rigidity of bones and teeth Chlorophyll is a complex of Magnesium (Mg2+)

Sulphur (S) containing amino acids enter proteins

Iron (Fe2+) combines with pigment porphyrin to form “Heme” compound in hemoglobin synthesis* Iron deficiency leads to Anemia

Inorganic Substances

Iodine (I-) --- Exists in many forms of mammals, Inorganic iodine, protein bound iodine of blood and thyroid hormones

* Dietary deficiency of iodine depresses thyroid activity and enlarges the thyroid gland resulting in Goitre

Mineral elements are required for enzyme action

E.g. Manganese required for activity of enzymes in synthesis of oligosaccharides and glycoproteins

Mitochondria is rich in manganese

Sodium (Na+) and Potassium (K+) ---- Maintenance of extracellular and intracellular fluids through osmosis, maintain membrane potential Also responsible for transmission of electrical impulses in nerve cells

Inorganic SubstancesWater

70% of body mass is water 2/3 of body is formed of water and 55% is confined to cells as intracellular

water Remainder found in extracellular fluids like blood, tissue fluid and lymph

Water is polar molecule, therefore passes readily through the membranes

2 electronegative atoms of oxygen of two water molecules share a hydrogen atom and become linked by a hydrogen bond

Hydrogen bonding of several water molecules result in fluidity of water

Inorganic Substances

Water acts like a “Solvent” in living organisms

Maintains molecular confirmation and stabilizes structural organization of living organisms

Helps in maintaining the constancy of internal environment of organism

Water aids in maintaining a constant pH

Organic Compounds

• Small and simple organic biological molecules may assemble is form large and complex molecules called “Macromolecules”

CarbohydratesLipidsProteinsNucleic Acids

• A polymerization is a process in which repeating subunits of monomers are bound into chains of different lengths called “Polymers”

CARBOHYDRATES

Carbohydrates

Carbohydrates are combination of Carbon, C and water (CH2O)n

In molecules, Carbon forms chains or rings with two or more hydroxyl groups and either an aldehyde or a ketone group

“Sugar” referes to a simple carbohydrate such as monosaccharide or disaccharide (Sweet taste)

Carbohydrates

A disaccharide is a combination of two monosaccharide molecules

Polysaccharides a polymer of more than two or more mono-saacharides bound in a linear or branched chain

Monosaccharide --- Glucose, fructose, galactose Disaccharide --- Maltose, Sucrose, Lactose Polysaccharide --- Starch, glycogen, cellulose

Glucose

Carbohydrates Subunits of disaccharide and polysaccharide are linked by

means of glycosidic bonds in which one sugar unit is bound to the oxygen atom of a hydroxyl of an adjacent sugar unit

Maltose is formed when number one carbon (1) on a glucose bonds to the (4)th carbon on a second glucose

Sucrose is formed when glucose and fructose join between their (1) and (2) carbons

Therefore once carbon gives up it’s OH groups and the other loses the hydrogen from its OH groups, this reaction is thus known as a dehydration synthesis (polymerization reactions)

Carbohydrates• Starch, Cellulose, and Glycogen are structurally and biochemically

distinct, although they are all polymers of the same glucose

• Synthesis and breakage of each type of covalent bond requires a specific enzyme

• Cellulose ---- Provides strength and rigidity in plants and algae as a cell wall

• Peptidoglycan is a class of polysaccharides providing structural support to the bacterial cell wall

• Lipopolysaccharide, complex of lipids and polysaccharide in gram (-) bacteria responsible for inducing symptoms such as fever and shock

• Polysaccharides on outer surface known as “sugar coating” also called glycocalyx used as site of receptors to receive and respond to stimuli

• Carbohydrates are also components of large protein molecules called Antibodies

• Small sugar molecules also account for differences in blood type

LIPIDS

Lipids

Long, complex hydrocarbon chains that are Non-polar and hydrophobic

Lipids are:--- Triglycerides Phospholipids Steroids Waxes

Lipids

Triglycerides:-

Triglycerides are composed of a single glycerol molecule bound to 3 fatty acids

Glycerol is a 3 carbon alcohol with 3 OH groups that serve as binding sites

Fatty acids are long chain hydrocarbon molecules with a carboxyl group (COOH) and one end which is free to bind to OH group of glycerol, forming an ester bond

Saturated Fat ----- Carbons in the chain are single bonded (Solid )

Unsaturated Fat ===== Carbons in the chain are double bonded (Liquid )

Structure of fatty acid is responsible for the physical nature of fats and oils giving a greasy texture

Solid fats (eg. Butter, animal fat) are saturated while oils are unsaturated

Triglycerides in most animal cells are stored as “Droplets”, Adipose cells

Phospholipids Membrane Lipids ---- Phospholipids

Major structural component of cell membrane Phospholipids contains only 2 fatty acids attached to

glycerol molecule while the 3rd glycerol binding site holds a phosphate group (PO4

2-)

These lipids have both hydrophillic and hydrophobic regions due to (-) charge on the phoric acid head of the molecule and lack of charge on the tail of the molecule

Forms a “bilayer”

Lipids

Steroids

Cholesterol helps reinforce the structure of cell membrane

Cholesterol, precursor for steroids such as “Sex Hormones”

CHOLESTEROL

Lipids

• WAX

• Esters formed between a long chain of alcohol and saturated fatty acids

• Pliable and soft when warm, but hard and water resistant when cold (e.g. Paraffin)

• Fur, feathers, fruits, leaves, skin, insect exoskeleton are naturally waterproofed with a coating of wax

• Bacteria such as Tuberculosis and Leprosy produce Wax-D that contributes to pathogenicity

PROTEINS

Proteins

• Most predominant organic molecule in cells which are chemically and physically most diverse

