1. BIOLOGICAL MOLECULES
2. BIOLOGICAL MOLECULES
a. CARBON (“C” on the periodic table)
b. Organic Chemistry is the study of carbon compounds (regardless of their
origin) though most naturally occurring organic compounds are produced by
organisms.
3. BIOLOGICAL MOLECULES
A. Organic Compounds: Compounds with covalent bonds between carbon and
hydrogen atoms.
B. HYDROCARBONS consist of only carbon and hydrogen.
C. Inorganic: describing a molecule that does not contain both carbon and
hydrogen.
D. Includes molecules: Carbon dioxide(CO2) and all molecules without carbon
4. OUR HERO – CARBON
A. Carbon has 4 electrons in the valence, therefore little tendency to “gain or
lose” an electron to form ionic bonds. CARBON LIKES TO SHARE. What type
of bond would that be?
B. CARBON: Acts like an intersection – can branch off in four directions (4
electrons in the valence shell) to form COVALENT BONDS.
C. Methane (CH4) a good example of carbon’s intersection. Methane is a
hydrocarbon.
5. CARBON SKELETON DIVERSITY
A. Vary in length.
B. Can be branched or unbranched.
C. May have double bonds, which vary in location.
D. Can be arranged in rings.
6. BIOLOGICAL MOLECULES
A. FOUR MAJOR ATOMIC COMPONENTS OF ORGANIC MOLECULES AND THEIR
VALENCES (ELECTRONS IN OUTERMOST SHELL – NUMBER OF BONDS ATOM
WILL FORM).
B. “CHON” – Carbon, Hydrogen, Oxygen, Nitrogen
7. LARGE COMPLEX MOLECULES ARE MADE BY PREASSEMBLED SMALLER
MOLECULES
A. Monomer: A small organic molecule, several of which may be bonded
together to form a chain called a polymer. Literally: “one part”.
B. Polymer: A molecule composed of three or more (perhaps thousands)
smaller subunits called monomers, which may be identical or a different.
Literally: “many parts”.
8. ATTACHED TO CARBON BACKBONES ARE FUNCTIONAL GROUPS.
A. FUNCTIONAL GROUPS:
B. One of several groups of atoms commonly found in an organic molecule that
determine the characteristics and chemical reactivity of the molecule.
page 1 of 8
biological molecules
beavers
9. TABLE OF IMPORTANT FUNCTIONAL GROUPS
A. Meet a Functional Family
10. MEET A FUNCTIONAL FAMILY
A. Methyl (big on making molecules hydrophobic - lipids) The fat relative.
B. Hydroxyl group (the party animal): Organic compounds containing hydroxyl
groups are called alcohols, and names usually end in –ol as in ethanol in
alcoholic beverages.
C. Seen as –OH or HO- . Do not confuse with our hydroxide ion OH-!
(Remember acids and bases).
11. Meet a Functional Family
A. Carbonyl – Look for a carbon atom double bonded to one oxygen. (Not on
our table)
B. The red-headed step-child – often not included in intro bio textbooks.
C. When carbonyl is on the end of a carbon skeleton, the organic compound is
called an aldehyde (formaldehyde – lab specimens).
D. Otherwise, it is called a ketone (acetone – removes nail polish).
12. MEET A FUNCTIONAL FAMILY
A. CARBOXYL GROUP: (The acid-tongued relative); Look for -COOH as his
nickname.
B. Compounds containing carboxyl groups are carboxylic acids or organic acids
– acetic acid the acid of vinegar.
C. AMINO GROUP: (Your “basic” relative) -NH2. Organic compounds in this
group are called amines.
13. BUILDING BIOLOGICAL MOLECULES- Meet a Functional Family
A. Valine is an amino acid that takes part in the building of proteins.
B. Sickle cell anemia is caused by a single nucleotide substitution that replaces
glutamic acid with valine.
14. MEET A FUNCTIONAL FAMILY
A. PHOSPHATE GROUP: (The backbone of the family); -H2PO4.
B. A phosphate with 4 bonds to oxygen, one being a double-bond. Don’t forget
hydrogen!
C. Combined with a deoxyribose sugar, the phosphate group makes up the
back bone of the double helix DNA molecule.
