Chemistry and Enzymes Review
AP Biology
The polarity of water molecules results in hydrogen bonding
The water molecule is a polar molecule: The opposite ends have opposite charges
Polarity allows water molecules to form hydrogen bonds with each other
Living systems depend on the properties of water that result from polarity and hydrogen bonding
Four of water’s properties that facilitate an environment for life:
Cohesion/adhesion
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent
Cohesion
Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion
Cohesion helps the transport of water against gravity in plants
Adhesion of water to plant cell walls also helps to counter gravity
Moderation of Temperature
Water can absorb or release a large amount of heat with only a slight change in its own temperature
Water’s high specific heat minimizes temperature fluctuations to within limits that permit life
Heat is absorbed when hydrogen bonds break
Heat is released when hydrogen bonds form
Evaporative Cooling
As a liquid evaporates, its remaining surface cools, a process called evaporative cooling
Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water
The Solvent of Life
Most biochemical reactions occur in water
Water is a versatile solvent due to its polarity
Water is an effective solvent because it readily forms hydrogen bonds
Water can dissolve both ionic and polar substances
Overview: The Molecules of Life
Within cells, small organic molecules are joined together to form larger molecules
A polymer is a long molecule consisting of many similar building blocks called monomers that are covalently
bonded together
Three of the four classes of life’s organic molecules are polymers:
Carbohydrates
Proteins
Nucleic acids
Atoms from the environment are needed to build biological molecules
Carbon moves from the environment into organisms were is used to build carbs, proteins, lipids and nucleic acids
Nitrogen is used to build proteins and nucleic acids
Phosphorus is used to build nucleic acids and phospholipids
Learning objective 2.8: The student is able to justify the selection of data regarding the types of molecules that an
animal, plant or bacterium will take up as necessary building blocks and excrete as waste products.
Learning objective 2.9: The student is able to represent graphically or model quantitatively the exchange of
molecules between an organism and its environment, and the subsequent use of these molecules to build new
molecules that facilitate dynamic homeostasis, growth and reproduction
The Synthesis and Breakdown of Polymers
Monomers form larger molecules by condensation reactions called dehydration reactions
Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration
reaction
The structure and function of polymers are derived from the way the polymers are assembled. (cellulose vs starch)
Directionality influences the structure and function of a polymer. (5’ vs 3’ ends of DNA)
Carbohydrates serve as fuel and building material
Carbohydrates include sugars and the polymers of sugars
The simplest carbohydrates are monosaccharides, or single sugars
Monosaccharides serve as a major fuel for cells and as raw material for building molecules
Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks
Polysaccharides
Polysaccharides, the polymers of sugars, have storage and structural roles
The structure and function of a polysaccharide are determined by its sugar monomers and the positions of the
bonds between them.
Storage Polysaccharides
Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
Plants store surplus starch as granules within chloroplasts and other plastids
Glycogen is a storage polysaccharide in animals
Humans and other vertebrates store glycogen mainly in liver and muscle cells
Structural Polysaccharides
Cellulose is a major component of the tough wall of plant cells
Like starch, cellulose is a polymer of glucose, but the bonds differ
The difference is based on two ring forms for glucose: alpha () and beta ()
Lipids are a diverse group of hydrophobic molecules
Lipids are the one class of large biological molecules that do not form polymers
The unifying feature of lipids is having little or no affinity for water
Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds
The most biologically important lipids are fats, phospholipids, and steroids
Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
Unsaturated fatty acids have one or more double bonds
The major function of fats is energy storage
Phospholipids
In a phospholipid, two fatty acids and a phosphate group are attached to glycerol
The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head
When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing
toward the interior
The structure of phospholipids results in a bilayer arrangement found in cell membranes
Phospholipids are the major component of all cell membranes
Polypeptides
Polypeptides are polymers of amino acids
A protein consists of one or more polypeptides
Amino Acid Monomers
Amino acids are organic molecules with carboxyl (-COOH) and amino (-NH2) groups
Amino acids differ in their properties due to differing side chains, called R groups
Cells use 20 amino acids to make thousands of proteins
Amino Acid Polymers
Amino acids are linked by peptide bonds
A polypeptide is a polymer of amino acids
Polypeptides range in length from a few monomers to more than a thousand
Each polypeptide has a unique linear sequence of amino acids
Four Levels of Protein Structure
The primary structure of a protein is its unique sequence of amino acids
Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain
Tertiary structure is determined by interactions among various side chains (R groups)
Quaternary structure results when a protein consists of multiple polypeptide chains
Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word
Primary structure is determined by inherited genetic information
The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the
polypeptide backbone
Typical secondary structures are a coil called an alpha helix and a folded structure called a beta pleated sheet
Tertiary structure is determined by interactions between R groups, rather than interactions between backbone
constituents
These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der
Waals interactions
Strong covalent bonds called disulfide bridges may reinforce the protein’s conformation
What Determines Protein Conformation?
