Biomolecules

Organization of Life

Entire organism

System Tissue Cells Organelle Molecules Atoms

Biomolecules are complex

Most Abundant Biomolecules of the Cell

Naturally Occurring Elements in Human Body

99% of the mass of most cells is H, O, N, and C

Biomolecules are Organic Compounds

Molecules containing Carbon, Hydrogen, Nitrogen, and often Oxygen. Organic molecules are complex molecules of life, built on a framework of carbon atoms all the biological macromolecules below have a carbon backbone Carbohydrates Lipids Proteins Nucleic acids

From Structure to Function

The function of organic molecules in biological systems begins with their structure.

The building and nucleic arrangements molecules to work.

blocks of carbohydrates, lipids, proteins, acids bond together in different to form different kinds of complex actually perform needed functions and

Basic Function of Biomolecules

Carbos
Energy Storage Structure Starch Glycogen Glucose Sucrose Cellulose

Lipids
Long term storage Insulation Protection Lipid Fats Oils Waxes

N. Acids
Genetic information

Proteins
Catalysts Hormones Structure Proteins Enzymes

DNA RNA

Functional Groups Are The Difference

Hydrocarbon An organic molecule that consists only of hydrogen and carbon atoms. Most biological molecules have at least one functional group (A cluster of atoms that imparts specific chemical properties to a molecule ex. polarity, acidity, ETOH, etc.)

Effects of Functional Groups: Sex Hormones

How Cells Form Large Molecules

Condensation:
It is a chemical process by which 2 molecules are joined together to make a larger, more complex, molecule, with the loss of water.

Glucose

Glucose

Maltose

Hydrolysis
Hydrolysis is the opposite to condensation. A large molecule is split into smaller sections by breaking a bond, adding -H to one section and -OH to the other. Results in the breakdown of polymer and release of energy.

What Cells Do With Organic Compounds

Monomers (mono means single) Single molecules used as subunits to build larger molecules (polymers)

Polymers (poly means more than one) Larger molecules that are chains of monomers May be split and used for energy Polymer example: starch is many glucose units joined together by condensation bonds

Structure Dictates Function

We define cells partly by their capacity to build complex carbohydrates and lipids, proteins, and nucleic acids. All of these organic compounds have functional groups attached to a backbone of carbon atoms

Carbohydrates
Carbohydrates include:
Small sugar molecules in soft drinks Long starch molecules in pasta and potatoes

Carbohydrates
Organic molecules that consist of carbon, hydrogen and oxygen in a ratio of 1:2:1. Formula (CH2O) Example: Glucose:- C6H12O6 Basic units of the carbohydrates are the monosacharides (simple sugars).

All monosacharides are white and water soluble.

Most taste sweet.

Carbohydrates
Depending on the presence of repeating unit of monosacharides, carbohydrates can be classified into three group. 1. Monosaccharides (mono=one unit) ex. Glucose 2. Oligosaccharides (oligo=few units) ex. sucrose 3. Polysaccharides (poly=many units) ex. Starch

Important Functions: 1. Energy storage. 2. Structural building material 3. Important structural elements in the backbone of both DNA and RNA

Simple Sugars
Monosaccharides (one sugar unit) are simple carbohydrates Used as an energy source or structure Backbones of 5 or 6 carbons Example: glucose is a 6-carbon sugar with red numbers showing carbon locations

Glucose

Glucose is found in sports drinks Fructose is found in fruits Honey contains both glucose & fructose Galactose is found in dairy products

Short-Chain Carbohydrates
Oligosaccharides
Short chains of monosaccharides Example: sucrose, a disaccharide (table sugar) Lactose, a disaccharide (in milk)

Lactose

Galactose

Glucose

Lactose

Complex Carbohydrates
Polysaccharides
Straight or branched chains of many sugar monomers joined by condensation bonds. The most common polysaccharides are cellulose, starch, and glycogen. All consist of joined glucose monomers. Each has a different pattern of covalent bonding, and different chemical properties and strength.

Cellulose, Starch, and Glycogen

Cellulose
It is a polysacharide consisting of a linear chain of several hundred to over ten thousand (1 4)linked glucose units. Cellulose is the structural component of the primary cell wall of green plants.