15. BIOLOGICAL MOLECULES Under construction – making biological molecules.
A. Making Biological Molecules
B. Dehydration reaction: (also called a condensation reaction) A chemical
reaction in which two molecules are joined by a covalent bond with the
simultaneous removal of a hydrogen from one molecule and a hydroxyl
group from the other, forming water.
page 2 of 8
biological molecules
beavers
16. BIOLOGICAL MOLECULES
Breaking Down Molecules
A. Hydrolysis: The chemical reaction that breaks down a covalent bond by
means of the addition of hydrogen to the atom on one side of the original
bond and a hydroxyl group to the atom on the other side; the reverse of
dehydration synthesis.
17. FOUR GENERAL CATEGORIES OF BIOLOGICAL MOLECULES
A. CARBOHYDRATES
B. LIPIDS
C. PROTEINS
D. NUCLEIC ACIDS
E. Linus Pauling
(1901-1994)
18. CARBOHYDRATE: A compound composed of carbon, hydrogen, and oxygen, with
the approximate chemical formula (CH2O)n; includes sugars and starches.
A. All carbohydrates are either small, water-soluble sugars, or polymers of
sugars, such as starch.
19. CARBOHYDRATES
A. MONOSACCHARIDE – the basic molecular unit of all carbohydrates normally
composed of a chain of carbon atoms bonded to hydrogen and hydroxyl
groups.
B. DISACCHARIDE –two monosaccharides covalently bonded – “two sugars”.
C. POLYSACCHARIDE: A polymer of many monosaccharides – “many sugars”.
20. MONOSACCHARIDES
A. GLUCOSE: The most common monosaccharide, with the molecular formula
C6H12O6; most polysaccharides, including cellulose, starch, and glycogen, are
made of glucose subunits covalently bonded together.
21. MONOSACCHARIDES
A. Fructose (corn syrup) and galactose (part of lactose). Fructose is an isomer
of glucose.
B. Isomer: molecules with the same molecular formula but different structures.
C. Ribose and deoxyribose have only 5 carbons. Part of RNA and DNA.
22. DISACCHARIDES – synthesized by dehydration
A. SUCROSE - A disaccharide composed of glucose and fructose. The most
plentiful sugar in nature.
B. LACTOSE – A disaccharide composed of glucose and galactose; found in
mammalian milk.
C. MALTOSE – A disaccharide composed of two glucose molecules.
23. STARCH –
page 3 of 8
biological molecules
beavers
A. STARCH: A polysaccharide that is composed of branched or unbranched
chains of glucose molecules; used by plants as a carbohydrate-storage
molecule.
24. GLYCOGEN
A. A long, branched polymer of glucose that is stored by animals in the muscles
and liver and metabolized as a source of energy.
B. Hydrolysis used to withdraw them from storage.
C. Glycogen extensively branched molecule.
25. CELLULOSE – An insoluble carbohydrate composed of glucose subunits; forms the
cell wall of plants.
26. CHITIN (KY-tin) – A compound found in the cell walls of fungi and the
exoskeletons of insects and some other arthropods; composed of chains of
nitrogen-containing, modified glucose molecules (an amino sugar).
27. LIPID: One of a number of organic molecules containing large non-polar regions
composed solely of carbon and hydrogen, which make lipids hydrophobic and
insoluble in water; includes oils, fats, waxes, phospholipids, and steroids.
A. LIPIDS: THREE MAJOR GROUPS
B. 1. OILS, FATS, WAXES.
C. 2. PHOSPHOLIPIDS.
D. 3. “FUSED-RING” FAMILY OF STEROIDS.
28. LIPIDS- Oils, Fats and Waxes
A. CONTAIN ONLY CARBON, HYDROGEN AND OXYGEN.
B. CONTAIN ONE OR MORE FATTY ACID SUBUNITS.
C. FATTY ACID: an organic molecule composed of a long chain of carbon
atoms, with a carboxylic acid (-COOH) group at one end, may be saturated
or unsaturated.
D. USUALLY DO NOT HAVE RING STRUCTURES.
29. FATS AND OILS: Formed by dehydration synthesis
A. FATS AND OILS: Formed through dehydration synthesis of one glycerol
molecule and three fatty acid subunits.
B. Glycerol: a three-carbon alcohol to which fatty acids are covalently bonded
to make fats and oils.
30. SATURATED AND UNSATURATED FATS
A. SATURATED FATS: fatty acids with the maximum number of hydrogen
atoms.
B. UNSATURATED FATS fatty acids with less than maximum number of
hydrogen atoms
31. LIPIDS – THE GOOD AND BAD REPUTATIONS OF FATS
A. BAD REPUTATION:
B. CARDIOVASCULAR DISEASE
page 4 of 8
biological molecules
beavers
C.
D.
E.
