1. Chapter 6 Honors Biology
Chemistry in Biology
Chapter 6
Honors Biology
EQ: How is chemistry related to the growth and survival of living organisms?

2. 6.1: Atoms, Elements, and Compounds
Chemistry is the study of matter.
Matter is anything that has mass and takes up space.
Atoms are the building blocks of matter.
THE STRUCTURE OF ATOMS:
Billions of atoms could fit on the head of a pin!
Atoms are made up of even smaller particles –
Neutrons
Protons
Electrons

3. The Structure of Atoms:
Nucleus – the center of an atom
Within this nucleus are protons and neutrons.
Neutrons – particles that have no charge
Protons – particles with a positive charge
Electrons – negatively charged particles located outside the nucleus.
Constantly move around the nucleus in energy levels.
Are attracted to the protons
Atoms contain an equal number of protons and neutrons so the overall charge of an atom is neutral.

4. An Atom:

5. Elements: Horizontal rows – called periods.
Vertical columns – called groups – similar chemical and physical properties.

6. Elements:
An element is a pure substance that cannot be broken down into other substances by chemical or physical means.
Are made of only one type of atom.
Information collected about each element has been organized into a chart called the periodic table of elements.
Organized into horizontal rows called periods,
And vertical columns called groups.

7. Isotopes:
Isotopes – atoms of the same element that have different numbers of neutrons.
Mass (A) = # of protons + # of neutrons
Atomic number (Z)= number of
protons
How many neutrons in Carbon 14?
14 (mass#) – 6 (atomic #) = 8 neutrons
Carbon 14 is a radioactive isotope.

8. Radioactive Isotopes:
A change in the number of neutrons CAN change the stability of the nucleus causing it to decay (or break apart).
When a nucleus decays, it gives off radiation that can be detected and used for many applications.
Isotopes that give off radiation are called radioactive isotopes.
Carbon 14 is a radioactive isotope found in all living things.
Half life – the amount of time it takes for half of the carbon 14 to decay.
Scientists can determine the age of an object by calculating how much carbon 14 remains in the sample.
Radioactive isotopes can be used for medical purposes (radiation therapy to treat cancer, radioactive labeling to track certain subsatnces).

9. Compounds Elements can combine to form more complex substances.
Compounds are pure substances formed when two or more different elements combine.
NaCl
CaCl
H2O
CO2

10. Chemical Bonds:
A chemical bond is the force that holds substances together.
Electrons are directly involved in forming chemical bonds.
Each energy level has a specific number of electrons that it can hold at any time.
The first energy level (the one closest to the nucleus) can hold up to two electrons.
The second energy level can hold up to eight electrons.

11. Chemical Bonds (continued)
A partially filled energy level is not as stable as an energy level that is empty or completely filled.
Atoms become more stable by losing electrons or attracting electrons from other atoms.
THIS RESULTS IN THE FORMATION OF CHEMICAL BONDS BETWEEN ATOMS.
It is the forming of chemical bonds that stores energy and the breaking of chemical bonds that provides energy for growth, development, adaptation, and reproduction in living things.

12. The Two Main Types of Chemical Bonds Are:
1. Covalent Bonds 2. Ionic Bonds
Covalent bond – the chemical bond that forms when electrons are shared. Most compounds in living organisms have covalent bonds holding them together.
Ionic bond – an electrical attraction between two oppositely charged atoms or groups of atoms called ions. Substances formed by ionic bonds are called ionic compounds.
Ion = an atom that has lost or gained one or more electrons; carries an electric charge.
Ions in living things include sodium, potassium, calcium, chloride, and carbonate ions. They help maintain homeostasis as they travel in and out of cells. In addition, ions help transmit signals among cells that allow you to see, taste, hear, feel, and smell.

13. Types of Compounds:
1. Molecule - a compound in which the atoms are held together by covalent bonds.
2. Ionic compound – a substance formed by ionic bonds.

14. Van Der Waals Forces:
Attractive forces between molecules due to the random movement of electrons which can cause an unequal distribution of electrons around the molecule.
Not as strong as a covalent bond or an ionic bond but they play a key role in biological processes.

15. Activity:
Turn to page 155 in the text and answer questions 1-6.

16. 6.2: Chemical Reactions
Chemical reactions allow living things to grow, develop, reproduce, and adapt.
The human body is a 24 hour reaction factory!
A chemical reaction is the process by which atoms or groups of atoms in substances are reorganized into different substances. Chemical bonds are broken and/or formed during chemical reactions.

