Study Guides (333,006)
CA (147,141)
UW (6,594)
PHYS (62)
Final

PHYS380 Study Guide - Final Guide: Beta Sheet, Polyproline Helix, Helix Bundle

20 pages243 viewsWinter 2013

Department
Physics
Course Code
PHYS380
Professor
Firas Mansour
Study Guide
Final

This preview shows pages 1-3. to view the full 20 pages of the document.
MODULE 1 Introduction to molecular physics
Fundamental properties of life:
Self-replication without it, you would remain stagnant
o Rate of self-replication the population within each generation is governed by an
exponential relative to time.
Death allows generations to be replaced
Mutation aspect of evolution from one form of life to another. Must have undergone specific
mutations, and death must have occurred.
Cellular structure and composition:
Cells can be prokaryotic or eukaryotic
Prokaryotes
o Present in lower organisms e.g., bacteria
o DNA molecule more randomly folded within the cell; has no enclosing structures
Eukaryotes present in complex organisms e.g., humans
o Genetic material is assembled in chromosomes (1-50) within nucleus
o Structural proteins are involved in the arrangement of the chromosomes.
MODULE 2 Introduction to basic protein structure
Covalent bonding:
Hydrogen is the simplest atom with 1s orbital that contains max 2e
Other atoms bond to H2 by donating an e to the 1s orbital, filling the shell
An e in an orbital close to the nucleus has an energy which is lower relative to an e in an orbital
further away from the nucleus.
E orbitals and quantum mechanics
Pauli exclusion principle no 2 e can have identical values for all 4 quantum #s
o N = principle quantum # (Shell) = 1, 2, 3…
o L = angular momentum (subshell) = 0, 1, 2, (n-1)… (s, p, d, f)
o M = magnetic quantum # (orientation) = 0, +/- 1, +/-2…
o Ms = spin quantum # = +/- 1/2
Hund’s rule – total energy of an atom with more than 1 e occupying a set of degenerate orbital
is lowest of electrons occupy different atomic orbitals and have parallel spin.
Bond lengths and energies:
C-H bond relatively strong; C-C bond weaker bond; C=C bond very strong
Amino acids:
20 principle amino acids, and are able to ionize in water.
There are 2 different conformations of the structure (stereoisomers = mirror images)
o L form (found in eukaryotes) R group is to the left of the path
o D form R group is to the right of the path
Polypeptide = amino acids joined by peptide bonds, water is always given off.
Peptide bond becomes non-rotating with resonance.
You're Reading a Preview

Unlock to view full version

Only half of the first page are available for preview. Some parts have been intentionally blurred.

Exam Q: Why does the charge redistribute with bond resonance?
o C=C bond takes on ~40% of single bond character, and the single bond takes on ~40%
double bond character, thus preventing it from rotating as easily as well.
Non polar/hydrophobic R groups
o Alanine Ala
o Valine Val
o Leucine Leu
o Isoleucine Ilu
o Proline Pro (only AA where R group prevents rotation of peptide bond)
o Phenylalanine Phe
o Trytophan Trp
o Methionine Met
Polar, uncharged R groups
Exam Q: Interact with water more easily. Water is an electric dipole which allows it to align its
polarity with that of the R group.
o Glycine Gly
o Serine Ser
o Threonine Thr
o Cysteine Cys
o Tyrosine Tyr
o Glutamine Glu
o Asparagine Asn
o Histidine His
Polar, acidic R groups negatively charged at pH 7
o Aspartic acid Asp
o Glutamic acid Glu
Polar, basic R groups positively charged at pH 7
o Lysine Lys
o Arginine Arg
Electrophoresis:
Used to measure charge properties of AA and proteins due to interaction between the medium
and protein causing resistance to motion. Frictional effects must also be considered.
Proteases:
Proteins that can break down peptide bonds and are found in GI tract.
Very specific on which bond they break.
E.g., Trypsin breaks peptide bond at carboxyl end of lys and arg (both + charged AA)
Polarity:
Generated by a particular charge distribution which is not spherically symmetric
Polar molecules have an affinity for water
You're Reading a Preview

Unlock to view full version

Only half of the first page are available for preview. Some parts have been intentionally blurred.

MODULE 3 Molecular interactions and energetics
Free energy:
Interactions between AA and those between AA and water are often weak = at the cellular level,
bonds must be broken and reformed on a continuous basis in order for large scale motion and
muscular contraction and relaxation to occur.
Gibbs free energy: - used for large quantities
ΔG = ΔH - T ΔS
o ΔG = G2 – G1
o ΔG < 0, bonds form
o ΔG > 0, bonds don’t form
o ΔG = 0, nothing happens.
2nd law of thermodynamics during a real process, the entropy of an isolated system always
increases. Heat is released and order tends to increase when bonds are formed.
Bond formation System favors minimum energy = ΔG is at a maximum where there is a
minimum energy and the bind is formed.
Bond breakage Total E= U + KE
o The ratio of ΔG/RT, bond energy to KE, will determine the fraction of bonded molecules.
o If ΔG = 0, Keq = 1 and formation and breakage of bonds are equally favored
o If ΔG < 0, Keq > 1, bond formation favored
o If ΔG >0, Keq <1, bond breakage favored
Weak bonds:
Ionic (electrostatic)
o If force is -, => attractive; if force is +, = repulsive
o Dielectric constant charges within the protein will not be evenly distributed (variable)
o Entropically driven reactions: ion-pair formation.
For aqueous solvents, the entropy of the water increases substantially so that
there is a net overall increase in entropy within the system”
ΔH for ion-pair formation is +
ΔS for ion-pair formation is
Dipole (permanent dipoles)
o Antiparallel attraction; parallel repulsion.
o Examples: OH, C=O, NH, peptide bond
Van der Waals (London dispersion forces)
o Occurs between 2 fluctuating, non-permanent dipoles
o In proximity, the electron cloud distribution can shift momentarily due to unpredictable
quantum fluctuations, producing a transient dipole-like interaction.
o Fluctuations continue in such a way that a net attraction exists.
o As atoms come close together, electron orbitals start to overlap and a repulsive force
will result in keeping with the Pauli exclusion principle = called the hard sphere potential
o You can also add 2 vanderwaal forces (+) + (-) = called the Lennard-Jones potential
Hydrogen bonds
o Strongest weak bond with energy of up to 5 kcals/mole
You're Reading a Preview

Unlock to view full version


Loved by over 2.2 million students

Over 90% improved by at least one letter grade.