Transcript Biology and computers

The digestive system, thermodynamics,
enzymes, and transport across membranes
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May 12, 2003
Learning objectives
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Be capable of manipulating protein structures using the
freeware, Deep View
Understand the structure of the alpha helix in proteins
Know the difference between anaerobic energy production
and aerobic energy production
Understand the major reactions in glycolysis, Krebs cycle
and oxidative phosphorylation
Workshop-Display tripeptide of a protein. Capture
the image, export to Power Point, label amino
terminus, etc.
Homework and reading assignment-see last slide
The Protein Data Bank
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Contains three-D coordinates for several thousand
proteins and other molecules.
This is experimentally-derived data from three
sources
1)
2)
3)
X-ray crystallography
Nuclear magnetic resonance
Ab initio calculations (very few)
•The Protein Data Bank contains records that consists of two
parts: header and content.
The header contains annotations and the content contains
the x, y, z coordinates of each atom in the protein
Content of 2HHB record in PDB
HEADER OXYGEN TRANSPORT 07-MAR-84 2HHB 2HHB 3
COMPND HEMOGLOBIN (DEOXY) 2HHB 4
SOURCE HUMAN (HOMO SAPIENS) 2HHB 5
AUTHOR G.FERMI,M.F.PERUTZ 2HHB 6
REVDAT 2 15-OCT-89 2HHBA 3 MTRIX 2HHBA 1 REVDAT 1 18-JUL-84 2HHB 0
2HHB 7
SPRSDE 18-JUL-84 2HHB 1HHB 2HHB 8
JRNL AUTH G.FERMI,M.F.PERUTZ,B.SHAANAN,R.FOURME 2HHB 9
JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN ..10
JRNL TITL 2 1.74 ANGSTROMS RESOLUTION 2HHB 11
JRNL REF J.MOL.BIOL. V. 175 159 1984 2HHB 12
JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 2HHB 13
REMARK 1 2HHB 14
REMARK 1 REFERENCE 1 2HHB 15
REMARK 1 AUTH M.F.PERUTZ,S.S.HASNAIN,P.J.DUKE,J.L.SESSLER, 2HHB 16
Content of 2HHB record in PDB
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1
2
3
4
5
6
7
N
CA
C
O
CB
CG1
CG2
VAL
VAL
VAL
VAL
VAL
VAL
VAL
A
A
A
A
A
A
A
1
1
1
1
1
1
1
X
Y
Z
6.130
6.870
8.377
8.820
6.345
6.745
4.826
16.559
17.784
17.548
16.980
18.763
20.188
18.612
4.905
4.702
4.913
5.922
5.731
5.356
5.847
7.00
6.00
6.00
8.00
6.00
6.00
6.00
41.29
41.33
31.64
38.31
52.26
52.75
58.75
2HHB
2HHB
2HHB
2HHB
2HHB
2HHB
2HHB
206
207
208
209
210
211
212
PDB file summary
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CATH: Structural Classification
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Class(C), Architecture(A), Topology(T) and
Homologous superfamily (H).
PDBSum: Summary of PDB Structure
SCOP: Structural Classification
Summary of PDB Structure
Heme
Deep View-an image display
program
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Created by Glaxo-Smith-Kline
Download to the self-extracting
file to desktop
Choose 1crn PDB file from
Download folder to display
Display the molecule and the
control panel
Instructions for Workshop
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Select the first alpha helix in the control panel
for display
Change view so that you are looking through
the “hole” of the alpha helix
Remove residues one at a time and add back
residues. Convince yourself that side chains
are on the outside of the helix.
Without the side chains display the H-bonds.
How many residues are interspersed within
the alpha chain between a pair of amino
acids bound by H-bonds?
Instructions for Workshop (2)
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Display a tripeptide.
Capture the image on the screen and import
into power point
Annotate the power point slide to point out
the amino terminus, carboxyl terminus and
side chain. Is your side chain hydrophobic or
hydrophilic?
Show your instructor when you are finished.
Metabolism-the sum of all the chemical changes taking
place in an organism
Cell respiration-decomposition pathway that provides
ATP for cellular functions.
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Three stages of cellular respiration-Glycolysis,
Krebs cycle, Electron transport (OxPhos)
Glycolysis
(cytoplasm)
Krebs cycle
(mitochondria
matrix)
Electron transport
(mitochondria
inner membrane)
Oxidation
Glucose + O2 + NAD+ 6CO2 + H2O + NADH
Used for electron
transport chain
Homework Due May 19
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Read pp 129-150. Answer Reviewing
Ideas on p. 50, problems 1, 2, 4-6;
Using Concepts on p. 151, problems 1,
2, 4, 6, 8, 9. Extensions on p. 151,
problem 1