A to Z in Biology and Biochemistry

Acetylation (or Succinylation) of Amino Groups on Proteins

Amino acids:

aliphatic

and peptides

and peptides, proteins, enzymes

aromatic
charged

chemico-physical properties, drawings, 3D models

metabolism

Phi and Psi angles (interactive, uses SGI Cosmo Player)

polar uncharged

properties

repository

selector

specialized products

structure and packing of the alpha helix

structure and packing of the beta pleated sheet

sulfur-containing

titration behavior (interactive)

Angiotensin Protein Kinase Assay (Fibroblasts)

Antibiotics database

Antibodies:

tutorial

ATP and ADP

ATPase assay: steady state, coupled Enzyme System

ATPase assays using³²P-ATP (1) (2)

Biocatalysis/Biodegradation Database

Biochemical Energetics Biochemical Techniques  -  see also specific topics

Biochemistry & Chemistry for biology

Biochemistry concepts

Biochemistry Databases

Bioenergetics

Bioinorganic Chemistry

Biological Macromolecules image library

Biological Macromolecules IMB Jena Image Library
Bioluminescence

Biomolecule basic chemistry

Blood Coagulation

Carbohydrate-Active enZYmes
Cellulase assays (gel diffusion and viscosity reduction methods) in fruits

Chemiluminescence immunoassays (with animations)

Chmiluminescence of luminol (movie, 4,94MB)

chemiluminescence of TCPO (movie, 4,85MB)

chemiluminescence emitters

chemiluminescence movies

Cholesterol and Bile Metabolism

Collagens

Computational Biochemistry Research Group

Crystallization of Biological Macromolecule Database

Cytoskeleton:

TUBULES & F ILAMENTS:

Actin & Myosin-Microscopic Observation of Muscle

Actin filaments (PDF)

Fluorescent Analysis of Microtubules

Further Studies

Histology of Extracellular Matrix

Introduction

Isolation of Actin and Myosin Filaments

Isolation of Microtubules (Bovine Brain)

Polymerization Induced Changes in Absorbance

SDS Gel Electrophoresis of Tubulin\MAPs

TEM Visualization of Microtubules

Viscosity & Polymeriztion of Microtubules

Cytric acid cycle animated

D-Amino Acid oxydase assay (PDF) in fruits

Deubiquitinating enzyme activity assay (HTML – PDF) in fruits

Energy conversion mechanisms in biology

Energy exchages & storing in organisms

Energy in Biology

Enzymes:

addition of enzyme inhibitors

advanced analysis of enzyme parameters

Compounds, and Reactions database (LIGAND)

computer simulation

determination of Km and Vmax

effects of ph

effects of temperature

enzyme concentration

introduction
extraction of tyrosinase

kinetic analysis

kinetics (part1) (part 2)

nomenclature Database (ExPASy)

preparation of standard curve

protein concentration/enzyme activity

structures database

Kinetics (interactive):

Enzyme Mechanisms
Michaelis-Menten Kinetics

Hanes-Woolf Kinetics

Lineweaver-Burk Kinetics

Reversible Inhibition

Glucosamine Rapid Assay in fruits

Gluconeogenesis

Glutathione micro-assay

Glycogen Metabolism (1) (2)

Glycolysis (see also in metab--)

Glycoprotein Synthesis

Glycoproteins detection on Blot

Glycoproteins Deglycosylation Using Endoglycosidases

Glycosaminoglycans

Growth Factors and Cytokines

Heme and Porphyrin Metabolism

Hemoglobin (tutorial)

Hormones

Hormones, Lipids, Sugars, Vitamims
Hydrophobic interactions in proteins

In-gel digestion of proteins for peptide fingerprint mapping

Interactive Biochemistry

ketone bodies

LDH isozymes separation from serum by SDS PAGE

Lipids:

crystal structures of membrane lipids

database

Data Bank

Eicosanoid Metabolism

Fatty Acids

Fatty Acid Oxidation

Glycosphingolipid analysis

LIPIDAG - Miscibility/Phase Diagram Database 

LIPIDAT - Phases and Phase Transitions Database

LMSD - Molecular Structures Database

Molecular Dynamics Simulations in membranes

Phospholipid Metabolism

Sphingolipid Metabolism

Structure of Fluid Lipid Bilayers

Lipoproteins

Luminol chemiluminescence

Macromolecular Museum (needs Firefox):

