AP Biology
Week 3 Notes
AP Biology --- WEEK 3
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Nucleic acids are polymers specialized for storage, transmission, and use of genetic information
o DNA – deoxyribonucleic acid
o RNA – ribonucleic acid
Monomers = nucleotides
Nucleotide: Pentose Sugar + N – containing base + Phosphate Group
Bases
o Pyrimidines = single rings
o Purines = double rings
Sugars:
o DNA has deoxyribose
o RNA has ribose
Nucleotides bond in condensation reactions to form phosphodiester linkages
Nucleic acids grown in the 5’ to 3’ direction
Complementary Base pairing
o A & T always pair
(Adenine and Thymine)
o C & G always pair
(Cytosine and Guanine)
Base pairs are linked by Hydrogen bonds
There are so many Hydrogen bonds in DNA and RNA that they form a strong attraction, but not
as strong as covalent bonds
Thus base pairs are separated with a small amount of energy
DNA is an informational molecule: genetic info is in the sequence of base pairs
DNA has two functions:
o Replication
o Gene Expression: base sequences are copied to RNA, and specify amino acids sequences
in proteins
DNA (through Transcription)  RNA (through Translation)  Polypeptide
DNA replication/transcription depends on the base pairings
o 5’ – TCAGCA – 3’
o 3’ – AGTCGT – 5’
Genome a complete set of DNA in a living organism
DNA base sequences reveal evolutionary relationship
o Closely related living species should have more similar base sequences than species that
are more distantly related
Scientists are now able to determine and compare entire genomes of organisms to study
evolutionary relationships
Page 1 of 4
Made By: Katie Frye
AP Biology
Week 3 Notes
3.2 Proteins are polymers with important structural metabolic roles
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Major functions of proteins;
o Enzymes – catalytic proteins
o Defensive proteins (e.g. antibodies)
o Hormonal and regulatory proteins – control physiological processes
o Receptor proteins – receive and respond to molecular signals
o Storage proteins – store amino acids
o Structural proteins – physical stability and movement
o Transport proteins – carry substances (e.g. Hemoglobin)
o Genetic regulatory proteins – regulate when, how, and to what extent a gene is
expressed
Protein monomers = amino acids
Amino and carboxylic acid functional groups allow them to act as both acid and base
The R group differs in each amino acid
Only 20 amino acids occur extensively in the proteins of all organisms
They are grouped according to properties conferred by the R groups
Cystine side chains can form covalent bonds – a disulfide bridge, or disulfide bond
Oligopeptides or Peptides: short polymers of 20 or less amino acids
o Polypeptides or proteins range in size from Insulin (51 amino acids) to Titin (34,350
amino acids)
Amino acids linked in condensation reactions to form peptide linkages or peptide bonds
Polymerization takes place in the amino to Carboxyl direction
Primary Structure of a protein – the sequence of amino acids
Secondary Structure – regular, repeated spatial patterns in different regions, resulting from
Hydrogen bonding
α (alpha) helix – right handed coil
β (beta) pleated sheet – 2 or more polypeptide chains are extended and aligned
Tertiary structure – polypeptide chain is bent and folded; results in the definitive 3D shape
o The outer surfaces present functional groups that can interact with other molecules
o Interactions btwn R groups determine tertiary structure
Disulfide Bridges hold a folded polypeptide together
Hydrogen Bonds stabilize folds
Hydrophobic side chains can aggregate
Van der Waals interactions btwn hydrophobic chains
Ionic interactions form salt bridges
Secondary and tertiary protein structure derive from primary structure
Denaturing - heat or chemicals are used to disrupt weaker interactions in a protein, destroying
secondary and tertiary structure
The protein can return to normal when cooled – all the info needed to specify the unique shape
is contained in the primary structure
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Made By: Katie Frye
AP Biology
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Week 3 Notes
Quaternary Structure – 2 or more polypeptide chains (subunits) bind together by hydrophobic
and ionic interactions, and hydrogen bonds
These weal interactions allow small changes that aid in the protein’s function
Factors that can disrupt the interactions that determine protein structure (denaturing):
o Temperature
o Concentration of H+
o High concentrations of polar substances
o Nonpolar substances
3.3 Some Proteins At As Enzymes To Speed Up Biochemical Reactions
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Living systems depend on reactions that occur spontaneously, at very slow rates
Catalysts are substances that speed up reactions without being permanently altered
NO catalyst makes a reaction occur that cannot otherwise occur
Most biological catalysts are proteins (enzymes)
In some exergonic reactions there is an energy barrier btwn reactants and products
An input of energy (the Activation Energy, EA) will put reactants into a transition state
Enzymes lower the activation energy – they allow reactants to come together and react more
easily
o Ex: a molecule of Sucrose in solution may hydrolyze in about 15 days. With sucrose
present, the same reaction occurs in about 1 second
Enzymes are highly specific – each one catalyzes only one chemical reaction
Reactants are substrates: they bind to a specific site on the enzyme, the Active Site
The enzyme-substrate complex (Es) is held together by Hydrogen bonding, electrical attraction,
or temporary covalent bonding
Binding of substrate to enzyme is like a baseball in a catcher’s mitt. Enzymes change shape to
make the binding tight – induced fit
Some enzymes require ions or other molecules in order to function:
o Cofactors = inorganic ions
o Coenzymes add or remove chemical groups from the substrate. They can participate in
many different reactions
o Prosthetic groups (non-amino acid groups) permanently bound to their enzymes
Rates of catalyzed reactions
o There is usually less enzyme than substrate present, so reaction rate levels off when the
enzyme becomes saturated
o Saturated – all enzyme molecules are bound to substrate molecules
Enzyme-catalyzed reactions are part of metabolic pathways – the product of one reaction is a
substrate for the next
o ABCD
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Made By: Katie Frye
AP Biology
Week 3 Notes
3.4
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Homeostasis – maintenance of stable internal conditions
Cells can regulate metabolism by controlling the amount of an enzyme
Cells often have the ability to turn the synthesis of enzymes off or on
Chemical inhibitors can bind to enzymes and slow reaction rates
Irreversible Inhibition – inhibitor covalently binds to a side chain in the active site. The enzyme is
permanently inactivated
Reversible inhibition
o A competitive inhibitor competes with natural substrate for active site
o A noncompetitive inhibitor binds at a site distinct from the active site – this causes
change in enzyme shape and function
Allosteric /regulation: non-substrate molecule binds at a site other than the active site
Enzymes are proteins
Protein kinases are enzymes that regulate responses to the environment by organisms
o They are subject to allosteric regulation
The active form regulates the activity of other enzymes, by phosphorylating allosteric or active
sites on other enzymes
Metabolic pathways
o The first reaction is the commitment step – other reactions then happen in sequence
o Feedback inhibition (end-product inhibition) – the final product acts as a
noncompetitive inhibitor of the first enzyme, which shuts down the pathway
Ph affects enzyme activity:
o Acidic side chains generate H+ and become anions
o Basic side chains attract H+ and become cations
Example:
o Glutamic acid – COOH  glutamic acid – COO - + H+
The law of mass action – the higher the H+ concentration the more reaction is driven to the left
to the less hydrophilic form
Protein tertiary structure (and thus function) is sensitive to the concentration of H+ (PH) in the
environment
All enzymes have an optimal PH for activity
Temperature affects enzyme activity
o Warming increases the rate of chemical reactions, but if temperature is too high, noncovalent bonds can break and inactivate enzymes
o All enzymes have an optimal temperature for activity
o Enzymes are temperature sensitive
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Made By: Katie Frye