1. Biomolecules 2

2. Most biological molecules are made from covalent combinations of six important elements,
whose chemical symbols are CHNOPS.
Biological molecules, or biomolecules, are mainly built by joining atoms through covalent bonds.
Although more than 25 types of elements can be found in biomolecules,
six elements are most common. These are called the CHNOPS elements;
the letters stand for the chemical abbreviations of
carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.

3. C, H, N, O , P, S

4. Valence and Covalent Bonding
Each element has a characteristic valence that determines the number of covalent bonds it can form.
The ability of an atom to combine with other atoms depends on
the number of electrons in the outer shells of the atoms. Some elements, the so-called noble gases,
have complete outer shells and do not share electrons.
Many elements will share electrons with other elements, such that each element completes
its outer electron shell capacity to effectively resemble nobel gases A shared electron pair is called a covalent bond. The number of covalent bonds that each element can form is
called its valence.
The CHNOPS atoms are shown above. Each valence position is represented by a stick protruding from the atom.

5. Hydrocarbons, the simplest organic molecules, contain only carbon and hydrogen atoms.
Because carbon can form simultaneous covalent bonds with up to four partners, an enormous number of carbon compounds are possible. Carbon chemistry is called organic chemistry.
Among the simplest organic compounds are those containing only hydrogen and carbon, or hydrocarbons. Hydrocarbons include methane gas, liquid gasoline, and solid paraffin wax in candles.
Simplest molecule is methane, CH4, in which one carbon atom shares electrons with four atoms of hydrogen. The four hydrogen atoms are oriented at the vertices of a tetrahedron.

6. Isomers
Organic molecules exist in three-dimensional space, and the same set of atoms can be put together in many recognizably different ways, resulting in molecules called isomers.
The atoms found in a simple sugar, with the structural formula C6H12O6, can be arranged in over a dozen different ways.
Even though many isomers can theoretically exist, cells are discriminating about which ones they will synthesize and recognize. For example, the sugar glucose (C6H12O6) is very abundant and can be used by almost all organisms as a quick energy source. By contrast, an isomer of glucose called tagatose (also C6H12O6) is rare and is not useful to most forms of life—same atoms, different shapes.
Three situations can lead to the existence of isomers:
Structural isomers: Variations in the position at which different atoms are joined together.
Enantiomers: Left-handed and right-handed variations resulting from the tetrahedral geometry of carbon.
Geometric isomers: Variations in the placement of atoms around carbon atoms joined by double covalent bonds.

7. L-

8. Polarity
Many combinations of different elements result in unequal
electron sharing, called polar bonding.
As was already seen, the sharing of electrons in covalent bonds is not always equal.
In a covalent bond, atoms especially such as oxygen contain a higher localization
of negative charge density than their atomic partners.
As a result, the electron distribution is asymmetric, or polar,
and the oxygen atom is said to be electronegative.
This asymmetry results in regions of slight negative and
positive charge in different regions of the molecule,
denoted by the Greek symbol δ, for "partial" charge.

9. The Functional Groups
The properties of different biological molecules depend on certain characteristic groupings of atoms called functional groups.
If you know the properties of some of the functional groups, you will be able to quickly look at many simple biological molecules and get some idea of their solubility and possible identity. The names of the six most important functional groups are:
Hydroxyl
Carbonyl
Carboxyl
Amino
Sulfhydryl
Phosphate

10. The Hydroxyl and Carbonyl Groups Two functional groups containing oxygen, the hydroxyl and carbonyl groups, contribute to water solubility. Oxygen occurs in these two common functional groups: Hydroxyl groups have one hydrogen paired with one oxygen atom (symbolized as -OH). Hydroxyl groups are not highly reactive, but they readily form hydrogen bonds and contribute to making molecules soluble in water. Alcohols and sugars are "loaded" with hydroxyl groups. Carbonyl groups have one oxygen atom double-bonded to a carbon atom (symbolized as C=O). Like hydroxyl groups, carbonyl groups contribute to making molecules water-soluble. All sugar molecules have one carbonyl group, in addition to hydroxyl groups on the other carbon atoms. Carbonyl groups exist in two forms: Aldehyde groups, where the C=O group is at the end of an organic molecule. A hydrogen atom is also located on the same carbon atom. Keto groups, where the C=O group is located within an organic molecule. All sugars have either a keto or an aldehyde group.