17. Two Examples of Chemical Reactions are:
The formation of rust on metal.
Glow sticks

18. Rust forms when oxygen in the air reacts with iron:
The rust on these gear components is a compound called iron oxide and it was formed when oxygen in the air reacted with the iron components.

19. A light stick consists of a
glass vial, containing one
chemical solution, housed
inside a larger plastic vial,
containing another solution.
When you bend the plastic vial,
the glass vial breaks, the two
solutions flow together, and the resulting chemical reaction
causes a fluorescent dye to emit
light.

20. Physical Changes
It’s important to know that substances can undergo changes that do not involve chemical reactions.
Water, for example, can undergo physical changes:
Water > Water Vapor > Water
Water > Ice > Water
The water is undergoing a physical change but it’s composition is not changed.

21. Reactants and Products
A chemical equation shows the reactants on the right side of an arrow, and the products on the left.
Reactants – the starting substances of a chemical reaction.
Products – The substances formed during the reaction.
Reactants Products
C6H12O6 + O CO2 + 6H2O

22. Balanced Equations: C6H12O6 + O2 6CO2 + 6H2O
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.
1. Use coefficients to make the number of atoms on each side of the equation equal.
2. Multiply the coefficient by the subscript for each element.
Is the above equation balanced?
No, the above equation is not balanced. To balance this equation you must put the coefficient 6 in front of the oxygen reactant.

23. Energy of Reactions
The key to starting a chemical reaction is energy.
Activation energy is the minimum amount of energy needed for reactants to form products in a chemical reaction.
The flame above provides the activation energy for the reaction of the substances in the candle wick with oxygen. Once the reaction begins, no further input of energy is required – the candle will continue to burn on its own. + =

24. Activation Energy Video Clip

25. Exothermic Reaction Progress of Reaction Energy Heat is given off
An exothermic reaction = the energy of the product is lower than the energy of the reactants and energy was released.
The peak in the graph represents the amount of energy that must be added to the system to make the reaction go. Some reactions never take place because they have a very high activation energy.
Progress of Reaction

26. Endothermic Reaction
An endothermic reaction – the energy of the products is higher than the energy of the reactants.
This type of reaction takes in heat so the reaction will feel cold.
When we added vinegar to baking soda, we created an endothermic reaction. Did you notice the reaction felt cold?

27. Enzymes
Sometimes, the activation energy required for a reaction to take place is too high. The reaction can’t take place unless additional substances are present to reduce the activation energy.
A catalyst is a substrate that lowers the activation energy needed to start a chemical reaction.
Does not increase how much product is made
Doesn’t get used up in a reaction
Enzymes – special proteins that act as biological catalysts to speed up the rate of reactions.
Enzymes are not used up by a chemical reaction. Once it has participated in a chemical reaction, it can be used again. Most enzymes are specific to one reaction.
Example: Amylase is an enzyme found in saliva. It breaks down amylose, one of two components of starch.

28. Enzymes Without Enzyme With Enzyme
Free energy released by the reaction
Compare the activation energy of the reaction without enzyme to the activation energy of the reaction with enzyme.

29. How Enzymes Work: Active Sites
The reactants that bind to the enzyme are called substrates.
Active site – the specific location where a substrate binds to an enzyme.
Active site and substrate have complimentary shapes. They are specific for each other.
The enzyme-substrate complex helps chemical bonds in the reactants to be broken and new bonds to form. The substrates react to form products. The enzyme then releases the products.
Active Sites

30. Factors that affect enzyme function:
Temperature – if….
Too high – enzyme will denature
Too cold – enzyme activity will slow
pH – enzymes will denature if pH is
Too acidic (H+ ions)
Too basic (OH- ions)

31. Section 6.3: Water and Solutions
Properties of water (H2O):
Water is a polar molecule – it has an unequal distribution of charges.
Hydrogen bonds – a weak attraction involving a hydrogen atom and an oxygen atom. Van der Waals forces are responsible for keeping water molecules together.
Water has surface tension due to Van der Waals forces.
Water striders can stand on water.
Water droplets can form.

32. Water is a Polar Molecule

33. Mixtures
A mixture is a combination of two or more substances in which each substance retains its individual characteristics and properties.
Homogenous mixture – uniform composition throughout
Heterogenous mixture – components remain distinct, do not dissolve
A solution is a homogenous mixture. Two components of a solution are:
Solvent – substance in which another substance is dissolved
Solute – the substance that is dissolved in the solvent.