Amino Acid Structures

Bacteriophage cro repressor

Beta-subunit of E. coli DNA polymerase III

Catabolite Activator Protein

Catalase

Chemical Bonds and Protein Structure

Cre Recombinase
DNA Conformers

DNA Structure

E. coli Porins: OMPF and Maltoporin (LamB)

Enzymes of Mismatch Repair:  MutS - MutH

Erythropoietin - Epo Receptor Complex

Erythropoietin Receptors

Eukaryotic DNA Polymerase Beta

Genetic Switch of Temperate Phages: cro - repressor

Hammerhead Ribozyme - Inhibitor DNA

HhaI DNA Methylase
Hin Recombinase
RecA (E. coli)

HIV Nef Protein/Fyn PTK SH3 Domain

HIV Reverse Transcriptase

HIV-1 Protease
HIV-1 Reverse Transcriptase
HIV-1 Integrase

HIV-1 Nef
HIV-1 gp120 and Flu Hemagglutinin
Influenza Hemagglutinin (Jmol)
Nitrogen Regulatory Protein C

Nucleosome Core Particle

Phage T7 DNA Replication Complex

Protein Tyrosine Phosphatase

PTP 1B

Restriction Endonuclease BamHI

Ribosome Structure

RNA Polymerase

RuvA Recombination Protein

Signal Recognition Particle Core (E. coli)

Topoisomerase I (E. coli)

Two Mg++-Catalyzed DNA Elongation

U1A Spliceosomal Protein: Interactions with RNAs

Medical biochemistry (1) (2)

Metabolic Pathways :

Citric Acid Cycle (TCA cycle)

Glycolysis

Pentose-Phosphate Pathway

Metabolism:

(IUBMB-Nicholson):

Animaps

Metabolic Maps

Minimaps:

The Hub of Metabolism GIF SVG GPDF

Glycolysis GIF SVG PDF

Lactic and Alcoholic Fermentation GIF SVG PDF

Glycolysis and TCA Cycle - Reactions GIF SVG PDF

Glycolysis and TCA Cycle - Products of Potential Energy GIF SVG PDF

Glycolysis and TCA Cycle - Enzymes and EC Reference Numbers GIF SVG PDF

Glycolysis and TCA Cycle - Compartmentation GIF SVG PDF

Glycolysis and TCA Cycle - Compartmentation (Simplified) GIF SVG PDF

Glycolysis and TCA Cycle - Shuttles GIF SVG PDF

Glycolysis and TCA Cycle - Regulation GIF SVG PDF

Mitochondrial ATP Formation GIF SVG PDF

ATP Yield GIF SVG PDF

Anaplerotic (Replenishing) Reactions of the TCA Cycle GIF SVG PDF

The Glyoxylate Pathway GIF SVG PDF

Gluconeogenesis and Glycolysis GIF SVG PDF

Gluconeogenesis and Glycolysis - Regulation GIF SVG PDF

Lipid Metabolism GIF SVG PDF

Deamination of Amino Acids - The Urea Cycle GIF SVG PDF

Purine Metabolism GIF SVG PDF

Pyrimidine Metabolism GIF SVG PDF

Pentose Phosphate Pathways GIF SVG PDF

Pentose Phosphate Pathways - Pathway II GIF SVG PDF

Photosynthesis in the Chloroplast GIF SVG PDF

Photosynthesis - Regulation GIF SVG PDF

Night-Life in the Chloroplast GIF SVG PDF

Basic Photosynthesis GIF SVG PDF

Photosynthesis - Calvin Cycle GIF SVG PDF

Folic Acid Metabolism GIF SVG PDF

Folic Acid Reactions GIF SVG PDF

Folic Acid and Early Chemotherapy GIF SVG PDF

Isoprene Metabolism GIF SVG PDF

Products of Isoprene Metabolism GIF SVG PDF

Heme Metabolism  GIF SVGPDF

Prostaglandins GIF SVG PDF

ATP and Histidine Interrelationships GIF SVG PDF

Biochemistry of Metabolism:

Sugars & Polysaccharides  
Lipids & Membranes 
Bioenergetics 
Membrane Transport  
K+ Channels
Calcium Signals 
Signal Transduction 
Glycolysis & Fermentation 
Glycogen Metabolism 
Gluconeogenesis 
Krebs Cycle 
Electron Transfer Chain 
Chemiosmotic Coupling 
F1Fo ATPase  

Pentose Phosphate Pathway 
Calvin Cycle 
Fatty acid catabolism 
Fatty acid synthesis 
Eicosanoid synthesis 
Cholesterol synthesis 
Lipoproteins 
Amino acid catabolism - N 
Amino acid catabolism - C
Heme synthesis 
tRNA and ribosomes 
Protein synthesis  
Protein degradation  

 

 

Metabolism of Major Non-Glucose sugars

Metalloprotein Database and Browser
Mitochondria (see also the Cell biology section):

Mitochondria preparation from Rat Liver

Oxygen measurement with polarography (Clarke electrode)

