chapter 6 notes. biochemistry chemistry is the study of matter, its composition and properties....

Chapter 6 Notes

Biochemistry

Chemistry is the study of matter, its composition and properties.

Matter is anything that has mass and takes up space.

Atoms- building blocks of matter

Atoms are made of three small particles called proton, electrons, and neutrons.

Protons= positive +Electrons = negative –Neutrons= neutral

Atoms contain an equal number of protons and electrons, therefore the overall charge of an atom is neutral.

• The first energy level holds 2 electrons.

• 2nd energy level holds 8 electrons.

• 3rd energy level holds 18 electrons.

• 4th energy level holds 32 electrons.

• 5th energy level holds 18 electrons.

• 6th energy level holds 1 electron.

Elements- pure substances that cannot be broken down into other substances by physical or chemical means

6.Each element has a unique name and symbol. What are the symbols for Carbon-Oxygen-Hydrogen-Nitrogen-

COHN

The elements are arranged on the periodic table by their atomic number, which is the number of protons for that element.

The periodic table of elements is organized into horizontal rows, called periods, and vertical columns, called groups.

Elements in the same group have similar chemical and physical properties.

Isotope- any atom of the same element that have different number of neutrons*The number of protons and electrons remain the same.Ex. Carbon-12 has 6 neutrons, most abundant Carbon-14 has 8 neutrons, radioactive, used for “carbon dating”• Changing the number of

neutrons can in fact affect the stability of the nucleus, sometimes causing it to decay or break apart. When this happens, the atom gives off radiation that can be detected.

Compound- pure substance formed when two or more different elements are combined

There are thousands of known compounds and more are discovered each year.Ex. Water- H₂O Salt/Sodium chloride- NaCl

Compounds have unique properties:1.Always formed from specific

combinations of elements in fixed ratios.

2.Cannot be broken down into simpler compounds or elements by physical means(tearing or breaking), but can be broken down by chemical means.

Chemical Bonds

Covalent bond-form when electrons are shared between two elements

Molecule- compound in which atoms are held together by covalent bonds

Ionic bond-electrical attraction between two oppositely charged atoms called ions, elements exchange electrons• Metals donate electrons• Nonmetals accept

electrons

Ion- atom that has lost or gained an electron

Water H₂OCovalent bond

Sharing electrons

Sodium chlorideNaClIonic bond

Exchanging electrons

van der Waals forces- attractions between molecules, not elements

These forces are what holds water molecules together to form droplets and water surface.

Geckos use van der Waals forces to climb surfaces due to the attraction of atoms making up tiny hair like structures on their toes and atoms making up the surface they are climbing.

6.2 Chemical Reactions

Chemical reaction- process where atoms or compounds are reorganized into different substances by breaking or forming chemical bonds

Chemical changeEx. Rust forming Fe + O₂ Fe₂O₃The iron and oxygen change forms to make rust/iron oxide

Physical changeEx. Water freezing or boiling, changes appearance but not composition

*A chemical change involves a change in the composition of the substance.

Chemical formulas describe the substances in the reaction and arrows indicate the process of change.

Chemical equations• Reactants- starting substances,

left side of arrow• Products- substances formed,

right side of arrowReactants ProductsEx. Photosynthesis equation

H₂O + CO₂ O₂ + C₆H₁₂O₆ Carbon dioxide + water Glucose + oxygen

*The arrow means yields.

The law of conservation of mass states matter cannot be created nor destroyed.

All chemical reactions must balance. *The number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side.

The coefficient is the number in front of the reactant or product.The subscript is the number of atoms.The coefficient times the subscript equals the total number of atoms.6CO₂ + 6H₂O C₆H₁₂O₆ + 6O₂

Activation energy- minimum amount of energy needed for reactants to form products in a chemical reaction• Exothermic- releases heat energy,

product energy is lower than reactants

• Endothermic- absorbs heat energy, product energy is higher than reactants Exothermic

Endothermic

Catalyst- substance that lowers the activation energy needed to start a chemical reaction. They are not used up in a reaction, but are re-used over and over again

Enzyme- special proteins that are catalysts in biological chemical reactions

Substrate- reactants that bind to enzymes

Active site- specific location where substrate binds to enzyme

Factors such as pH, temperature, and other substances affect enzyme activity.

6.3 Water and Solutions

Polar molecule have unequal distribution of charges or oppositely charged poles/ends.Polarity is the property of having two opposite poles. Water is a polar compound.

• Hydrogen bond- weak interaction involving hydrogen and a fluorine, oxygen, or nitrogen atom.

Why is it that water and oil do not mix?Water is a polar molecule as compared to oilThe answer behind this puzzle is that oil does not dissolve in water because of the way molecules of each of these substances interact with each other. Water is a polar molecule. This means this is a molecule that likes to take sides. One side of the molecule is positively charged, while the other is negatively charged. The two atoms of oxygen cling to each other with the single hydrogen atom on the other side. Oil on the other hand is made of carbon atoms bonded to hydrogen atoms forming hydrocarbon chains, this makes them non-polar. What this means is that oil molecules are attracted to each other more than water molecules.There is a particular saying in chemistry called 'Like dissolves like' which basically means polar substances will only dissolve polar substances and so is the same for non-polar substances.Size does matterDid you know that water molecules are much smaller than other molecules? So a number of water molecules have to break their hydrogen bonds to accommodate oil molecules, which is another reason why oil doesn't easily mix with water.

Mixture- combination of two or more substances in which each substance retains its individual characteristics

Homogeneous mixture- uniform composition, also called a solution

Solution = Solute + Solvent

Solute- substance that is dissolvedSolvent- substance that the solute is dissolved intoEx. Kool-Aid, salt water, saliva

• Water is the universal solvent because many substances dissolve in it.

• Water is adhesive (sticks to surfaces) which allows it to travel up the stem of a plant.

• Water is cohesive (molecules stick together) which causes water to form droplets.

Heterogeneous mixture- components remain distinctEx. salad

Suspension- heterogeneous mixture in which the particles settle out over timeEx. sand and water

Colloid- heterogeneous mixture where the particles do not settleEx. Fog, milk, blood

Acids & Bases

Acid-substance that releases hydrogen ions (H+) when dissolved in waterEx. Vinegar, bananas, stomach acid

Base- substance that releases hydroxide ions (OH-) when dissolved in waterEx. Sodium hydroxide, baking soda, sea water

pH & Buffers

The measure of concentration of hydrogen(H+) ions in a solution is called pH.Acidic solutions have pH values lower than 7.Basic solutions have pH values higher than 7.Buffers are mixtures that can react with acids or bases to keep the pH within a particular range.

6.4 Organic Chemistry

The element carbon is a component of almost all biological molecules.

Carbon has four electrons in its outermost energy level.

One carbon atom can form four covalent bonds with other atoms. This enables carbon atoms to bond to each other which results in a variety of important organic compounds.

Macromolecule- large molecules that are formed by joining smaller organic molecules togetherPolymers- molecules made from repeating units of identical compounds called monomers4 majors types:•Carbohydrates• Lipids•Proteins•Nucleic acids

Group orMacromolecule

Example Function Monomer Components

Bread Stores energyStructural support

monosaccharide

Lipids Store energy steroidswaterproofs coatings

Fatty acid and C, H

Hemoglobin transports substancesspeeds reaction structural supporthormones

C,N, O,H, S

Nucleic acids Stores and communicates genetic information

PhosphateN-baseRibose sugar

Carbohydrates

Proteins

C, H, O

Fats, oils, waxes triglyceride

Amino acids

DNA, RNA, ATP

nucleotides

Carbohydrate- compound composed of carbon, hydrogen, and oxygenCH₂O ratio- 1 carbon: 2 hydrogen: 1 oxygen

Monosaccharide- simple sugars, can be linked to form larger moleculesDisaccharide- two monosaccharides linked togetherex. Glucose, sucrose, lactosePolysaccharide- longer chains, more than three monosaccharides linked togetherex. Glycogen

Lipids- molecules mostly made carbon and hydrogen, made of fatty acidsEx. Fats, oils, and waxes

The primary function of lipids is to store energy.

A triglyceride is a fat if it is solid at room temperature and an oil if it is liquid at room temperature.

Saturated fats- fatty acid chain with tails made with single bonds between carbons

Unsaturated fats- fatty acid chain with tails made with at least one double bond between carbonsFats with more than one double bond in the tail are called polyunsaturated fats.

Phospholipids- makes up the structure of plasma membranes

Lipids are hydrophobic, which means they do not dissolve in water.

Proteins- compound made of small carbon compounds called amino acids

Amino acids are made of carbon, nitrogen, oxygen, hydrogen, and sometimes sulfur

Amino acids have a central carbon atom. One of the four carbons bond with a hydrogen atom. The other three are with an amino group(NH₂), a carboxyl group(-COOH), and a variable group(-R)

Nucleic acid- complex molecules that store and transmit genetic information

Nucleic acids are made of smaller repeating subunits called nucleotides. Nucleotides are composed of three units- a phosphate group, a nitrogenous base, and a ribose sugarTwo types of nucleic acids:DNA-DeoxyribonucleicacidRNA- Ribonucleicacid