Chemistry

 Why is studying chemistry important in Biology?

 All organism are chemical machines

Atoms

 What does all matter have in common?

 It is all made up of atoms

 Atoms- is the smallest unit of matter that cannot be broken down by chemical means

 Consist of protons, neutrons, and electrons

Atoms

 Protons and Neutrons make up the atom’s nucleus

 The electrons make up the electron cloud that orbit the nucleus

 Protons (+), Neutrons (no charge), and Electrons are (-)

 Usually the number of protons and electrons are equal, since they are equal the atom has no overall charge

Elements

 Element- pure substance made of only one kind of atom

 Elements differ in the number of protons they have

 Atoms of an element that have a different number of neutrons are called isotopes

Chemical Bonding

 Atoms can join with other atoms to form stable substances

 A force that joins the 2 is called chemical bonding

 Compound- is a substance made of joined atoms of 2 or more different elements

 EX: Na + Cl = NaCl “Table Salt”

Covalent Bonding

 Covalent bonding- when 2 or more atoms share electrons to form a molecule

 Molecule- is a group of atoms held together by covalent bonds

 Because the number of protons = the number of electrons the molecule has no net electrical charge EX: CO2

Covalent Bonding

 The arrangement of their electrons determines how atoms bond together

 Electrons are grouped into levels; the levels close to the nucleus have less energy than those farther away

 Electron levels have limits on the number of electrons they can hold; some 2 some 8

Covalent Bonding

 An atom becomes stable when its outer level is full

 If the outer level isn’t full it will react with other atoms to fill its need

 Ex: water H2O hydrogen has 1 electron in its outer shell and oxygen has 6 = 8

 2 hydrogen join 1 oxygen

Hydrogen Bonds

 Electrons in a water molecule are shared between hydrogen and oxygen, but the shared electrons are more
attracted to oxygen nucleus than the hydrogen nucleus

 The water molecule therefore has partially positive and negative ends, or poles

Hydrogen Bonds

 The partially positive of one end of the water molecule is attracted to negative end of another water molecule

 This is what we call polar molecules

 These attraction between 2 water molecules is an example of a hydrogen bond- a weak chemical attraction
between polar molecules

Ionic Bonds

 Sometimes atoms gain or lose electrons

 An atom or molecule has gained or lost one or more electrons are called Ions

 Ions have an electrical charge b/c they contain an unequal number of electrons and protons
Ionic Bonds

 An atom that has lost electrons are POSITIVELY CHARGED

 An atom that has gain electrons are NEGATIVELY CHARGED

 Ions of opposite charges can interact to form Ionic Bonds

Ionic Bonds

 Na is unstable because it has only 1 electron in its outer level, Na readily gives up this electron to become stable
(Na+); Cl has 6 electrons in its outer level

 Cl readily accepts an electron to become stable (Cl-)

 Opposites attract to form Na+Cl-

Water and Solutions “Storage of Heat”

 Water heats more slowly and retains heat longer than many other substances

 Many organisms release heat through water evaporation (sweating); carries heat away from the body

 The ability to control an internal temp. despite of external temps.

 Water helps maintain Homeostasis

Water and Solutions “Cohesion and Adhesion”

 The hydrogen bonds between water molecules cause the cohesion of liquid water

 Cohesion- is an attraction between substances of the same kind

 B/c of cohesion water forms thin films and drops (surface tension)

 Surface tension prevents the surface of water from stretching or breaking

Water and Solutions “Cohesion and Adhesion”

 Water molecules are also attracted to many other similarly polar substances

 Adhesion- is an attraction between different substances

 B/c of adhesion some substances get wet

 Adhesion powers capillary action; like water moving up the stems of a plant

Water and Solutions “Cohesion and Adhesion”

 Water is sucked up b/c the force of gravity is less than the power of water clinging to the walls of the xylem

 Water moves upward from through the plant from roots to leaves b/c of capillary action, cohesion, and etc….
Aqueous Solutions

 Many things dissolve in water; like when salt is added to water it is called a saltwater solution

 Solution- is a mixture in which 1 or more substances are evenly distributed in another substances

 Many important substances are dissolved in your blood

Aqueous Solutions

 B/c the substances can dissolve in water, they can easily move within and between your cells