Metabolic Poisons

Recommended experiments

Polaragraphic Studies of Isolated Mitochondria

Molecules in Action

Molecules of light

Muscle Biochemistry

Myosin-Actin model

Nitrogen Metabolism and the Urea cycle

Nuclear Receptor Resource

Nucleotide Metabolism

Oxidative Phosphorylation

Pentose Phosphate Pathway

Peptidyl-prolyl bonds

Peptide Hormones and Receptors

Pheromones

Phospholipids:

Phospholipid Metabolism

Phosphoprotein Database

Photosynthesis animations (light reactions) (dark reactions)

Photosynthesis / photolysis and carbon fixation

PHOTOSYNTHESIS / RESPIRATION:

Introduction

Isolation of Chloroplasts from Spinach Leaves

ChlorophyII Content

The Hill Reaction

Isolation of Mitochondria

Respiration: Succinic Dehydrogenase

Cytochrome Oxidase Manometric Analysis

Respiration of Mitochondria

Photosynthesis by Respirometry

Protein Data Bank

Proteins:

and amino acids in pdb (Rasmol) format

Crystal Growth data NASA Archive

Electrophoresis Databases:

SWISS-2D: Two-Dimensional Polyacrylamide Gel Electrophoresis Database

membrane protein assembly

membrane proteins of known 3D structure

Modifications and Targeting

NMR of Paramagnetic Proteins

NMR spectroscopic data (BioMagResBank)

Protein-Protein Interactions

Purification:

Preparation of Brain Acetone Powder

Extraction of Brain Actin from Acetone Powder

Preparation of Muscle Acetone Powder

Extraction of Muscle Actin from the Acetone Powder

Preparation of Skeletal Muscle Myosin

Preparation of Gizzard Myosin

Preparation of Myosin II Heavy Meromyosin and Light Meromyosin

Preparation of Myosin II S1 and Rod

Preparation of Gizzard Alpha-actin and Vinculin

Preparation of Thymus Alpha-Actinin

Preparation of Brain Profilin and Profilin-Actin Complexes

Preparation of Brain Calmodulin

Preparation of Brain Tubulin

Preparation of Cellular Fibronectin

Sequence Databases:

CATH

DBGET.

Genobase

Swiss Prot

PIR -- The Protein Information Resource

OWL-Web

GenQuest

ExPASy Molecular Biology Server.

PRODOM

Blocks

SBASE

Structural Imaging and Analysis

Structure: concepts

Structure databases

Structure Prediction From Primary Sequence (PDF)

Structure Resources:

Chemical MIME connection

NRL-3D

image library of biological macromolecules

protein motions database

Structures (interactive,with Chemscape Chime)

Structure

Synthesis

variety

Proteins, peptides & peptide activity, assembling, bonding, synthesis

Proteoglycans (1) (2)

Protocol Books

Receptors & Signaling:

Wnts and the TGFs-b/BMP Families

Signal Transduction

Skeletal muscle contraction

Smooth muscle

Sphingomyelin Mass Measurement

Sphingomyelinase Assay

Superoxide dismutase activity assay by combining electrophoresis and densitometry

Sphingolipid Metabolism

Steroid Hormones and Receptors

Sugars

TCA Cycle and PDH

TGFs-b/BMP Families

Urea Cycle

Vitamins and Co-enzymes

                           

Actin cytoskeleton  
Myosin 
Microtubules 
Microtubule motors

Preparation of Dialysis Tubing

Drop Freezing

Miscellaneous

Biochemistry of Nerve Transmission

+ Metabolism, Neurotransmitters, Signal Transduction

      

NIH MoleculesR Us -  - NIH Molecules R US Utililty. This facility combines a full text

 (Georgetown University) - Collection of individual databases on members of the steroid and thyroid

 (PPDB)

 (PDB) - Archive of experimentally-determined, biological macromolecule 3-D structures from the Brookhaven

UM-BBD:  - Search data on biodegradation pathways, microbial enzyme-catalyzed reactions and

                       

                                           

Molecular Tools of Medicine

Oncogenes and Cancer

 

Table of Common Vertebrate

Tumor Suppressors and Cancer

Biomolecular Structures

Biochemistry Techniques

Molecules of Life introduces the techniques used to examine protein structure and discusses DNA, proteins and protein folding.

Molekularbiologie-Repetitorium (Universität Bern)

THCME Medical Biochemistry Page (Indiana State University) - Designed principally as a teaching tool for students of Medical Biochemistry. However, any student taking Biochemistry will benefit.

Tutorials in Molecular Biology  - Very nice graphical demonstrations of molecular processes & techniques from UCLA. A little slow loading - requires at least Netscape 3.01 with Shockwave Plug-in.