BIOCHEMISTRY I General Chemistry August 2014

CHEMISTRY OF LIFE Atom: the actual basic unit - composed of protons, neutrons, and electronsAtom: the actual basic unit - composed of protons, neutrons, and electrons

THE ATOM Just like cells are the basic unit of life, the ATOM is the basic unit of matter. Just like cells are the basic unit of life, the ATOM is the basic unit of matter. They are very small. If placed side by side one million would stretch a distance of 1cm. They are very small. If placed side by side one million would stretch a distance of 1cm. The atom is made up of three particles. The atom is made up of three particles. ParticleCharge PROTON PROTON+ NEUTRON NEUTRAL (0) ELECTRON-

Electrons are not present within the atom. Instead, they revolve around the nucleus of the atom and form the ELECTRON CLOUD Electrons are not present within the atom. Instead, they revolve around the nucleus of the atom and form the ELECTRON CLOUD Below is a diagram of a helium atom. Below is a diagram of a helium atom PROTONS NEUTRONS ELECTRONS ATOMIC # = 2 (PROTONS) ATOMIC MASS = 4 (PROTONS & NEUTRONS)

The Element Elements: simplest form of a substance - cannot be broken down any further without changing what it is Elements: simplest form of a substance - cannot be broken down any further without changing what it is It is a substance composed of one type of atom It is a substance composed of one type of atom There are 92 living elements There are 92 living elements – 11 in living things

Living Elements 99% of atoms in the body are: – Nitrogen (N) – Oxygen (O) – Carbon (C) – Hydrogen (H) – Sulfur (S) – Phosphorus (P)

Role in Biogeochemical Cycles These six elements play important roles in the biogeochemical cycles – Biogeochemical cycle: A pathway by which a chemical element or molecule moves through the living and non- living parts of Earth The major cycles include: Carbon, Nitrogen, Oxygen, Phosphorus, Sulfur, and Water water (molecule)

COMPOUNDS A substance formed by the chemical combination of 2 or more elements in definite proportions A substance formed by the chemical combination of 2 or more elements in definite proportions – Ex: water, salt, glucose, carbon dioxide

The cell is a COMPLEX CHEMICAL FACTORY containing some of the same elements found in the nonliving environment. The cell is a COMPLEX CHEMICAL FACTORY containing some of the same elements found in the nonliving environment. carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatest percentages carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatest percentages

TWO TYPES OF COMPOUNDS Organic - Contain Carbon bonded to other Carbons, H and O in some ratio (usually referred to as chemicals of life) Organic - Contain Carbon bonded to other Carbons, H and O in some ratio (usually referred to as chemicals of life) – Carbohydrates, Proteins, Lipids, Nucleic Acids Inorganic - usually "support" life - no specific ratio of C, H, and O Inorganic - usually "support" life - no specific ratio of C, H, and O – Water (H2O), Carbon Dioxide (CO2)

Molecule Vs. Compound A molecule is formed when two or more atoms join together chemically – Can be the same or different atoms – Ex: Hydrogen (H 2 ), Oxygen (O 2 ), and Water (H 2 O) A compound is a molecule that contains at least two different elements – Ex: Water (H 2 O), Carbon dioxide (CO 2 ) *All compounds are molecules but not all molecules are compounds

CHEMICAL BONDS Chemical bonds hold the atoms in a molecule together. Chemical bonds hold the atoms in a molecule together. There are 2 main types of chemical bonds: IONIC and COVALENT There are 2 main types of chemical bonds: IONIC and COVALENT

IONIC BONDS Occur when 1 or more electrons are TRANSFERRED from one atom to another. Occur when 1 or more electrons are TRANSFERRED from one atom to another. When an atom loses an electron it is a POSITIVE charge. When an atom loses an electron it is a POSITIVE charge. When an atom gains an electron it is a NEGATIVE charge When an atom gains an electron it is a NEGATIVE charge These newly charged atoms are now called IONS These newly charged atoms are now called IONS – Example: NaCl (SALT)

COVALENT BONDS Occur when electrons are SHARED by atoms. Occur when electrons are SHARED by atoms. These new structures that result from covalent bonds are called MOLECULES These new structures that result from covalent bonds are called MOLECULES ** In general, the more chemical bonds a molecule has the more energy it contains ** In general, the more chemical bonds a molecule has the more energy it contains SHARING IS CARING!