• The structure, behavior and unique qualities of all living beings are the consequences of the protein they contain

• Building blocks of proteins are “Amino Acids”

Proteins Amino acids exist in about 20 different naturally occurring forms Essential (body cannot synthesize) vs Non-essential amino acids Various combination of amino acids contribute to the variety of

proteins

All amino acids have a basic skeleton consisting of 1. Carbon (alpha) linked to an 2. Amino group (NH2) and a 3. Carboxyl

group (COOH) and a 4. Hydrogen atom (H)

Variations among the amino acids occur at the 5. “R group”, which is different in each amino acid

R group imparts the unique characteristic to the molecule and to the protein that contains it

Proteins

• Peptide Bond forms between the amino group of one amino acid and the carboxyl group of another amino acid

• “Peptide” refers to a molecule composed of a short chain of amino acids

• “Polypeptide” refers to more than 20 amino acids

Protein Structure Protein is synthesized on the ribosome as a linear sequence of

amino acids which are held together by peptide bonds

After synthesis, protein “Folds” into a three dimensional form

Four levels of organization have been recognized:

1. Primary

2. Secondary

3. Tertiary

4. Quaternary

Proteins

• First protein to have its primary structure determined was Insulin, the pancreatic hormone that regulates glucose metabolism in mammals

• Secondary protein structure arises when functional groups exposed on outer surface of the molecule interact by forming hydrogen bonds. This causes the amino acid chain or peptide to twist into a coiled configuration called “alpha-helix” or to fold into a flat “beta-pleated sheet”

• Held by hydrogen bonds

• Tertiary protein structure arises when the secondary level proteins undergo twisting torsion. This is created by additional bonds (See next Image) between functional groups.

• Quaternary protein structure contains more than one polypeptide chain forming a large multi unit protein. (Eg. collagen, hemoglobin. See images below)

Tertiary Structure showing different interactions

Collagen fibers – Connective Tissue

What is Sickle Cell Anemia??

PROTEIN

• Bonding and folding of a proteins will allow to react only with molecules that complement or fit its particular surface features like a lock and key

• A high degree of specificity E.g. Enzymes

• Antibodies are complex glycoproteins with specific regions of attachment for bacteria

• Keratin

Lysozyme ----- Enzyme Protein in tears, saliva, etc (Recognition and binding to target)

• Protein “Chaperones” – Assist in folding process of the proteins

Protein Denaturation

• pH• Salt Concentration • Temperature

• Environmental factors if altered can weaken the different chemical bonds and interactions, destroying the protein

• Eg. Chemical treatment, excessive heat can denature a protein

Nucleic Acids

• DNA === Deoxyribonucleic acid• RNA === Ribonucleic acid• DNA contains coded genetic program with

detailed and specific instructions for each organism’s hereditary

• Nucleic acids are polymers of repeating units called “Nucleotides”

Nucleic Acids• Nucleotides:

• Nucleotides are composed of three smaller subunits:

• 1. Nitrogen Base • 2. Pentose ( 5 carbon sugar)• 3. Phosphate

• Nitrogen Base is a cyclic compound that can be of any two formes ---- Purines ( 2 rings) and Pyrimidines ( 1 Ring)

Nitrogen base is covalently bonded to the sugar ribose in RNA, and to deoxyribose (one less oxygen than ribose) in DNA

Nucleic Acids

Pyrimidines ==== Thymine (T) and Cytosine (C) and Uracil (U)

Purines ===== Adenine (A) and Guanine (G)

Uracil differentiates RNA from DNA DNA contains all nitrogen bases except Uracil RNA contains all nitrogen bases except Thymine

Backbone of nucleic acid strand is a chain of alternative phosphate-sugar-phosphate-sugar molecule

Double Helix of DNA

DNA is a long molecule formed by two long polynucleotide strands held together by hydrogen bonds

Bonds occur between complementary pairs of nitrogen bases

Pairing------- How? Answer: Pattern

Adenine ==Thymine ( 2 hydrogen bonds)

Cytosine === Guanine (3 hydrogen bonds)

DNA

Sugar- Phosphate backbone represent the rails

Paired nitrogen bases represent the “Steps”

Configuration therefore is a “Double Helix that looks like a spiral staircase”

RNA

“Single strand” Ribose sugar and uracil instead of thymine

3 major types of RNA: 1. mRNA (messenger RNA) -- Copy of gene from DNA

gives the sequence of a type of amino acid to sythesize a protein

2. tRNA (transfer RNA) --- Carrier that delivers the correct amino acids for protein assembly

3. rRNA (ribosomal RNA) --- Component of ribosomes

Summary

Hormones Substance that is synthesized in minute quantities in one tissue and transported

by circulatory system to another organ

The tissue or organ where they are produced are called “Effectors” and those where they exert their influence are called “Targets”

Based on their site of action, hormones are classified as : Local and General

Local hormones have specific local effects

General hormones are secreted by endocrine glands are transported through blood to cause physiological action at points away from their place of origin (E.g. Growth hormone, Thyroid hormone)

Hormone effects --- Variety of regulatory functions such as growth, sexual development, metabolism , etc.

At the cellular level, the hormone action begins by binding to a specific receptor

VITAMINS

Organic molecules in food that are required in minute quantities for normal metabolism but cannot be synthesized adequately

Deficiency of any one of the vitamins lead to a specific set of disease that can be corrected by administration of that vitamin alone

Classification:

Water Soluble Vitamins ------ B complex group of Vitamins, Vitamin C• Function as coenzyme or cofactor and are required in minute quantities for

normal metabolism

Present in whole grain cereals, legumes, leafy green vegetables, meat and dairy products

Fat Soluble Vitamins ----- Vitamins A, D, E, K Present in fatty meats, liver, yolks, dairy fats, vegetable oils