11. The Carboxyl Group: Acids Carboxyl groups are weak acids, dissociating partially to release hydrogen ions. The carboxyl group (symbolized as COOH) has both a carbonyl and a hydroxyl group attached to the same carbon atom, resulting in new properties. Carboxyl groups frequently ionize, releasing the H from the hydroxyl group as a free proton (H+), with the remaining O carrying a negative charge. This charge "flip-flops" back and forth between the two oxygen atoms, which makes this ionized state relatively stable. (Hydroxyl groups sometimes ionize momentarily, but the resulting ionic forms are not stable and the ions immediately rejoin.) Molecules containing carboxyl groups are called carboxylic acids and dissociate partially into H+ and COO−. Carboxyl groups are common in many biological molecules, including amino acids and fatty acids. A simple 2-carbon acid found in vinegar is acetic acid (below). The carboxyl group ionizes and the resulting ionized group is stabilized by the negative charge flip-flopping between the two oxygen atoms.

12. The Amino Group: Bases
Nitrogen in biological molecules usually occurs in the form of basic amino groups.
Nitrogen is another abundant element in biological molecules. Having a valence of 3, nitrogen normally forms three covalent bonds, either single, double, or triple bonds.
By convention, nitrogen atoms are represented by blue spheres in molecular models.
Amino groups (-NH2) are common functional groups containing nitrogen. Amino groups become often ionized by the addition of a hydrogen ion (H+), forming positively charged amino groups (-NH3+).

13. 1s22s22p63s23p4 
The Sulfhydryl Group
Sulfur is found mainly in proteins in the form of sulfhydryl groups or disulfide groups.
Like oxygen, sulfur typically has a valence of 2, although it can also have a valence of 6, as in sulfuric acid.
Sulfur is found in certain amino acids and proteins in the form of sulfhydryl groups (symbolized as -SH). Two sulfhydryl groups can interact to form a disulfide group (symbolized as -S-S-).
By convention, sulfur atoms are represented by yellow spheres in molecular models.
The figure above illustrates two molecules: one with a sulfhydryl group and one with a disulfide group.

14. The Phosphate Group
In biological molecules, phosphorus occurs mainly in the form of acidic phosphate groups.
Phosphorus normally has a valence of 5. Its most common functional group in organic molecules is as a phosphate group (symbolized as -PO42−). Phosphorus is covalently paired to 4 oxygen atoms in phosphate groups: one P=O bond and three P-O− bonds.
In molecular models, phosphorus atoms are represented by orange spheres.
The compound H3PO4 is phosphoric acid, a strong acid that ionizes readily to give H2PO4− and hydrogen ion (H+). This compound can further ionize to HPO42− and H+, and still further to PO43− and H+.
Although all these chemical forms coexist in equilibrium in water, the convention in biology is to represent the phosphate ion in its doubly charged form HPO43−, often abbreviated by the symbol Pi, "inorganic phosphate." This form is shown in the figure below.
Phosphate groups are found in DNA and RNA, and in certain lipids. They are involved in the biological storage and release of energy.

15. 1. Which of the following elements is not one of the six most abundant elements found in all living cells?
a. oxygen
b. nitrogen
c. sulfur
d. potassium
e. carbon

16. 2. What is the valence of carbon?1 2 3 4 5

17. 3. The correct shorthand to symbolize a carboxyl group is:
-NH2
-COOH
-OH
-C=O
-SH

18. 4. Which of the following functional groups is acidic (ionizes to liberate H+ ions)?
H3PO4
-COOH
-OH
all of the above
a and b, but not c

19. 5. Which functional group(s) are basic (accept H+ ions)?
carboxyl groups
hydroxyl groups
keto groups
amino groups
sulfhydryl groups

20. 6. Which of the following molecules contains a triple bond?
NH3
HCCH
CH4
C(H3)C(H2)CH3
all of the above

