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Biochem Exam 1


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the total heat content of a system

- H = exothermic
+ H = endothermic

derived from 1st law of thermodynamics:
energy cannot be created or destroyed.
mesures the degree disorder in a system.

Derived from 2nd Law of thermodynamics:
universe tends to become more disordered.
Free energy (delta G)
energy available to do chemical work.
G = H - TS

only gives spontinaity, does not tell anything about the rate of the reaction.
open system vs. closed system
open system both energy and matter are exchanged.

closed system only energy is exchanged between the system and its surroundings.

Living organisms are open systems.
Entropy can be used to predict spontaneity and direction.
entropy change is poitive for spontaneous reaction.
entropy is the driving force behind irreversible processes.
Non-covalent interactions:

1) H+ bonds:
H+ donors - H+ covalently bonded to O,N,S.
H+ acceptors - lone pairs of electrons on O,N,S.

2) Vander Waals forces
elecrostatic interactions between polar groups with no charge.
includes Dipole-Dipole interactions and london dispersion.

3) Ionic interactions
the stongest of the non-covalent
occurs between ionizable groups.
pH of solution can be altered by addition of acid/base.
strong acid or base will completely dissovle in the solution
So, biologically relavent acids and bases are weak that do not completely ionize.
pKa =
pKa = -log Ka
Henderson-Hassalbach equation
pH = pKa + log [base]/[acid]
can combine with and release H+ to prevent a change in pH.

common buffers consist of a weak acid and its conj. base.
Buffering capacity
depends on the molar concentration of [H-] and [HA], the more that is present that better the buffer.
Also, the ratio of acid to conj. base
most effective buffers have equal conc. of both.
Bohr Effect
CO2 + H2O = H2CO3 = HCO3- + H
Most common amino acid sterioisomer
Common feature or structure of amino acid
alpha carbon
H atom
R side chain
carboxyl group
amino group
What is the isoelectric point and how do you find it?
Ip= is the pH where the specied has no net charge.
when the neutral species exists in the highest conc.

pI = pKa1 + pKa2 / 2
Peptide bond
also called the amide bond - formed by the condensation of 2 amino acids.
RCO2- + +NH3R gives
pH =
pH = -log [H+]
Native conf.
teh biologically active conf. of the protein.
Many conf. are possible but there is only one native structure.
denaturation is the loss of the native structure.
Primary structure
sequence of amino acids in the polypeptide chain.
Linear sequence of amino acids.
Secondary structure
the spatial arrangment of peptice backbone.
includes the alpha and beta sheets.
Also involves the H bonds.
Tertiary structure
the 3-D structure of peptide chain.
THis includes the side chains and the non-amino acid components.
Quaternary stucture
spatial arrangment of peptide chain in proteins with more than one chain.
The realationship of sepearte peptide chains to one another.
What does the primary structure of a protein determine?
The primary structure determines the properties of the protein.
And the amino acid sequence determines the primary structure.
Molecular diseases are mutations in which structure of the protein?
Mutations in the primary structure.
Replacement of one amino acid for a diff amino acid.
Ex: Sickle Cell anemia
The conformation of the peptide bond determines which protein structure.
Conf. of the peptide bond determines the secondary protein structure.

Rotation at the alpha carbon allows for the secondary strucuture.

The secondary structure is reqular and repeating and involves the H+ bonds.
Structure of alpha helix
usually right hand.
H+ between every 4th residue.
the carbonyl oxygen forms a H bond with the backbone NH 4 residues away.
Effects of Proline and Glycine on alphs helix.
Proline breaks the alpha helix because it contains a imine and the Glycine has a small R group (H+) that allow for the helix to bend.
Structure of beta-sheets
H-bonding between adjacent sheets.
can be parallel or antiparallel
they form pleated sheets due to the planar amide bond.
alpha helix with crosslinking disulfide bonds.
the single peptides form a left handed helix and conbine to form a very stable/strong right-handed alpha helix.
consists of glycine, proline, and hydroxyproline residues.
Scurveys is caused by a lack of hydroxyproline - which weakens collagen.
What is protein folding determined by?
H bonding
Hydrophobic interactions
complexes with metal ions
Hydrophobic interactions determine which structure of the protien.
Determine the tertiary structure and the 3-D arrangment.

Hydrophobic interactions determine the 3-D structure of the protein.
The primary structure determines the function of the protein.
consists of prostetic group -heme (prophoryn ring and Fe II)

The free floating His prevents perpendicular binding of O2.
So, O2 binds in bend conf. to prevent oxidation of FeII.

Myoglobin consists of a hyperbolic curve. So, binding of O2 has no affect on subsequent O2 binding.
T/F All the info for protein folding is available in the amino acid sequence.

Yes, ALL the info.
Urea is used to do what?
To break disulfide bonds and denature the protien from its native conf.
Chapperone Proteins
required for sequential folding of the native conformation.
Allow for the correct and timely folding of a protein.
consists of alpha and beta subunits. (2 of each)

When O2 binds to Hb, the O2 pulls the His residue up toward the ring and flattens out the porphoryn ring. This changes the quaternary structure and the confomation of adjacent subunits, opening up the O2 binding site.
cooperative binding - giving a sigmoidal curve.
required for Hb to participate in cooperative binding.

Binds to Hb and stabalizes the deoxy form.

W/O this glycerate the Hb globin curve resembles the Mb curve.

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