34. Acids and Bases:
Acids are substances that release hydrogen ions when dissolved in water.
The more hydrogen ions a substance releases, the more acidic the solution becomes.
Substances that release hydroxide ions (OH-) when dissolved in water are called bases.
NaOH is a common base that breaks apart in water to release Na+ and OH- ions. The more OH- ions present, the more basic a solution is.

35. pH: The amount of hydrogen ions
or hydroxide ions in a solution determines the strength of an acid or a base.
We can easily measure the pH of a solution using a pH meter or pH paper.
See the pH scale to the right.
Water is neutral (pH 7)
Acids have a pH lower than that of water.
Bases have a pH higher than that of water.
What’s a buffer?
The majority of biological processes carried out by cells occur between pH 6.5 and In order to maintain homeostasis, it’s important to control H+ levels.
Buffers are mixtures that can react with acids or bases to keep the pH in a cell within the 6.5 to 7.5 pH range.

36. 6.4: The Building Blocks of Life
Organisms are made up of carbon-based molecules.
Carbon is a component of almost all biological molecules.
Organic chemistry – the study of organic compounds (compounds containing carbon).

37. Carbon:
Has 4 electrons in its outer energy level. This energy level can hold 8 electrons so one carbon atom…
Can form 4 covalent bonds with other atoms.
Carbon atoms can bond to each other in different ways:
Straight chain molecules:
Branched molecules:
Ring molecules:

38. Macromolecules -
Are large molecules that are formed by joining smaller organic molecules together.
Monomer – a single molecule that can bind
to several others just like it to form a polymer.
Polymer – many monomers linked together
by covalent bonds.

39. There are 4 major categories of macromolecules:
Carbohydrates
Lipids
Proteins
Nucleic Acids

40. Carbohydrates
Compounds composed of carbon, hydrogen, and oxygen (CH2O)n.
This glucose monosaccharide plays
a central role as an energy source for
organisms.
Monosaccharides can be linked to
form disaccharides (sucrose) or
Polysaccharides.
CHO’s:
monosaccharide = glucose
disaccharides = sucrose (table sugar)
lactose (milk sugar)
polysaccharide – glycogen is an energy storage form of glucose found in the liver and muscles.
When the body needs energy and no glucose is available, the body will break glycogen down into glucose.
Plants – cellulose is a carbohydrate which provides structural support for the plant’s cell walls.
Glucose
(Monosaccharide)

41. Lipids
Fats, oils, waxes
Lipid molecules are made up of carbon and hydrogen.
Store energy
Basic structure of a lipid includes fatty acid chains (tails):
Tails are chains of carbon bonded together by either single or double bonds. Hydrogen atoms are bonded to the carbon atoms.
Saturated – single bonds between carbon atoms so no more hydrogens can bond.
Unsaturated – one double bond between C atoms, so at least one hydrogen can bond.
Polyunsaturated fats are fats with more than one double bond in the tail.

43. Phospholipids and Steroids
Phospholipid bilayer
Steroids
Cholesterol
Hormones

44. Proteins Compounds made of small carbon compounds called amino acids.
Amino acids are small compounds made of carbon, nitrogen, oxygen, hydrogen and sometimes sulfur.
All amino acids share the same general structure:
Central carbon atom
Amino group
Carboxyl group
Variable side chain – there are 20 different ones
Several covalent bonds called peptide bonds join aa’s together to form protein chains.
Peptide bonds

45. Proteins (cont.) Can have up to 4 levels of structure:
Primary
Secondary
Helix
pleat
Tertiary – a globular arrangement (hemoglobin)
Quaternary – proteins bound to other proteins
Structure depends on the number of amino acids in a chain and how they are arranged.

47. Proteins (cont.) Muscle, skin, hair are made up of proteins
Are involved in almost every function of your body
Cells contain 10,000 different proteins that provide
Structural support
Transport substances
Communicate signals between cells
Catalysts for enzymatic reactions
Control cell growth

48. Nucleic Acids:
Nucleic acids are complex macromolecules that store and transmit genetic information. Two types:
DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
Made of smaller repeating subunits called nucleotides which are composed of
Carbon
Nitrogen
Oxygen
Phosphorus
Hydrogen

49. Nucleotide: