BCH 3053 General Biochemistry Exam #1 Study GuideSpring 2021

Chapter 2 (interactions and buffers):

• Identify and distinguish types of interactions that occur between molecules. Including
intermolecular forces such as: H-bonding, dipole-dipole, ionic, Van der Waals interactions
-H bonding: between the oxygen of one water molecule and the H of another. Strongest
when the bonded molecules are in a straight line.
-Dipole-dipole: attraction between partial charges in nearby molecules
-Ionic: complete transfer of valence electrons between metal and non metal atoms.
Generates two oppositely charged ions.
-Van der Waals: (includes dipole dipole and London dispersion) includes attraction and
repulsion between atoms, molecules, and surfaces,as well as other intermolecular forces.
• Identity and define hydrophobic interactions and describe the role they play in the creation of
micelles.
-Hydrophobic interactions: a type of van der waals interactions. When nonpolar
molecules repel water, causing non polar regions to cluster together to present the smallest
hydrophobic area to the solvent, while the polar regions are arranged to maximize interaction
with the solvent.
-Micelles: formed in aqueous solution by hydrophobic interaction when the polar regions
face the outside surface and the nonpolar regions face the core.
• Discuss how weak acids and bases behave in water and how pKa can be used to indicate the
relative strength of an acid. Responsible for delivering hydrophilic and hydrophobic agents.
• Be able to use the Henderson-Hasselbalch equation to calculate pKa or pH for a solution.
-Henderson hasselbalch:

• Discuss how buffers work and why they are used.

-Buffers: aqueous solutions that tend to resist changes in PH in the presence of small
amounts of acid or base. Biological buffers are mixtures of weak acids and their conjugate bases
-Buffers maintain the pH of a solution by adjusting the direction of their chemical
reactions (dissociating or re-associating) in response to increases or decreases in hydrogen ion
concentration caused by a substance entering or exiting the solution.

Chapter 3(amino acids):

•Define the common features of all amino acids.
-are all alpha amino acids
-have a carboxyl group and an amino group bonded to the same alpha carbon atom
-They differ from each other in their side chains (r groups) which can vary in structure,
size, charge, and solubility.
•Identify the structure and names (and 1 and 3 letter codes) of the 20 common amino acids.
-see image
•Classification of the R groups of the amino acids and how the properties of these groups can
affect reactivity and structure.
-nonpolar, aliphatic r groups:
-alanina, valine, leucine, isoleucine: tend to cluster together in proteins, stabilizing
their structure through hydrophobic effect
-glycine: has the simplest structure, easiest to group here, side chain has no real
contribution to hydrophobic effect
-methionine: contains sulfur, has a slightly non polar thioether group in its side
chain
-proline: has an aliphatic side chain with a cyclic structure, secondary group is
held in a rigid conformation that reduces structural flexibility of polypeptide regions that
contain it
-Aromatic r groups:
-phenylalanine, tyrosine, tryptophan: relatively nonpolar, all can contribute to the
hydrophobic effect
-Polar, uncharged R groups:
-serine, threonine, cysteine, asparagine, glutamine: more soluble/hydrophilic
because their functional groups can form H bonds with water.
-serine and threonine gains polarity from their hydroxyl group
-cysteine: polarity from the sulfhydryl group is much more modest than others,
but it is a weak acid and can make H bonds with oxygen or nitrogen. Can be readily
oxidized to cystine (AA, 2 cysteine molecules joined by a disulfide bond)
-asparagine and glutamine are the amides of aspartate and glutamate, which they
can be readily hydrolyzed to by an acid or base
-Positively charged (basic) R groups:
-the most hydrophilic r groups are those that are positively or negatively charged
-AA’s with significant positive charge at pH 7 are lysine, arginine, histidine
-Histidine has an ionizable side chain w/ a pka near neutrality, so it can have a
positive or negative charge at neutral ph
-Negatively charged (acidic) r groups:
-have R groups with a net negative charge at ph 7: aspartate, glutamate (has a 2nd
carboxyl group)
•Read a titration curve of an amino acid or buffer and identify pKas of each ionizable group
(including R groups).
•Calculate pI for an amino acid using pKa values.
-isoelectric point (pH at which the amino acid does not migrate in an electric field, pH at
which the amino acid is neutral)

