Chemistry in Biology - Abhinandan Chowdhury

Chemistry in Biology - Abhinandan Chowdhury

Chemistry in Biology Abhinandan Chowdhury (Ach) Life depends on chemistry! When you eat food or inhale oxygen, your body uses these materials in chemical reactions that keep you alive. Just as buildings are made from bricks, steel, glass, and wood, living things are made from chemical compounds.

Atom The study of chemistry begins with the basic unit of matterthe ATOM History Greeks were first to try to explain chemical reactions 400 BC: thought all matter composed of:

Fire Earth Water Air Democritus first used word atomos, meaning indivisible Atom It the smallest component of an element having the chemical properties of the element

It consisting of a nucleus containing combinations of neutrons and protons and one or more electrons bound to the nucleus by electrical attraction The number of protons determines the identity of the element. Atoms have equal numbers of electrons and protons. Because these subatomic particles have equal but opposite charges, atoms are

Elements An element is a substance consisting of atoms which all have the same number of protons - i.e. the same atomic number. Elements are chemically the simplest substances and hence cannot be broken down using chemical methods. Elements can only be changed into other elements using nuclear methods. Atomic Theory of Matter Protons Neutrons Electrons 6

6 6 6 7 6 6

8 6 How many protons, neutrons and electrons in each of the following: protons neutrons electrons 23Na 11 11

12 14N 7 7 7 18 20 18 38Ar 35Cl 17

18 17 36Cl-1 17 19 18 56Fe 26 30 26

More About Atomic Structure The center of the atom is called the nucleus. Electrons live in something called shells. Shells are areas that surround the center of an atom. A shell is sometimes called an orbital or energy level.

Atomic Mass Mass of an atom. Approximately equal to the number of protons and neutrons Find number of neutrons by subtracting the number of protons from the mass. Review: An element's atomic number tells how many protons are in its atoms.

An element's mass number tells how many protons and neutrons are in its atoms. Isotopes Although an element's atoms must all have the same number of protons, they can have different numbers of neutrons and hence different masses. When atoms of the same element have different numbers of neutrons, they are called isotopes. Isotopes are atoms that have the same atomic number but different mass number. Most elements have two or more isotopes.

Same chemical properties because the electron number does not change. More about isotopes: Some isotopes have unstable nuclei which break down over time. They are called radioactive isotopes Some radiations are harmful. Valence Electrons The electrons on the

outside edge of the atom This is where bonding takes place Atoms have no more than 8 valence electrons Terminologies Atom : Particle that is a fundamental building block of matter Atomic number: Number of protons in the atomic nucleus; determines the identity of

element. Charge: Electrical property of some subatomic particles. Opposite charges attract; like charges repel. Electron: Negatively charged subatomic particle that occupies orbitals around the atomic nucleus. Element: A pure substance that consists only of atoms with the same number of protons. Isotopes: Forms of an element that differ in the number of neutrons their atoms carry Mass number: Total number of protons and neutrons in the nucleus of an element's atoms. Neutron: Uncharged subatomic particle in the atomic nucleus. Nucleus: Core of an atom; occupied by protons and neutrons. Proton: Positively charged subatomic particle that occurs in the nucleus of all atoms.

Radioactive decay: Process by which atoms of a radioisotope spontaneously emit energy and subatomic particles when their nucleus disintegrates. Radioisotope: Isotope with an unstable nucleus. 12 Compound Two or more elements chemically combined in specific proportions Examples: Water Salt

Sugar H 2O NaCl C6H12O6 Chemical Formulas are used to represent compounds

Two types of compounds: Ionic Covalent Ionic Compounds Form when electrons are transferred from one atom to another. Ions - Atoms with a net charge due to gaining or losing electrons Gaining electrons gives an ion a negative charge

Losing electrons gives an ion a positive charge Covalent Bonds Formed when a pair of electrons is shared between two atoms. Sometimes the atoms share two pairs of electrons and form a double bond, or three pairs of electrons to form a triple bond.

Ionic compounds form between metals and nonmetals Covalent compounds form between 2 nonmetals Ionization Ionization: breakup of molecules held together by ionic bonding when dissolved

in water (solvent), producing separate positive (cation) and negative (anion) ions These ions conduct electricity and thus called electrolytes Van der Waals Forces There are small attractive forces between all atoms Help to hold molecules to

each other Ex: Gecko Electronegativity The attraction of a particular atom for the electrons of another atom in a covalent bond is called its electronegativity. Atoms in a molecule attract shared electrons to varying degrees, depending on the element. The more electronegative an atom is, the more strongly it pulls shared electrons toward itself. Polar Covalent Bond: Molecule in

which electrons are shared unevenly between atoms, causing each end of the molecule to have a slight charge Non Polar Covalent Bond: The atoms participating in the bond are sharing electrons equally. There is no difference in charge between the two ends of such bonds. Hydrogen Bonds A hydrogen bond is a weak attraction

between a hydrogen atom and another atom taking part in a separate polar covalent bond Like ionic bonds, hydrogen bonds form by the mutual attraction of opposite charges. Unlike ionic bonds, hydrogen bonds do not make molecules out of atoms, so they are not chemical bonds its an attraction Hydrogen bonds form and break much more easily