21. 7. A substance that is polar:
is able to dissolve in water
contains an asymmetric distribution of electrical charge
involves unequal sharing of electrons
can be involved in hydrogen bonding
all of the above

22. 8. Which of the following types of chemical groups is not polar?
-OH
-COOH
-NH2
-CH3
phosphate group

23. Macromolecules “Large” molecule
As said, living things are made of 5 main atoms carbon, hydrogen oxygen, nitrogen, phosphorus
Inorganic molecules USUALLY do not have carbon. i.e. H2O, NaCl
Carbon dioxide (CO2) is the exception. It has carbon but is inorganic
Macromolecules
“Large” molecule
Formed by monomers (small molecules) bonding together
Large molecule with many monomers is a polymer

24. There are four main macromolecules in living things
Carbohydrates, lipids, nucleic acids, proteins
Carbohydrates
Sugars and starches
Made of 3 atoms: carbon, hydrogen and oxygen
Most carbohydrates have a C1:H2:O1 ratio (1:2:1)
Monosaccharides are the monomer.
Simple Sugars such as Glucose (C6H12O6)

25. Monosaccharides bond together to form polysaccharides Disaccharides
SUCROSE
Two molecules together
Ex) Maltose, lactose
Formed from dehydration synthesis
Understand how dissacarides are formed in dehydration synthesis, small molecules so they can dissolve in water *

27. Glucose most common sugar in cells
Carbohydrates have two main functions.
1. Usable (short-term) energy storage
2. Structure and support
Sugars (monosaccharides) are usable energy for cells. (glucose, fructose, sucrose)
Glucose most common sugar in cells

28. Polysaccharides provide short term energy storage.
Plants use starch (in roots and stems)
Animals store glycogen in the liver.

29. Structural Support
Polysaccharides can also support both plants and animals.
Cellulose is in the cell wall of plant cells to make them stronger. (indigestible)
Chitin is a polysaccharide used in the exoskeletons of insects and crabs

30. Notice the positions of the oxygens, large molecules can’t dissolve in water*

31. All lipids do not dissolve in water = hydrophobic
Long term energy storage/insulation & padding (fats). Six times more energy storage than carbohydrates. (fats, oils, waxes)
Cellular Membranes- phospholipids
Chemical Messengers- steroids and cholesterol (hormones)

32. Types Fatty Acids Chain of carbons ending in COOH
Fatty acids can be saturated, unsaturated, or polyunsaturated
Saturated Fatty Acids
Solid at room temperature
Bad for health
Unsaturated Fatty Acids
Contain double bonds
Liquid at room temperature
Saturated fats have only single bonds between the carbons on the long fatty acid chains.
Found in animals
Solid at room temperature

33. Types Triclycerides Neutral Fats Glycerol + 3 Fatty Acids
Can be saturated or unsaturated
Not polar = no dissolving in water *

34. Polyunsaturated Fats
Polyunsaturated fats have two or more double bonds between the carbons on the long carbon chain of the fatty acid.

35. Liquid at room temperature Better for you, but don’t taste as good.
Unsat. & Polyunsat Fats
Found in plants
Called oils
Liquid at room temperature
Better for you, but don’t taste as good.

36. Phospholipids Found in cell membrane Same structure as
triglyceride but one fatty acid is
replaced with a phosphate
group (polar)
Hydrophilic phosphate head,
hydrophobic fatty acid tail
Can dissolve in water – water surrounds hydrophilic part and hydrophobic part bunches together. Emulsification and soap example *

37. Phospholipids Phospholipids are found in a bilayer (two layers).
The long carbon chains face the middle and the phosphate groups face the outsides.