 Sugar is dissolved in water, so that it can reach your cells to make energy

Aqueous Solutions “Polarity”

 The polarity of water allows many substances to be dissolved in it

 Ionic compounds and polar molecules dissolve best in water

 Polar water molecules attract to other positive and negative ends of other compounds which evenly distributes
ions or molecules in the water

Aqueous Solutions “Polarity”

 Nonpolar molecules do not dissolve well in water

 Oil is nonpolar; water attracts to other polar molecules instead of the oil (don’t mix); the nonpolar molecules are
shoved together

The inability of nonpolar molecules to dissolve in polar molecules is very important to organisms

Aqueous Solutions “Polarity”

 It is important b/c, the shape and function of cell membranes depend on the interaction of polar water with
nonpolar membrane molecules

Aqueous Solutions “Acids and Bases”

 While the bonds in a water molecule are strong, at any given time a tiny fraction of those bonds might break,
forming a hydrogen ion H+, and a hydroxide ion, OH-

 H2O H+ + OH-

Aqueous Solutions “Acids and Bases”

 As a result, pure water always has a low concentration of hydrogen ions and hydroxide ions, which are present
in equal numbers

 Acids- are compounds that form hydrogen ions when dissolved in water

 When an acid is added to water, the concentration of hydrogen in the solution is increased above that of pure
water

Aqueous Solutions “Acids and Bases”

 Bases- are compounds that reduce the concentration of hydrogen ions when dissolved in water

 Many bases form hydroxide ions when dissolved in water, *Such bases lower the concentration of hydrogen
ions b/c hydroxide ions react with hydrogen ions to form water molecules
Aqueous Solutions “Acids and Bases”

 pH scale measures the concentration of hydrogen ions in solutions

 All are between 0 – 14

 Pure Water= 7

 Acidic= less than 7

 Basic= more than 7

Chemistry of Cells “ Carbon Compounds”

 Other than your water, your body is mostly made up of organic compounds

 Organic compounds contain carbon atoms that are covalently bonded to other elements- typically hydrogen and
oxygen

Chemistry of Cells “ Carbon Compounds”

 4 principal classes of organic compounds are found in living things:

 1. Carbohydrates

 2. Lipids (Fats)

 3. Proteins

 4. Nucleic Acids

Carbohydrates

 Carbohydrates- are organic compounds made of carbon, hydrogen, and oxygen atoms in the proportion of 1:2:1

 Key source of energy; found in fruits, veggies, and grains

 The building blocks of carbs are called monosacchrides; Ex: Glucose C6H12O6

Carbohydrates

 Monosaccharides are simple sugars

 Disaccharides are double sugars joined when 2 monosaccharides join together; Ex: Sucrose = glucose + fructose

 Polysaccharides= 3 or more monosaccharides join Ex: STARCH and CELLULOSE

Carbohydrates

 Polysaccharide is an example of a macromolecule, a large molecule made of many smaller molecules

 Polysaccharides can function as storehouses of energy

Carbohydrates

 Include sugars, starches, cellulose, and gums

 End in “OSE” Glucose

 Monosaccharides

Pentose- 5 sided; deoxyribose,ribose, ribulose

Hexose- 6 sided; glucose, galactose, fructose

Carbohydrates

 Disaccharides

Maltose= glucose + glucose

Sucrose= glucose + fructose

Lactose= glucose + galactose

Carbohydrates

 Polysaccharides

1. Storage polysaccharides store energy

a. starch in plants

b. glycogen in animals

2. Structural polysaccharides- give support and protection

a. cellulose in cell wall

b. chitin in fungal cell wall and anthropod exoskeleton

Lipids

 Lipids- are nonpolar molecules that aren’t soluble in water; they include steroids, phospholipids, and waxes

 Very important in structure and function of cellular membranes

 Phospholipids make up the bilayer of the cell membrane

Lipids

 Steroids include cholesterol, which is found in animal cell membranes

 Other lipids include pigments, such as chlorophyll

 Fats are lipids that store energy (2 times of carbohydrates)

 A typical fat includes 3 fatty acids bonded to a glycerol molecule backbone

Lipids

 A fatty acid is a long chain of carbon atoms with hydrogen atoms bonded to them

 Saturated Fatty Acid- all carbon are bonded to 2 hydrogen atoms except for the end which has 3 hydrogen
atoms; generally straight; solid at room temp.; butter, lard, grease, and animal fat

Lipids

 Unsaturated Fatty Acid- some carbon atoms are “double covalently bonded;” produces kinks in the chain

 Liquid at room temp.