•Predict the charge (structure) of an amino acid at a pH based on its pKa values.
2 pka values: uncharged side chains
3: ionizable side chain
•Discuss methods that can be used to separate and analyze peptides according to the properties.
-peptides can be named using full names, three letter codes, or one letter codes of their
amino acids
-the sequence and arrangement of amino acids gives the polypeptide chemical character.
They can thus be separated by charge, size, affinity for a ligand, solubility, hydrophobicity, and
thermal stability.
-chromatography is commonly used for preparative separation in which the protein is
able to remain fully folded. Proteins with a lower affinity for the solid phase wash off first, while
those with higher affinity will retain the column longer and wash off later.
-separation by charge: ion exchange. Proteins move through a protein containing cation
exchangers at rates determined by their net charge at a specified pH. Proteins with more negative
charge will move faster.
-separation by size: protein mixture is added to columns containing cross linked polymer,
protein molecules separate by size with larger molecules passing more freely.
Chapter 4 (protein structure):

• Describe how the primary sequence (amino acid sequence) of a protein can determine its
tertiary (3D shape) and its function.
-the organization around the peptide bond, paired with the identity of the R groups,
determines the secondary structure of the protein
-drives the folding and intramolecular bonding of the chain, which determines the 3D
shape
-folded proteins are stabilized by non covalent bonds between amino acids
• Discuss the interactions that stabilize a protein conformation: Hydrogen bonding, van der
waals, hydrophobic, disulfide bonds, ionic, etc.
-hydrophobic: the release of water molecules rom the structured solvation layer around
the molecule as protein folds increases the net entropy
-Hydrogen bonds: interaction of N-H and C double to O of the peptide bond leads to local
regular structures such as alpha helices and beta sheets
-London dispersion: medium range weak attraction between all atoms contributes
significantly to the stability in the interior of the protein
-electrostatic interactions: long range strong interactions between permanently charged
groups. Salt bridges, especially those buried in the hydrophobic environment strongly stabilize
the protein.
• Identify and discuss the important secondary structures including: α helices, β sheets (parallel
and antiparallel), and beta turns. Including:
• Structural features of each structure
• Amino acids prevalent in each structure
• Interactions that stabilize these structures
-Alpha helices: stabilized by hydrogen bonds between nearby residues (n and n+4).
Peptide bonds are aligned roughly parallel with the helical azis. Can be right or left handed. Side
chains point out and are roughly perpendicular with the axis. Small hydrophobic residues such as
ala and leu are strong helix formers. Pro acts as a helix breaker because the rotation is
impossible. Gly acts as a helix breaker because the tiny R group supports other conformations.
-Beta sheets: stabilized by hydrogen bonds between adjacent segments (backbone amides
in different strains) that may not be nearby. The planarity of the peptide bond and tetrahedral
geometry of the alpha carbon create a pleated sheet like structure. Side chains protrude from the
sheet, alternating in an up and down direction. Sheets are held together by the hydrogen bonding
of amide and carbonyl groups of the peptide bond from opposite strands. Can be parallel or
antiparallel. In parallel sheets, the h bond strands run in the same direction (hydrogen bonds
-beta turns:occur whenever strands in beta sheets change the direction, the 180 degree
turn is accomplished over four amino acids and is stabilized by a H bond from a carbonyl oxygen
to amide proton three residues down the sequence. Proline in position 2 or glycine in position 3
are common in beta turns.
• Tertiary structures of proteins including classifications of proteins as globular or fibrous.
-refers to the overall spatial arrangement of atoms in a protein. Stabilized by numerous
weak interactions between amino acid side chains, largely hydrophobic and polar interactions.
-fibrous:
1. alpha helix, cross linked by disulfide bonds: tough, insoluble protective structures
of varying hardness and flexibility.
2. Beta conformation: soft, flexible filaments,
3. Collagen triple helix: high tensile strength, without stretch
-globular
1. Contain protein segments that lack definable structure, composed of aminoacids
whose higher concentration forces less define structure (lys, arg, glu,pro),
disordered regions can conform to many different proteins, facilitating interaction
with numerous different partner proteins.
• Identify and define the term native conformation when referencing a protein.
-thermodynamically most stable conformation
• Discuss quaternary structure and what is referenced
- A quaternary structure is formed by the assembly of individual polypeptides into a larger
functional cluster
• Discuss the process and importance of denaturation and some of the conditions that may lead to
a protein denaturing.
-denaturation:loss of structural integrity with accompanying loss of activity
-caused by: heat or cold, ph extremes, organic solvents, chaotropic agents (urea and
guanidinium hydrochloride)
• Discuss the use and role of chaperones in protein folding.
-prevent misfolding and aggregation of unfolded peptides, facilitate folding

Chapter 5 (ligands)

• Identify the methods and forces involved in the binding of ligands and proteins.
-ligands:molecules that reversibly bind to proteins
-binding occurs by intermolecular forces such as ionic bonds, hydrogen bonds, and van
der waals forces
-affinity: rate of binding
• Describe the theory of induced fit.
-ligand binding is often coupled to conformational changes, sometimes quite
dramatically. This allows for a tighter binding of the ligand, and for high affinity for different
ligands. Both the ligand and the protein can change their conformations.
• Describe and / identify cooperative and allosteric binding of a protein system binding of a
protein
-cooperativity: in multisubunit proteins, conformational changes in one subunit can affect
the others
-Positive cooperativity: first binding event increases affinity at remaining sites,
recognized by sigmoidal binding curves.
-negative cooperativity: first binding event reduces affinity at remaining sites.
-allosteric regulation: binds somewhere other than the active site
-allosteric protein: binding of a ligand to one site affects the binding properties of a
different site on the same protein, can be positive or negative.
-homotropic: the normal ligand of the protein is the allosteric regulator.
-heterotropic: a different ligand affect binding of the normal ligand.

• Describe the importance of temporary interactions between the ligand and binding site. Discuss
why temporary binding is important and what and how specific interactions allow the binding to
be temporary.
-In globin (oxygen binding proteins), the protein side chain lacks an affinity for )2, some
transition metals will bind it well, but these would generate free radicals in solution.
Organometallic compounds like heme are more suitable but Fe2+ in free heme could be oxidized
to the highly reactive Fe3+. The solution is to capture the oxygen molecule with a heme that is
protein bound
-Oxygen transport, immune function, muscle contraction
-transient nature is critical to life, allows an organism to respond rapidly and reversibly to
changing environmental and metabolic circumstances.

Chapter 6 (enzymes):

• Describe the physiological significance of enzymes.

-catalysts: increase reaction rates without being used up
-most are globular proteins or RNA
-high reaction specificity, which avoids side productis
-milder reaction conditions, conducive to conditions in cells
-higher reaction rates, biologically useful timeframe
-capacity for regulation, control of biological pathways
• Discuss the ways that enzymes can accelerate chemical reactions.
-enzymes increase reaction rate by lowering activation barriers
-enzymes organize reactive groups into close proximity and proper orientation with the
binding energy of substrates
• Identify the chemical mechanisms of catalysis.
-acid-base catalysis: give and take protons
 -covalent catalysis: change reaction path, transient covalent bond between the enzyme
and the substrate. Requires a nucleophile on the enzyme. Can be a reactive serine,
thiolate, amine, or carboxylate
-metal ion catalysis: use redox cofactors, pka shifters . Involves a metal bound to the
enzyme, interacts with substrate to facilitatie binding and stabilizes negative changes,
participates in oxidation reactions.
• Define and use Km and the Michaelis-Menten equation. Use equation to solve for Km or Vmax
when given information.

E+S><ES>E+P
Etot= concentration of E +ES
• Define an enzyme inhibitor and classify it into type.
-inhibitors decrease an enzyme's activity
-irreversible inhibitors: ract with the enzyme, can permanently shut off one enzyme
molecule. They are often powerful toxins, but may also be used as drugs.
-reversible inhibitors: bind to and can dissociate from the enzyme.They are often
structural analogs of substrates or products, often used as drugs to slow down a specific enzyme.
Can bind to a free enzyme and prevent the binding of the substrate.
 -competitive inhibitor:competes with substrate for binding, binds active site, does not
affect catalysis.
-uncompetitive inhibition: only binds to enzyme substrate complex, does not affect
substrate binding, but inhibits catalytic function
-mixed inhibition:binds enzymes with or without substrate. Binds to regulatory sites,
inhibits both substrate binding and catalysis.
• Identify how enzyme activity can be regulated.
-noncovalent modification (allosteric regulators)- generally small chemicals, can be
positive or negative, and improve or reduce enzyme catalysis respectively.
-covalent modification
-irreversible
-reversible