In addition to primary structure, physical and chemical conditions can affect conformation
Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel
This loss of a protein’s native conformation is called denaturation
A denatured protein is biologically inactive
Nucleic acids store and transmit hereditary information
The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
Genes are made of DNA, a nucleic acid
The Structure of Nucleic Acids
Nucleic acids are polymers called polynucleotides
Each polynucleotide is made of monomers called nucleotides
Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group
Nucleotide Monomers
Nucleotide monomers are made up of nucleosides and phosphate groups
Nucleoside = nitrogenous base + sugar
In DNA, the sugar is deoxyribose
In RNA, the sugar is ribose
Nucleotide Polymers
Nucleotide polymers are linked together, building a polynucleotide
Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one
nucleotide and the phosphate on the 5´ carbon on the next
These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
The sequence of bases along a DNA or mRNA polymer is unique for each gene
The DNA Double Helix
A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix
In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement
referred to as antiparallel
One DNA molecule includes many genes
The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always
with C
Learning objective 4.1: The student is able to explain the connection between the sequence an the subcomponents
of a biological polymer and its properties.
Learning objective 4.2: The student is able to refine representations and models to explain how the
subcomponents of a biological polymer and their sequence determine the properties of that polymer.
Learning objective 4.3: The student is able to use models to predict and justify that changes in the subcomponents
of a biological polymer affect the functionality of the molecule.
Enzymes
Proteins that catalyze chemical reactions in living things by lowering the activation energy required to start a
reaction
They allow reactions to occur at body temp
Only work on one specific molecule--its substrate
Are not used up
Have optimal pH and temperature ranges
Each has a specific job
Function is determined by its 3-D structure
Enzyme action
Active site of the enzyme binds to the substrate and changes shape slightly to hold it (induced fit)
Enzyme holds substrate in place so the reaction can happen
Enzyme lets go of the products and reverts to its original shape so it can catalyze another reaction
Inhibition of Enzyme activity
Can be reversible or irreversible
Competitive inhibitors
Block the active site from the substrate
Non-competitive inhibitors
Bind to a different part of the enzyme causing it to change shape so the active site no longer can bind to the
substrate
Regulation of metabolic pathways
Allosteric regulation
Allosteric enzymes have 2 forms: active and inactive
Most are made of 2 or more polypeptide chains
Binding of an activator to the allosteric site stabilizes the active form
Binding of an inhibitor stabilizes the inactive form
Feedback inhibition: regulated by the end product of the metabolic pathway
Prevents a cell from wasting resources by producing to much of a substance
End product is typically an allosteric inhibitor of an enzyme in the pathway
Learning Objective 4.3: The student is able to use models to predict and justify that changes in the subcomponents
of a biological polymer affect the functionality of the molecule.
Learning Objective 4.17: The student is able to analyze data to identify how molecular interactions affect structure
and function.