Starch and Glycogen

Starch Glycogen It is a polysacharide consisting of a branched chain of several hundred to over ten thousand (1 4) and (1 6) linked glucose units. Starch is the main energy reserve in plants. Glycogen is the main energy reserve in animals.

Chitin A Carbohydrate of Strength

Chitin (a hard, durable carbohydrate).

A nitrogen-containing polysaccharide that strengthens hard parts of animals such as crabs, and cell walls of fungi

Lipid
Fatty, oily, or waxy organic compounds that are insoluble in water need a nonpolar solvent . Functions: They store and transport metabolic energy in chemical form. serve as structural elements, e.g., in the cell membrane. They also form protective surface and fatty layers. cell-cell recognition

Fatty Acids
Many lipids incorporate fatty acids. Simple organic compounds with a carboxyl group joined to a backbone of 4 to 36 carbon atoms

Essential fatty acids are not made by the body and must come from food. Omega-3 and omega-6 fatty acids are examples of essential fatty acids

Fatty Acid Examples

Fatty acids are saturated, monounsaturated, or polyunsaturated on basis of their bonds Saturated no d-bond Mono one d-bond Poly multi d-bonds Double bonds can attach other atoms

Characteristics of Fats
Fats Lipids with one, two, or three fatty acid tails attached to glycerol. Triglycerides Neutral fats with three fatty acids attached to glycerol.

The most abundant energy source in vertebrates.

Concentrated in adipose tissues (for insulation and cushioning).

Triglyceride

Fats store energy, help to insulate the body, and cushion and protect organs

Saturated and Unsaturated Fats

Saturated fats (animal fats)

Fatty acids with only single covalent bonds

Pack tightly; are solid at room temperature

Unsaturated fats (vegetable oils)

Fatty acids with one or more double bonds

Liquid at room temperature

Phospholipids
Molecules with a polar head containing a phosphate
and two nonpolar fatty acid tails. Heads are hydrophilic, tails are hydrophobic

The most abundant lipid in cell membranes

Note that cell membrane is a double layer with the

hydrophilic heads pointing out while hydrophobic

tails point in.

Phospholipid Structure of Cell Membrane

Waxes Natures Waterproofing

Waxes Complex mixtures with long fatty-acid tails bonded to long-chain alcohols or carbon rings. Protective, water-repellant covering, many uses

Cholesterol And Other Steroids

Steroids
Lipids with a rigid backbone of four carbon rings and no

fatty-acid tails.
Cholesterol an important steroid in humans Component of eukaryotic cell membranes. Remodeled into bile salts, vitamin D, and steroid hormones (estrogens and testosterone). Excessive cholesterol can be bad for health

Proteins
Proteins are the most diverse biological molecules (examples: there are structural, nutritious, enzyme, transport, communication, and defense proteins). Cells build thousands of different proteins by stringing together amino acids according to the directions found in the DNA.

Key is the flexibility of proteins allowing them to perform many functions in the organism.

Proteins And Amino Acids

Protein An organic compound composed of one or more chains of amino acids joined by peptide bonds. Amino acid A small organic compound with an amine group ( NH3+), a carboxyl group (COO-, the acid), and one or more variable groups (R group).

It is the R group that makes each of the 20 naturally occurring amino acids different

Amino Acid Structure Examples

Amino Acid

Valine

R above is functional group; valine is example of amino acid.

Polypeptides From Amino Acids

Polypeptide A chain of amino acids bonded together by peptide bonds in a condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid. Remember: the condensation bond is made by extracting water from the two amino acids and thus linking them together.

Peptide Bond Formation

How long are the polypeptide chains in proteins?

Protein Composition
Proteins can be classified based on the number of polypeptides used Monomeric : only a single polypeptide is present Oligomeric: two or more polypeptides are present. The subunit peptide chains are held together by non-covalent interactions

Polypeptides have unique amino acid composition

Protein Composition
Proteins are also classified based on their composition. Simple proteins: Only amino acids eg RNAse and chymotrypsinogen. Conjugated proteins: other chemical groups in addition to amino acids. This nonamino acid part is known as prosthetic group.