 Olive oil and fish oil

 Some unsaturated can become saturated by adding hydrogens creating “Hydrogenated Vegetable Oils”

Lipids

 Steroids- are lipids that function as hormones

 Waxes- protection for plant/animal structures

Proteins

 Protein- large molecule formed by joining amino acids

 Amino acids- building blocks of proteins; 20 different amino acids found in proteins

 Proteins tend to fold depending on how the amino acids react with water and one another

Proteins

 Some proteins are enzymes which promote chemical reactions; some are for structure

 Antibodies are proteins that defend your body from infection

 Proteins in your muscles cause them to contract

 Hemoglobin in your blood is a protein that carries oxygen throughout your body, from your lungs to body tissues

Nucleic Acids

 All your cells contain nucleic acids

 Nucleic acid- is a long chain of smaller molecules called nucleotides

 Nucleotides- has 3 parts: a sugar, a base, and a phosphate group (which contains phosphorous and oxygen)

 There are 2 types of nucleic acids:1. DNA and 2. RNA; and each type contain 4 nucleotides

Nucleic Acids

 DNA- deoxyribonucleic acid, consists of 2 strands of nucleotides that spiral around each other

 Chromosomes contain long strands of DNA. Which stores hereditary information

Nucleic Acids

 RNA- ribonucleic acid; single strand of nucleotides

 Play many key roles in making proteins

 Can act as an enzyme, promoting the chemical reactions that link amino acids forming proteins

Energy and Chemical Reactions

 Energy- the ability to move or change matter

 We are surrounded by energy; electrical, kinetic, mechanical, thermal, and chemical

 One can be converted into the other

 Energy can be stored and released by chemical reactions

Chemical Reaction

 Chemical Reaction- is a process during which chemical bonds between atoms are broken and new ones are
formed, producing 1 or more different substances

 Reactant- starting material

 Product- finishing material

 Chemical Reactions are written by chemical equations

Chemical Reaction

 A Chemical Reaction is written like this:

Reactants Products

The arrow means “forms or changes”

Energy in Chemical Reactions

 Energy is absorbed or released when bonds are broken and formed

 Metabolism- all the chemical reactions that occur within an organism

 Your cells get most of the energy needed for metabolism from the food you eat; food is digested and chemical
reactions convert the chemical energy in food to energy for cells

Activiation Energy

 Activiation Energy- energy needed to start a chemical reaction

 For a log to burn, ya gotta heat it up

Enzymes

 Most biochemical reactions- chemical reactions that occur in cells, need activation energy to begin

 The chemical reactions in cells occur quickly and at a relatively low temp. due to enzymes

 Enzyme- are substances that increase the speed of a chemical reaction ( by reducing the amount of activation
energy)
Enzymes

 Enzymes help organisms maintain homeostasis

 W/out enzymes chemical reactions wouldn’t occur fast enough to sustain life

 p.40 gives an example

Enzyme Specificity

 Substrate- a substance on which an enzyme acts during a chemical reaction

 Enzymes act only on specific substrates

 An enzymes shape determines its activity

 An enzymes is typically a large protein with folds on its surface

 These folds form pockets called active sites

Enzyme Specificity

 Step 1- when an enzyme first attaches to a substrate during a chemical reaction, the enzyme shapes changes
slightly so that substrate fit more tightly in the enzyme’s active site

 Step 2- at an active site, an enzyme and a substrate interact in a way that reduces the activation energy of a
reaction, making the substrate more likely to react

 Step 3- the reaction is complete when products have formed. The enzyme is now free to catalyze further
reactions

Factors in Enzyme Activity

 Any factor that can change the shape of the enzyme can change its effectiveness

 Usually have a temp range that they like, certain pH levels

 Those can change the bond which change its shape

 The enzymes that are active at any one time in a cell determine what happens in that cell