Download AP Biology, Chapter 5, 9th ed. The Structure and Function of Large

AP Biology, Chapter 5, 9th ed.
The Structure and Function of Large Biological molecules
The Molecules of Life
1. List the four major classes of biological macromolecules in all known life forms.
Carbohydrates
Lipids
Proteins
Nucleic acids
1.D.2.b. Molecular and genetic evidence from extant and extinct organisms indicates that all
organisms on Earth share a common ancestral origin of life.
1.D.2.b.1. Scientific evidence includes molecular building blocks that are common to all
life forms.
1.D.2.b.2. Scientific evidence includes a common genetic code.
5.1 Macromolecules and polymers, built from monomers
Intro
The Synthesis and Breakdown of Polymers
2. Describe the construction and deconstruction of biological polymers.
Polymers ("many part") are made from monomers ("one part")
Put together by condensation by removing water = dehydration
Taken apart by adding water = hydrolysis
The Diversity of Polymers
3. Explain how organic polymers contribute to biological diversity.
Organisms use 40-50 common monomers
There are many combinations of those in long linear sequences
5.2 Carbohydrates serve as fuel and building material
Intro
Sugars
4. Describe the distinguishing characteristics of carbohydrates and explain how they are
classified.
Chemical characteristics
Polyhydroxylated (1C:2H:1O) aldehydes, ketones, alcohols and acids
Very polar while carrying appreciable energy
Provide carbon skeletons for biosynthesis
Classification
Number of carbon atoms per monomer (triose, tetrose, pentose,
hexose)
Number of monomers (mono-, di-, polysaccharide)
Position of carbonyl (aldose vs. ketose)
5. Distinguish significant monosaccharides and disaccharides.
Mono-: a single sugar unit
Glucose
A hexose
Import for energy, raw material for biosynthesis
Found in ring form
Ribose and deoxyribose are the pentoses of nucleic acids
Di-: two monosaccharides with a glycosidic linkage
Maltose = two glucoses
Lactose = glucose + galactose; milk sugar
Sucrose = glucose +fructose; transported in plants
6. Identify a glycosidic linkage and describe how it is formed.
Glycosidic linkages form between hydroxyl groups
Water is removed, one O atom link sugars
Polysaccharides
Intro
Storage Polysaccharides
7. Describe the structure and functions of polysaccharides.
Storage
Starch
Helical 1-4 linked glucose polymers, may be branched
Energy storage in plants
Hydrolysed using amylase
Glycogen
Highly branched glucose polymers
Energy storage in liver and muscle
Structural Polysaccharides
Structural
Cellulose: very long, unbranched, 1-4 linked, beta glucose in
plants; “insoluble” fiber
Chitin: many linked acetylglucosamine in arthropod and fungus
cell walls
Chondroitin: polymers of acetylgalactosamine and glucuronic
acid in cartilage
8. Distinguish the glycosidic linkages found in starch and cellulose and explain
why the difference is biologically important.
Starch: glucose in alpha rings; 1-4 linkages digestible by us
Cellulose: glucose in beta rings; 1-4 linkages not digestible by us
4.A.1: The subcomponents of biological molecules and their sequence
determine the properties of that molecule.
4.A.1.a. Structure and function of polymers are derived from the way
their monomers are assembled.
4. Carbohydrates are composed of sugar monomers whose
structures and bonding with each other by dehydration synthesis
determine the properties and functions of the molecules.
Illustrative examples include: cellulose versus starch.
4.A.1.b. Directionality influences structure and function of the polymer.
3. The nature of the bonding between carbohydrate subunits
determines their relative orientation in the carbohydrate, which then
determines the secondary structure of the carbohydrate.
5.3 Lipids are a diverse group of hydrophobic molecules
Intro
9. Describe what distinguishes lipids from other major classes of macromolecules.
"Does not include polymers"; but fatty acids are made from 2C units
Generally hydrophobic; except for steroid hormones
Mostly hydrocarbon
Generally small
Fats
10. Describe the building-block molecules, unique properties, and biological importance
of fats, phospholipids, and steroids.