Protein Solubility
It is determined by the type of the amino acids and their side chains are involved. Water soluble: globular proteins eg hemoglobin. Water insoluble: keratin, Fibrous proteins eg

Protein Structure (Primary & Secondary)

Primary structure The unique amino acid sequence of a protein (list of amino acids contained in protein). Secondary structure The polypeptide chain can fold and it forms hydrogen bonds between the amino acids

Protein Structure (Tertiary & Quaternary)

Tertiary structure (more complex) A secondary structure is compacted into structurally stable units. Forms a functional protein Quaternary structure (most complex) Some proteins consist of two or more folded polypeptide chains in close association Example: hemoglobin

Why Is Protein Structure So Important?

When a proteins structure goes awry, so does its function (example: fried egg white cannot return it to unfried condition). A really scary example is the brain prion that is involved in mad cow disease and similar cases in which the normal protein structure of the prion becomes distorted and literally starts destruction of the surrounding tissue.

Sickle-Cell Disease: A Simple Change in Primary Structure

Hemoglobin Hemoglobin contains four globin chains, each with an iron-containing heme group that binds oxygen and carries it to body cells.

Sickle Cell Anemia

A single change in primary structure can affect protein conformation and function. Example-Sickel Cell Anemia Mutation in DNA that causes substitution of one amino acid. Glutamic acid Valine

Results into abnormal beta chain of hemoglobin.

Abnormal hemoglobin molecules tend to crystallize, deforming some of the cell into sickel shape.

Proteins In General Structurally and functionally, proteins are the most diverse molecules of life. They include enzymes, materials, and transporters. structural

A proteins function arises directly from its structure.

Nucleic Acids
Nucleic acids are biological molecules essential for life, and include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information.

Nucleotides
Nucleotides are building Blocks of Nucleic Acids. Nucleotides that have a sugar, nitrogen base, and phosphate.

Nitrogenous Base

PO4 Sugar

Nucleoside Nucleotide

Nitrogenous Base
Derivatives of purine and pyramidine.

Sugar Molecule
Ribose is pentose.

Nucleotide

Adenosine Triphosphate (ATP)

A nucleotide with three phosphate groups . Important in phosphate-group (energy) transfer. ATP is the energy ATM of the cell it is used to store and release energy as needed.

Polymerization of Nucleotides
Phosphodiester Bonds
In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon atom of another. A phosphodiesterase is an enzyme that catalyzes the hydrolysis of phosphodiester bonds

DNA Architect For Life

DNA (deoxyribonucleic acid)
Two chains of nucleotides twisted together into a double helix with links of hydrogen bonds.
Contains all inherited information necessary to build/maintain an organism, coded in the order of the nucleotide bases, with each three base letters forming a genetic code word . All living organisms have DNA.

The DNA Molecule

Double Helix Model of DNA

1. Two polynucleotide chains wrapped helically around each other.
2. Nucleotide chains are anti-parallel: 5 3 3 5 3. Sugar-phosphate backbones are on the outside of the double helix, and the bases are oriented towards the central axis. 4. Complementary base pairs from opposite strands are bound together by weak hydrogen bonds. A pairs with T (2 H-bonds), and G pairs with C (3 H-bonds). 5-TATTCCGA-3 3-ATAAGGCT-5 5. Base pairs are 0.34 nm apart. One complete turn of the helix requires 3.4 nm (10 bases/turn). 6. Sugar-phosphate backbones are not equally-spaced, resulting in major and minor grooves.

Double Helix

Base Pairing

Chargaffs rules 1. The base composition of DNA generally varies from one species to another.

2. DNA specimens isolated from different tissues of the same species have the same base composition.

Chargaffs rules
The base composition of DNA in a given species does not change with an organisms age, nutritional state, or changing environment. In all cellular DNAs, regardless of the species, A = T, and G = C). Sum of the purine residues equals the sum of the pyrimidine residues.

DNA to Protein
Genome: the complete set of information in an organisms DNA. Total length of DNA is about 2 meters long in a human cell, encoding about 30000 proteins.