F.
G.
APPEARANCE WAS ONCE FAVORABLE
GOOD REPUTATION:
COMPACT ENERGY STORAGE
VITAL ORGAN CUSHION
INSULATION
32. Calorie versus calorie: measurements of energy
A. calorie: (already defined earlier) – the amount of energy required to raise
the temperature of 1 gram of water by 1 degree Celsius.
B. Calorie: a unit of energy, in which the energy content of foods is measured;
the amount of energy required to raise the temperature of 1 liter of water 1
degree Celsius; also called a kilocalorie, equal to 1000 calories.
33. WAXES – DO NOT EAT
A. Chemically similar to fats.
B. Most animals lack appropriate enzymes to digest wax.
C. Highly saturated (what does that mean?)
D. Solid at normal outdoor temperatures.
34. PHOSPHOLIPIDS: A lipid consisting of glycerol bonded to two fatty acids and one
phosphate group, which bears another group of atoms, typically charged and
containing nitrogen. A double layer of phospholipids is a component of all cellular
membranes.
35. PHOSPHOLIPIDS Structurally related to fats.
A. Difference: two fatty acids rather than three. The 3rd hydroxyl group of
glycerol joined to a phosphate group with a short, polar functional group
(often containing nitrogen.)
B. Water soluble heads
C. Water-insoluble tails
36. PHOSPHOLIPIDS
A. Two structures formed by self-assembly of phospholipids in water.
B. Top picture – a micelle; an aggregate of surfactant molecules (secreted in
lungs)
C. Bottom picture: Phospholipid bilayer, main fabric of biological membranes.
37. ALL STEROIDS COMPOSED OF 4 RINGS OF CARBON FUSED TOGETHER.
A. DIFFERENCE IN STEROID FUNCTIONS IS DUE TO DIFFERENT FUNCTIONAL
GROUPS.
38. PROTEINS VISUALIZED
A. Proteins are polymers of amino acids, joined by peptide bonds.
B. They are composed of a central carbon atom bonded to an amino group (NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable group of
atoms denoted by the letter “R”.
C. Amino acids all have the same fundamental structure:
page 5 of 8
biological molecules
beavers
D. Central carbon bonded to four different functional groups: -NH2, -COOH, H,
and “R” (a variable group).
39. AMINO ACIDS are JOINED by PEPTIDE BONDS TO FORM CHAINS THROUGH
DEHYDRATION SYNTHESIS.
A. PEPTIDE BONDS: The covalent bond between the amino group’s nitrogen of
one amino acid and the carboxyl group’s carbon of a second amino acid,
joining the two amino acids together in a “peptide”.
B. RESULTING PEPTIDE: A SHORT CHAIN OF AMINO ACIDS, 2 UP TO 50.
C. LONGER CHAINS ARE CALLED POLYPEPTIDES.
40. THE MANY FUNCTIONS OF PROTEINS
41. SOME SNAKE’S VENOM IS AN ENZYME PROTEIN.
42. ENZYME: A protein that serves as a biological catalyst that speeds up the rate of
specific biological reactions.
A. CATALYST: A substance that speeds up a chemical reaction without itself
being permanently changed in the process.
43. 20 AMINO ACIDS COMMONLY FOUND IN PROTEINS OF ORGANISMS
44. WHAT CAN YOU DO WITH A STRING OF AMINO ACIDS????
A. PROTEINS ARE HIGHLY ORGANIZED MOLECULES THAT COME IN A VARIETY
OF SHAPES:
B. PRIMARY
C. SECONDARY (HELIX, PLEATED SHEETS)
D. TERTIARY
E. QUATERNARY
45. PROTEINS – PRIMARY STRUCTURE
A. UNIQUE SEQUENCE OF AMINO ACIDS LINKED BY PEPTIDE BONDS MAKES
UP PROTEIN.
B. SEQUENCE IS DETERMINED BY INHERITED INFORMATION IN MOLECULES
OF DNA.
C. DIFFERENT PROTEINS HAVE DIFFERENT SEQUENCES.
46. PROTEINS: SECONDARY STRUCTURE
A. POLYPEPTIDE CHAINS ACQUIRE ONE OR BOTH OF TWO SIMPLE, REPEATING
SECONDARY STRUCTURES.
page 6 of 8
biological molecules
beavers
B. HYDROGEN BONDS BETWEEN THE POLAR MOLECULES OF THE AMINO
ACIDS GIVE RISE TO TWO STRUCTURES.