Fats = glycerol + 3 fatty acids with ester linkages = triacylglycerol
Saturated (with H): no double bonds, straight, solid
Unsaturated: double bonds, kinked, liquid
Ester linkages are largely hidden; whole molecule is nonpolar
Functions
Stores > twices as much energy as carbodrates
Insoluble in water so conserves water
Insulates and cushions
Phospholipids
Triglyceride with one fatty acid replaced by PO4
PO4 is charged and hydrophilic, fatty acids are hydrophobic
Forms membranes and micelles with PO4 sticking out
Steroids
Composed of four fused HC rings; hydrophilic functional groups may be added
Cholesterol stabilizes membrane structure
Steroid hormones have >1 hydrophilic functional group
4.A.1: The subcomponents of biological molecules and their sequence determine the
properties of that molecule.
4.A.1.a. Structure and function of polymers are derived from the way their
monomers are assembled.
3. In general, lipids are nonpolar; however, phospholipids exhibit structural
properties, with polar regions that interact with other polar molecules such as
water, and with nonpolar regions where differences in saturation determine the
structure and function of lipids.
5.4 Proteins include a diversity of structures, resulting in a wide range of functions
Intro
11. Describe the characteristics that distinguish proteins from the other major classes of
macromolecules and explain the biologically important functions of this group.
Composed of 20 amino acids; the most structurally diverse
Functions
Structural support (collagen)
Transport of other substances (hemoglobin)
Signaling (insulin)
Movement (myosin and actin)
Defense (antibodies)
Catalysts (enzymes)
Polypeptides
Intro
12. Differentiate polypeptide and protein.
Polypeptide = a chain of amino acids
Protein = folded, trimmed, combined, modified (finished), functional
Amino Acid Monomers
13. List the four major components of an amino acid. Explain how amino acids
may be grouped according to the physical and chemical properties of the side
chains.
Components: amino, carboxyl, H, R (variable) group
Side chain classes: nonpolar, polar, acidic, basic
Amino Acid Polymers
14. Identify a peptide bond and explain how it is formed.
Peptide bond links amino and carboxyl groups on adjacent amino acids
In a structure: N-C w/double bonded O
Amide bond is formed by dehydration
Protein Structure and Function
Intro
15. Explain what determines protein conformation and why it is important.
Amino acid sequence mainly determines conformation
Matching shapes determine interactions between molecules
Substrate-enzyme
Hormone-receptor protein
Antibiotic-target protein
Four Levels of Protein Structure
16. Define primary structure and describe how it may be deduced in the
laboratory.
Primary structure = amino acid sequence
Determination (Sanger, 1958)
Cut with sequence-specific proteases, characterize fragments
Identify the amino- and carboxy-terminal amino acids
4.A.1.b. Directionality influences structure and function of the polymer.
2. Proteins have an amino (NH2) end and a carboxyl (COOH)
end, and consist of a linear sequence of amino acids connected by the
formation of peptide bonds by dehydration synthesis between the
amino and carboxyl groups of adjacent monomers.
17. Describe the two types of secondary protein structure. Explain the role of
hydrogen bonds in maintaining the structure.
α helix: coil stabilized by H-bonds between every fourth amino acid
β pleated sheet
Parallel straight stretches of amino acids, carbonyls staggered
Carbonyls H-bond with aligned strand
18. Define tertiary structure and list the stabilizing interactions.
Sequence folds between secondary structures
Interactions between R-groups
Hydrophobic side chains fold in for water soluble proteins
Hydrogen bonds
Van der Waals interactions stabilize at close range
Disulfide bridges form between non-adjacent cysteines
Ionic bonds between basic and acidic side chains
19. Using collagen and hemoglobin as examples, describe quaternary protein
structure.
Quaternary = more than one amino acid chain bound together
Collagen: three helical amino acid chains wound into a triple helix
Hemoglobin: 2 alpha + 2 beta chains + 4 hemes
4.A.1: The subcomponents of biological molecules and their sequence determine the
properties of that molecule.
4.A.1.a. Structure and function of polymers are derived from the way their
monomers are assembled.