RNA Carries Out DNA Instructions

RNA (ribonucleic acid)
It contains four kinds of nitrogenous base adenine, guanine, cytosine and uracil. Important for protein synthesis.
The non genetic RNA is single stranded. Non genetic RNA carry the order of DNA

RNA
RNA acts as an intermediary by using the information encoded in DNA to specify the amino acid sequence of a functional protein. All cellular organisms use messenger RNA (mRNA) to carry the genetic information that directs the synthesis of proteins. transfer RNA (tRNA) molecules deliver amino acids to the ribosome, where ribosomal RNA (rRNA) links amino acids together to form proteins.

The Search for Genetic Material

In 1928, Frederick Griffith, in a series of experiments with Streptococcus pneumoniae (bacterium responsible for pneumonia), witnessed a miraculous transformation in the bacteria.

This must be due to the transfer of the genetic material. However, the biochemical nature of genetic material was not defined from his experiments.

Biochemical Characterization of Transforming Principle

Prior to the work of Oswald Avery, Colin MacLeod and Maclyn
McCarty (1933-44), the genetic material was thought to be a protein. They worked to determine the biochemical nature of transforming principle in Griffith's experiment. They purified biochemicals (proteins, DNA, RNA, etc.) from the heatkilled S cells to see which ones could transform live R cells into S cells.

DNA Is The Genetic Material

The unequivocal proof that DNA is the genetic material came from the experiments of Alfred Hershey and Martha Chase (1952). They worked with viruses that infect bacteria called bacteriophages. Hershey and Chase worked to discover whether it was protein or DNA from the viruses that entered the bacteria. They grew some viruses on a medium that contained radioactive phosphorus and some others on medium that contained radioactive sulfur.

Radioactive phages were allowed to attach to E. coli bacteria. The virus particles were separated from the bacteria by spinning them in a centrifuge. Bacteria which was infected with viruses that had radioactive DNA were radioactive, indicating that DNA was the material that passed from the virus to the bacteria. Bacteria that were infected with viruses that had radioactive proteins were not radioactive. This indicates that proteins did not enter the bacteria from the viruses. DNA is therefore the genetic material that is passed from virus to bacteria.

A molecule that can act as a genetic material must fulfill the following criteria:
1. It should be able to generate its replica (Replication).
2. It should chemically and structurally be stable. 3. It should provide the scope for slow changes (mutation) that are required for evolution.

Packaging of DNA Helix

Taken the distance between two consecutive base pairs as 0.34 nm (0.34 109 m), if the length of DNA double helix in a typical mammalian cell is calculated (simply by multiplying the total number of bp with distance between two consecutive bp, that is, 6.6 109 bp 0.34 10-9m/bp), it comes out to be approximately 2.2 metres. A length that is far greater than the dimension of a typical nucleus (approximately 106 m). How is such a long polymer packaged in a cell?

In prokaryotes, such as, E. coli, though they do not have a defined nucleus, the DNA is not scattered throughout the cell. DNA (being negatively charged) is held with some proteins (that have positive charges) in a region termed as

nucleoid. The DNA in nucleoid is organized in large loops held by

proteins.

Packaging of DNA Helix

Nucleosome

Nucleosomes constitute the repeating unit of a structure in nucleus called chromatin. The nucleosomes in chromatin are seen as beads-onstring structure when viewed under electron microscope (EM).
The beads-on-string structure in chromatin is packaged to form chromatin fibers that are further coiled and condensed at metaphase stage of cell division to form chromosomes.

The packaging of chromatin at higher level requires additional set of proteins that collectively are referred to as Non-histone Chromosomal (NHC) proteins. In a typical nucleus, some region of chromatin are loosely packed (and stains light) and are referred to as Euchromatin. The chromatin that is more densely packed and stains dark are called as Heterochromatin

Assignment
Q 1. The composition (in mole fraction units) of one of the strands of a double-helical DNA molecule is [A]=0.30 and [G]=0.24. (a)What can you say about [T] and [C] for the same strand? (b) What can you say about [A], [G], [T] and [C] of the complementary strand?