MIXTURES Water is not always pure. It is often found as part of a mixture. Water is not always pure. It is often found as part of a mixture. Mixture: a material made of two or more elements or compounds that are physically mixed Mixture: a material made of two or more elements or compounds that are physically mixed – Ex: salt & pepper mixed, sugar and sand – can be easily separated

SOLUTION Cannot be separated once mixed Two parts: SOLUTE – substance that is being dissolved (sugar, salt) SOLUTE – substance that is being dissolved (sugar, salt) SOLVENT - the substance in which the solute dissolves SOLVENT - the substance in which the solute dissolves Materials that do not dissolve are known as SUSPENSIONS. Materials that do not dissolve are known as SUSPENSIONS. – Blood is the most common example of a suspension. – Cells & other particles remain in suspension.

FORMULA The chemical symbols and numbers that compose a compound ("recipe") The chemical symbols and numbers that compose a compound ("recipe") Structural Formula – Line drawings of the compound that shows the elements in proportion and how they are bonded Structural Formula – Line drawings of the compound that shows the elements in proportion and how they are bonded Molecular Formula – the ACTUAL formula for a compound Molecular Formula – the ACTUAL formula for a compound C2H6OC2H6OC2H6OC2H6O

Chemical Equations The beginning substances (reactants) are changed into other substances (products) CH 4 (g) + 2 O 2 (g)  CO 2 (g) + H 2 O (g) Reactants Products

WATER (H 2 O) The most important inorganic compound for living organisms Most cellular activities take place in water solutions Water is most often what substances dissolve in

Water is a Polar Molecule Polar molecule: molecule in which the charges are unevenly spread Because of its positive and negative charge, water molecules are attracted to each other The atoms bind in such a way that there are excess electrons on the Oxygen side and an excess of positive charges on the Hydrogen side

Non-Polar Molecules Non-polar molecules have electrons distributed more symmetrically and so do not have an abundance of charges at the opposite sides – All charges cancel each other out Examples: Methane, Gasoline

Hydrogen Bonds of Water Because of its partial positive and negative charges, water molecules can attract each other Hydrogen bond: the pull between a partially positive hydrogen atom on one molecule and a partially negative oxygen atom on another – Form between the H 2 atoms and O 2 atoms of different water molecules

Hydrogen Bonds of Water Hydrogen bonds are not as strong as covalent or ionic bonds – But, they give water 3 special properties…

Adhesion Water molecules stick to other substances This causes water to be higher on edges of a graduated cylinder than in the middle

Grab a graduated cylinder and add water. Draw your observation on the diagram

Cohesion Water molecules stick together – Water is attracted to water

Surface Tension This is the measure of the difficulty to break or stretch the surface of a liquid Water has strong surface tension because of the hydrogen bonds between water molecules at the water’s surface – Causes a film that can support the weight of some animals

Water: The Universal Solvent It is capable of dissolving a variety of substances It dissolves more substances than any other liquid This is important to every living thing on Earth Wherever water goes (eg. the ground, our bodies), it takes along valuable chemicals, minerals and nutrients

ACIDS & BASES Acids: always (almost) begin with "H" because of the excess of H+ ions (hydrogen) Acids: always (almost) begin with "H" because of the excess of H+ ions (hydrogen) – Ex: lemon juice (6), stomach acid (1.5), acid rain (4.5), normal rain (6) – HCL, H 2 SO 4 Facts about Acids Acids usually taste SOUR. Acids usually taste SOUR. You eat acids daily You eat acids daily Examples: coffee, vinegar, soda, spicy foods, etc… Examples: coffee, vinegar, soda, spicy foods, etc…

ACIDS & BASES Bases: always (almost) end with -OH because of the excess of hydroxide ions (Oxygen & Hydrogen) Bases: always (almost) end with -OH because of the excess of hydroxide ions (Oxygen & Hydrogen) – EX: oven cleaner, bleach, ammonia, sea water, blood, pure water – NaOH, Ca(OH) 2 Facts about Bases Bases usually feel SLIPPERY to touch and taste BITTER. Bases usually feel SLIPPERY to touch and taste BITTER.

pH SCALE measures degree of substance alkalinity or acidity measures degree of substance alkalinity or acidity Ranges from 0 to 14 Ranges from 0 to 14 0 – 5 strong acid 0 – 5 strong acid 6-7 neutral 6-7 neutral 8-14 strong base 8-14 strong base

The goal of the body is to maintain HOMEOSTASIS (neutrality) – to do this when pH is concerned, we add weak acids & bases to prevent sharp changes in pH. The goal of the body is to maintain HOMEOSTASIS (neutrality) – to do this when pH is concerned, we add weak acids & bases to prevent sharp changes in pH. These are called BUFFERS These are called BUFFERS