47. PROTEINS: SECONDARY STRUCTURE – The Helix
A. PICTURED HERE IS THE HELIX.
B. SEEN IN PROTEINS LIKE HEMOGLOBIN SUBUNITS AND KERATIN.
C. HYDROGEN BONDS BETWEEN POLAR MOLECULES HOLD COIL TOGETHER.
48. PROTEINS: SECONDARY STRUCTURE – The Pleated Sheet
A. PLEATED SHEET ARRANGEMENT IS THE OTHER SECONDARY STRUCTURE
ALSO HELD TOGETHER BY HYDROGEN BONDS.
B. PROTEINS SUCH AS SILK CONSIST OF POLYPEPTIDE CHAINS THAT
REPEATEDLY FOLD BACK UPON THEMSELVES.
49. PROTEINS SECONDARY STRUCTURES : Helix and Pleated Sheet
50. PROTEINS - TERTIARY STRUCTURES
A. TERTIARY STRUCTURE DETERMINES FINAL CONFIGURATION OF
POLYPEPTIDE.
B. MOST IMPORTANT INFLUENCE OF TERTIARY STRUCTURE IS CELLULAR
ENVIRONMENT LEADING TO HYDROPHILIC AND HYDROPHOBIC
INTERACTIONS BETWEEN SIDE CHAINS (FUNCTIONAL GROUPS – “R”
GROUPS).
C. DISULFIDE BRIDGES CAUSE PROTEIN TO FOLD OR BEND.
51. PROTEINS: TERTIARY STRUCTURES DISULFIDE BRIDGES
A. DISULFIDE BRIDGE: The covalent bond formed between the sulfur atoms of
two cysteines in a protein; typically causes the protein to fold by bringing
otherwise distant parts of the protein close together.
52. PROTEINS - TERTIARY STRUCTURES
53. AN DER WAALS INTERACTION
A. Created by Johannes Diderik van der Waals (1837-1923), a Dutch physicist.
B. When two atoms approach each other, there is an attraction between their
opposite charges that stabilize them (van der Waals forces).
C. But, if two atoms come too close to each other – they are strained (van der
Waals strain), the energy (heat) of the system increases.
D. NOT TOO CLOSE, NOT TOO FAR.
E. NOT ON TEST.
54. QUATERNARY STRUCTURE
A. Individual polypeptides can be linked together to create a quaternary
structure.
B. 4 peptides holding a heme that binds one oxygen molecule.
C. Hemoglobin – the oxygen-carrying molecule is a quaternary structure.
55. WHERE CAN IT GO WRONG?
page 7 of 8
biological molecules
beavers
A. Primary structure: Wrong nucleotide in DNA creating wrong codon that
forms wrong amino acid in Sickle Cell Anemia. AMINO ACIDS MUST BE IN
PROPER SEQUENCE.
B. Proteins must have the correct secondary and tertiary structures so amino
acids are correctly positioned within protein.
C. When these structures are altered the protein is said to be DENATURED, and
is no longer functional.
D. DENATURE: To disrupt the secondary and/or tertiary structure of a protein
while leaving its amino acid sequence intact. Denatured proteins can no
longer perform their biological functions.
56. NUCLEIC ACIDS
A. NUCLEIC ACIDS: An organic molecule composed of nucleotide subunits; the
two common types of nucleic acids are ribonucleic acid (RNA) and
deoxyribonucleic acid (DNA).
B. PICTURED: DNA
57. NUCLEOTIDES – Subunits of NUCLEIC ACIDS
A. Nucleotides: a subunit of which nucleic acids are composed; a phosphate
group bonded to a sugar (deoxyribose in DNA), which is in turn bonded to a
nitrogen-containing base (adenine, guanine, cytosine or thymine in DNA).
58. NUCLEIC ACIDS
A. Nucleotides are linked together, forming a strand of nucleic acid. Bonds
between the phosphate of one nucleotide link to the sugar of the next
nucleotide.
59. The building blocks of DNA and RNA: Five nitrogen containing bases, 2 sugars and
phosphate.
60. DNA AND RNA
A. The Molecules of Heredity
B. Deoxyribose nucleotides form chains millions of units long called DNA
(deoxyribonucleic acid).
C. DNA is found in the chromosomes of all living things.
D. Watson & Crick with discovery of the structure of DNA in 1953.
61. DNA to RNA to PROTEIN
A. DNA’s sequence of nucleotides spells out the genetic information needed to
construct proteins.
B. Information flow in a cell
page 8 of 8
biological molecules
beavers