2. In proteins, the specific order of amino acids in a polypeptide
(primary structure) interacts with the environment to determine the
overall shape of the protein, which also involves secondary tertiary and
quaternary structure and, thus, its function. The R group of an amino
acid can be categorized by chemical properties (hydrophobic,
hydrophilic and ionic), and the interactions of these R groups determine
structure and function of that region of the protein.
Sickle-Cell Disease: A Change in Primary Structure
20. Exemplify the significance of even slight changes in primary structure.
Sickle-cell: one amino acid changed
Changed protein shape, altered cell shape  symptoms
What Determines Protein Structure?
21. Define denaturation and explain how proteins may be denatured.
Denaturation of protein = loss of shape and therefore function
By heat, change in pH, organic solvents, polar solutes like urea
Protein Folding in the Cell
22. Define the protein folding problem.
So far, not able to predict protein structure from primary sequence
Stages, intermediate structures involved
23. Describe the role of chaperonins in protein folding.
= cylindrical chambers that accept unfolded polypeptides
Provide folding environment without interfering influences
5.5 Nucleic acids store, transmit, and help express hereditary information
Intro
24. Define gene in the traditional sense.
Segment of DNA that defines the primary structure of a polypeptide
25. Describe the characteristics that distinguish nucleic acids from the other major
groups of macromolecules.
Polymers of 4 nucleotides
Order = coded information
Complementary strands allow replication
The Roles of Nucleic Acids
26. Summarize the functions of nucleic acids.
DNA is a stable, stored form of information giving traits
RNAs are working copies of the information in DNA
Semi-conservative replication allows transmission to offspring
The Components of Nucleic Acids
27. List the major components of a nucleotide, and describe how these monomers are
linked to form a nucleic acid.
Nucleotide = nitrogen base+pentose+phosphate
Phosphates link the 3' and 5' carbons on adjacent pentoses
28. Distinguish pyrimidine and purine nitrogen bases.
Pyrimidine bases
One ring
Thymine, cytosine, uracil
Purine bases
Two rings
Adenine, guanine
Nucleotide Polymers
The Structures of DNA and RNA Molecules
29. Differentiate the three-dimensional structures of DNA and RNA.
DNA
Double helix
Strands anti-parallel: 3’ 5’, 5’  3’
Complementary base pairs in center: A-T, G-C
RNA
Mainly single stranded
May fold back on itself and base pair
4.A.1.b. Directionality influences structure and function of the polymer.
1. Nucleic acids have ends, defined by the 3' and 5' carbons of
the sugar in the nucleotide, that determine the direction in which
complementary nucleotides are added during DNA synthesis and the
direction in which transcription occurs (from 5' to 3').
3.A.1.b. DNA and RNA molecules have structural similarities and differences that
define function.
1. Both have three components — sugar, phosphate and a
nitrogenous base — which form nucleotide units that are connected by
covalent bonds to form a linear molecule with 3' and 5' ends, with the
nitrogenous bases perpendicular to the sugar-phosphate backbone.
2. The basic structural differences include:
i. DNA contains deoxyribose (RNA contains ribose).
ii. RNA contains uracil in lieu of thymine in DNA.
iii. DNA is usually double stranded, RNA is usually single stranded.
iv. The two DNA strands in double-stranded DNA are antiparallel
in directionality.
3. Both DNA and RNA exhibit specific nucleotide base pairing
that is conserved through evolution: adenine pairs with thymine or
uracil (A-T or A-U) and cytosine pairs with guanine (C-G).
i. Purines (G and A) have a double ring structure.
ii. Pyrimidines (C, T and U) have a single ring structure.
DNA and Proteins as Tape Measures of Evolution
30. Explain how the structure of DNA and proteins can be used to document the
hereditary background of an organism.
Assume descent with modification and a constant rate of mutation
Phyogenetic trees showing relatedness can be constructed
Number of changes is proportional to time since divergence
4.A.1: The subcomponents of biological molecules and their sequence determine the
properties of that molecule.
4.A.1.a. Structure and function of polymers are derived from the way their monomers
are assembled.
1. In nucleic acids, biological information is encoded in sequences of nucleotide
monomers. Each nucleotide has structural components: a five-carbon sugar
(deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine,
guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in
structure, and these structural differences account for the differing functions.
The Theme of Emergent Properties in the Chemistry of Life