Appendix – Biology for Bioinformatics
Fig A1.1 A typical biomembrane showing the organization of lipid bilayers and
embedded proteins and carbohydrates
Fig A1.2 Schematic representation of of the nuclear envelope which contains two lipid
bilayers. A mammalian nucleus has about 4000 nuclear pores, each is formed by over
100 different proteins.
Fig A1.3 Schematic of typical animal cell, showing subcellular components. Organelles:
(1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (ER) (6)
Golgi apparatus (7) Cytoskeleton (8) smooth ER (9) mitochondria (10) vacuole (11)
cytoplasm (12) lysosome (13) centrioles
Fig. A1.4 A cartoon of a subunit in the capsid of foot-and-mouth-disease virus. The
capsid is an icosahedron, comprising 60 subunits. Each subunit is made up of four
proteins: VP1, VP2, VP3 and VP4
Fig. A1.6 Structure of the complex formed by HIV gp120, CD4 and an antibody against
chemokine receptors. PDB ID = 1GC1.
Fig. A1.7 Structure of
Fig. A1.8 Formation of peptide bond and rotational freedom in it
Fig A1.
- Ψ angles. The red line formed by the
repeating -Ca-C-N-Ca- is the backbone of the peptide chain
Figure A1.13 Schematic drawing of DNA's two strands.
Fig A1.16 The condensed structure of chromatin
Table A1.4 The genetic code, which was deciphered by Marshall Nirenberg and his
colleagues in early 1960s.
Fig A1.17 General organization of exons and introns on the DNA sequence
Fig. A1.18 Illustration of satellite bands using buoyant density gradient centrifugation
Fig. A1.20 Basic organization of LINEs
Fig. A1.21 Comparison between direct repeats and inverted repeats
Fig. A1.22 Central dogma depicting steps involved in the expression of protein genes
Figure A1.23 Schematic illustration of transcription
Figure A1.24 The chemical reaction catalyzed by RNA polymerases.
Fig A1.25 Simplified presentation for the chain elongation. The vertical line represents
the pentose and the slanting line denotes the phosphodiester bond. Bases are
designated as N1, N2, etc.
Fig. A1.26 The structure of Sigma 70 and its DNA binding site. Note that residues Y425,
Y430, W433 and W434 are directly involved in the unwinding (melting) of the double helix.
Fig A1.26 Human β globin gene cluster, where elements in blue are the enhancers
Figure A1.27 Gene organization in eukaryotes
Fig A1.28 The lac operon and its working
Fig. A1.29 RNA processing for protein genes
Fig. A1.30 consensus sequence for splicing. Pu = A or G; Py = C or U
Fig. A1.31 Formation of spliceosome during RNA splicing
Fig. A1.32 Frameshift indels. Note that the translated amino acids are entirely different
after the insertion point.
Fig A1.33 Pairing between (A) tRNA's anticodon and mRNA's codon, the wobble
position where base pairing does not obey the standard rule. (B) All possible base
pairings at the wobble position.
Figure A1.34 Major pathways for signals interaction in a cell
Fig A1.35 Sodium ion channel is a voltage gated channel. (A) the protein has four
homologous domains containing multiple potential α-helical transmembrane segments. The
fourth transmembrane segment (S4) of each domain is highly positively charged, and
thought to be a voltage sensor (B) The ionic pore formed from the protein has a large
aqueous cavity, with a gate close to the interior and a selectivity filter on the outer vestibule
Fig A1.36 (A) Schematic drawing of the transmembrane topology of the G-proteincoupled receptor, which is characterized by seven transmembrane segments. (B) None
of the structures of G-protein-coupled receptors has been determined yet, but their
transmembrane structures are expected to be similar to bacteriorhodopsin (a proton
pump) PDB ID = 1AT9
Fig A1.37 Active and inactive forms of caspases.
Fig A1.38 Schematic drawing of the DNA replication process. DNA replication involves
unwinding of the double helix. New strands are synthesized by DNA polymerases using
the old strands as template. Unwinding of a DNA molecule looks like a "fork" growing in
one direction
Fig A1.39 Donut shaped structure formed by two b subunits of the E. coli DNA
polymerase III
Fig A1.40 End Replication Problem
Fig A1.41 Simplistic overview of the signal transduction from critically short telomeres to
irreversible growth arrest at the G1/S transition of the cell cycle.
Fig A1.42 The essential steps in DNA cloning using plasmids as vectors
Fig A1.44 Process of Southern Blotting