20 Chemical Bonding Description Bond Strength Example Ionic

Oppositely charged ions Moderate are attracted to each other Bond between Na+ and Cl- in salt Covalent Two atoms share electrons Strong

Bonding of Oxygen and Hydrogen in H2O Hydrogen Forms between oppositely charged portions of covalently bonded hydrogen atoms Bonds between water

molecules Weak 21 Organic Compounds Organic compounds are a class of complex molecules that are characterized by their use of carbon as a molecular backbone. Carbon is able to bond with up to four other atoms, which makes it ideal for building up the

complicated molecules typical of organic chemistry. Adhesion Hydrogen Bonds In Water Are Responsible For: Attraction between molecules of different substances Graduated cylinder

Cohesion Attraction between molecules of the same substance Drops of water on a penny Ex: Surface Tension Jesus Lizard Diffusion and Osmosis In animals and plants the process of diffusion is involved in the transfer of materials within the cells Diffusion is a feature of many processes that control and supply vital substances to the

living body. Example: Respiration - Oxygen is passed from lungs to cells by a process of diffusion.The carbon dioxide excreted by the cells is diffused to the lungs. Excretion -When there is excess water it is diffused to the kidneys, and when there is less water it is diffused back to the body. Diffusion : The process by which molecules spread from areas of high concentration to areas of low concentration. Osmosis The diffusion of water across a semipermeable membrane

Water will move in the direction from low solute concentration ( higher concentration of water) to high solute concentration (and hence a lower concentration of water) Diffusion and Osmosis Tonicity Living cells may be thought of as microscopically small bags of solutions contained within semipermeable membranes. For the cell to survive, the concentration of solutes within the cell must

stay within a safe range. Tonicity is the effect of a solution on the osmotic movement of water Three types: Isotonic Hypotonic Hypertonic Tonicity Isotonic Concentration of solute equal on both sides

Water will move back and forth but wont have any result on the overall amount of water on either side Hypotonic Concentration of solute is lower outside the cell Water will move into the cell Hypertonic Concentration of solute is higher outside the cell

Water will move out of the cell Tonicity and living cells Tonicity and living cells Cells have shrunk Cells are normal Cells have swollen

37 Acids and Bases Acids are molecules that can split apart in water and release hydrogen ions (H ). + Example: hydrochloric acid (HCl) HCl

H++ Cl- Bases are molecules that can split apart in water and release hydroxide ions (OH-) Example: sodium hydroxide (NaOH) NaOH Na+ OH- Charged particles, like hydrogen and hydroxide ions, can interfere with the chemical bonds

that hold molecules together Because living things are made of molecules, strong acids and bases can release enough of these ions to cause damage Even water can split apart to create hydrogen and hydroxide ions. H2O H+OH- In pure water, the number of hydrogen ions and hydroxide ions are balanced, so they dont do any damage to living things.

Acids and pHBases It is the hydrogen ion concentration in a solution pH = -log10 c c is the hydrogen ion concentration in moles per liter The pH scale goes from 1 to 14. pH of 7 is neutral - the amount of hydrogen ions and hydroxide ions in a solution is equal, just like in pure water pH <7 Acidic solution - A solution that contains more hydrogen ions than hydroxide ions

If a molecule releases hydrogen ions in water, its an acid. The more hydrogen ions it releases, the stronger the acid, and the lower the pH value. pH >7 Basic solution - A solution that contains more hydroxide ions than hydrogen ions Bases dissociate (break apart) into hydroxide ions (OH) and a positive ion. The OH can combine with H+ to form water Because the hydrogen ions are used, the number of hydrogen ions in the solution decreases, making the solution less acidic and therefore more

39 pH of common substances Acids and Bases Buffer Living things are made of molecules - strong acids and bases can release enough of these ions to cause damage. Buffer: a solution that resists changes in pH when acid or alkali is added to it.

Buffers typically involve a weak acid or alkali together with one of its salts. Buffers keep solutions at a steady pH by combining with excess hydrogen or hydroxide ions. They help in homeostasis. Think of them as sponges for hydrogen and hydroxide ions. If a substance releases these ions into a buffered solution, the buffers will soak up the extra ions. If buffer system doesnt work, an organism can develop: Acidosis (blood becomes too acidic): the pH drops too low Alkalosis (blood becomes too basic): the pH gets too high

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