Chapter 13
Basic concepts of thermodynamics
(Here is a PDF file of the figure)
Formal Oxidation states of carbon
Chapter 6
Enzymes enhance chemical rates
Enzymes stabilize transition states
Factors effecting enzyme efficiency
Some classic enzyme mechanisms
Serine proteases
Details
of transition
state
stabilization
Chymotrypsin animation
Convergent Evolution of serine proteases
Compare subtilisin and chymotrypsin
Glycohydrolases:
SN1 or SN2? probably SN2
Retaining
and
Inverting Mechanisms
Vitamin-derived cofactors for special enzyme reactions
Kinetics
Free energy and kinetic constants
Use of first order rates in Biochemistry
Michaelis-Menten kinetics (derivation)
Some catalytic parameters for enzymes
Enzyme Regulation
Allostery
- binding at other sites (catalytic or regulatory chains)
Use of regulatory sites
Most
allosteric enzymes show cooperative
kinetics
A specific example
ATCase,
Another kind of regulation:
Zymogens:
an example
Compare chymotrypsin with its zymogen
And yet another kind:
covalent
modification
Phosphorylation
Kinase sites
Other Covalent modulators
Chapter 7
Glycosaminoglycans and cell structure
Size
and structure of
carbohydrates
Carbohydrates carry
information: routing and interactions
Cells interact with the extracellular matrix
Cell
Adhesion
Lectins are proteins
that bind specific sugars
Details of RTB
Example: Lymphocyte
recruitment
Other interesting
aspects of carbohydrates
Bacterial
cell walls
Chapter 8
Base pairing in antiparallel strands
Nucleic acid conformation DEMO
DNA replication
Palindromes
etc
Nonstandard base
pairs
Triple helices
Secondary
structure of RNA
Another view of yeast Phe-tRNA
Ribosomes
Nucleic
Acid Chemistry
DNA melting
Base
mutations
Thymine
Dimers
DNA Sequencing
Animation of DNA
sequencing
Chapter
9
Restriction
enzymes cleave DNA at specific
sequences
Plasmids are self replicating
DNA units
Foreign DNA can be inserted
into plasmids
Cloning and screening recombinant DNA
Animation
of
molecular cloning in bacteria
Site directed
mutagenesis of
cloned genes
Animation
of polymerase chain
reaction, PCR
Chapter 10
Prostaglandin synthesis and COX Inhibitors
Chapter
11
Description of membranes
Membrane
overview
Membrane
compostion
Lipid asymmetry in biological membranes
Glycophorin:
an integral
membrane
protein
classes
of integral
membrane
proteins
The structure of bacteriorhodopsin
Structure of the membrane photosystem
Porin
structure - Beta barrels
A
gallery of integral membrane pores
Structure
of two membrane
pores-DEMO
A
role for Trp and Tyr
Protein-membrane
anchors
Diffusion
in bilayers
Internal
membrane
frameworks
Cell-cell membrane interactions
Membrane
fusion:flu virus
Version
from the text
Membrane
transport
The thermodynamics of transport
Cartoon mechanism of glucose T1-transporter
Hypothetical structure of the GluT1 transporter
Kinetics of glucose facilitated diffusion
Insulin and the GluT4 transporter
The chloride-bicarbonate antiporter
Mechanism of the Na/K-transporter
The energetics of solute movement across membranes
The Na/K ATPase & membrane-potential
In E. coli,
Lactose uses a proton
gradient
A
very selective ion channel
Headlines in neuron conductance