38. Steroids Ringed structures made from cholesterol
Chemical messengers and form hormones
Ex) Cholesterol, Testosterone, Estrogen
Cholesterol is four rings - hormones have different things sticking off of those rings *

39. Proteins Structure Movement Enzymes Transport Antibodies Hormones
Keratin and collagen
Movement
Actin and myosin
Enzymes
Speed up chemical reactions
Transport
Hemoglobin to carry oxygen in blood, proteins across cell membrane
Antibodies
Fight disease
Hormones
Maintain cell function – insulin

40. Structure of Proteins Made of Amino Acids
Amine (NH3); Acid (COOH)
20 different amino acids have different R groups
Must recognize the two groups on the end; 8 essential amino acids – we have to eat these in our diet *

41. Structure of Proteins
Amino acids undergo dehydration synthesis to form
Dipeptides (2 amino acids)
Polypeptides (~3-20 amino acids)
Proteins (many amino acids)
Peptide bond is formed (polar)
Be able to identify peptide bonds in long strings of amino acids *

42. Structure of Proteins (4 Levels)
Primary Structure
Linear sequence of amino acids
Secondary Structure
Hydrogen bonding between amino acids
Causes folding
Alpha helix and beta sheets
Draw helix and sheets to properly show H bonding. Identify the peptide bond (covalent) versus the hydrogen bonds *

43. Tertiary Structure
3D arrangement of amino acid chain
Caused by covalent, ionic, and hydrogen bonding between R groups
Precise shape = specific function
Quaternary Structure
More than one polypeptide chain grouped together

44. Denaturing Proteins Cause protein to lose shape = not function
pH, temperature, chemicals and heavy metals disrupt bonds
Ex Heating an egg, adding vinegar to milk
Know what denatures proteins *

45. Proteins
When you look at someone, the main things you see are proteins.
Proteins do many jobs for living things
Structure- found in hair, horns and spider’s silk.
Transport- moving materials
Defense- antibodies
Enzymes- helping chemical reactions

46. Nucleic Acids
DNA and RNA

47. Nucleic Acids Nucleic Acids have two main functions-
Genetic material for all life forms (DNA, RNA)
Energy for all life forms (ATP)

48. Nucleic Acids The monomer for a nucleic acid is a nucleotide.
Nucleotides made of three parts
phosphate group
5 carbon (pentose) sugar
Nitrogenous Base

49. DNA Deoxyribonucleic acid Stores genetic information
Codes for the order of amino acids in proteins
Made of nucleotides
5 carbon sugar (deoxyribose)
Phosphate
Nitrogenous bases
Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G)

50. DNA Structure The sugar and phosphate bond to form a backbone
Bases stick out and hydrogen bond with a second strand – antiparallel
Strands wind around in a double helix

52. RNA Ribonucleic acid Helps in protein synthesis Made of nucleotides
5 carbon sugar (ribose)
Phosphate
Nitrogenous bases
Adenine (A)
Uracil (U)
Cytosine (C)
Guanine (G)
Single stranded

54. ATP Adenosine Triphosphate Molecule of ENERGY
Energy is released during hydrolysis

55. Amino Acids
A protein is made of up to a few hundred amino acids bonded together.
The bonds between amino acids are peptide bonds and the long chains of amino acids are called polypeptide chains
There are 20 different amino acids.
The differences are changes in the R group on the amino acid.

56. Peptide Bond
Amino Acids

58. Enzymes One of the most critical types of proteins are enzymes.
Enzymes help chemical reactions happen inside the body.
An enzyme is called a biological catalyst.
Catalysts are chemicals that helps to lower the amount of energy needed for a chemical reaction to start.
If a chemical reaction is to happen, energy is required to start the reaction
It is called activation energy
Catalase, Lactase, Amylase, ATP Synthase are all examples of human enzymes

59. Activation Energy Graph
Energy Available
An enzyme or catalyst does the job of lowering the activation energy needed to start chemical reactions.

60. Enzymes
An enzyme is not changed during the reaction. This allows the enzyme to be reused over and over.
Enzymes are used to break molecules apart
Enzymes synthesize (build) new molecules from smaller pieces

61. Synthesis Reaction

62. Degradation Reaction

63. Enzymes are also specific in nature
Enzymes are also specific in nature. They will only work with a single molecule or chemical. (lock and key)

64. Enzyme Environment
Enzymes require specific environments to do their job.
Two major factors affect enzyme activity.
Temperature
pH (acidic or basic)
The environment can cause an enzyme to change its shape and make it ineffective
If an enzyme has changed its shape, it has become Denatured
If an enzyme has become denatured, it’s active site will also change and will not be able to attach to the substrate.