Download Bi-150-molbiol

Bi 150 Lecture 0
October 4, 2012
An introduction to molecular biology . . .
but you will learn the cell biology in this course
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3 x 109 base pairs
Lander et al
Humans have 22 pairs of chromosomes, plus the X and Y.
Males are XY; females are XX.
A. Each chromosome is “painted” with a
unique combination of fluorescent dyes
B. We have arranged the chromosomes
to form pairs.
© Garland; Little Alberts Fig 5-12
Genes can be localized crudely
by
hybridizing a fluorescent nucleotide probe to chromosomes
2 mm
6 distinct genes are
probed in this image
Little Alberts Fig 10-16
Seuss 1959
Complete DNA sequence as scripture (surf NCBI)
single-nucleotide
polymorphisms (SNPs)
chromosomal location
orthologs in
other species
mutations that
cause disease
basic sequence
RNA splicing
RNA sequence
proteins that bind to
the sequence and
regulate expression
RNA abundance
protein sequence
protein function
protein structure
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How much coding sequence is in the genome?
22,000 genes x 400 codons/protein x 3 bases/codon
= 26.4 million base pairs, or < 1% of the genome!
The remainder . . .
1.
Repetitive elements (junk? selfish DNA?)
2.
Regulatory regions
3.
Introns
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Gene activation involves regulatory regions
Little Alberts Fig. 8-15
© Garland publishing
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Components of Expression
coding sequences
Gene (DNA)
exon
noncoding sequences
intron
transcription (mRNA synthesis)
splicing (introns removed)
messenger RNA (mRNA)
translated sequences
untranslated sequences
translation
protein
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Protein synthesis and degradation
A. synthesis
B. degradation
“proteolysis”
protein + Greek, breakdown
Modified from Little Alberts Panel 2-5
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the tRNA synthetase translates the
genetic code, because it contacts
(a) the amino acid
(c) in some cases,
other parts of the
tRNA
(b) the anticodon loop
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receptor
a molecule on the cell surface or in the cell interior that has an affinity for
a specific molecule (the ligand).
Latin,
“to tie”
Most drug receptors are proteins.
Greek, “first”
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shortest: 9
longest: 5500
“peptide”
or
amide bonds
20 types
side chains
link the
“backbone”
or
“main chain”
or
“a-carbons”
Little Alberts Figure 2-22
© Garland publishing
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Proteins contain a few structural motifs:
a helices
b sheets
(A protein viewer must be
installed on your computer)
http://www.its.caltech.edu/~lester/Bi
-1/alpha-helix-alphabetical.pdb
http://www.its.caltech.edu/~lester/Bi
-1/beta-sheet-antiparallel.pdb
Hide side chains
Show H-bonds and distances
Show ribbons & arrows
Show side chains
Show Van der Waals radii
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Most drug receptors are membrane proteins
Outside the cell
nicotinic
acetylcholine
receptor
nicotine,
another agonist
natural ligand
(agonist)
~ 100 Å
= 10 nm
Membrane = lipid bilayer
Inside the cell = cytosol
(view in ~1995)
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Protein Folding vs. “Inverse Folding” = Computational Protein Design
Protein Folding
(no degeneracy)
Set of All
Structures
Inverse Folding
(large degeneracy)
Individual
amino acids
Set of All
Sequences
Several ways to
make an arch
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A future Lecture
outside
receptor
membrane
b 
G protein
i q s t
a
b 
a
inside
effector
channel enzyme
The pathway from a
G protein-coupled receptor
(GPCR)
to
gene activation
intracellular
messenger
Ca2+ cAMP
cytosol
kinase
phosphorylated
protein
nucleus
How fast?
10 s to days
How far?
Up to 1 m
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Protein degradation is accomplished primarily by proteolytic enzymes
The genome encodes hundreds of proteolytic enzymes.
They vary in
-- sequence specificity for the “cut”
-- cellular expression
-- organelle of expression
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Cells often mark proteins for proteolysis by attaching strings of the protein, ubiquitin.
strings of ubiquitiin
other
protein
to be
proteolyzed
modified from Little Alberts Fig 18-7
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Controlled proteolysis takes place in the proteasome
shorter
modified from Little Alberts 1st edition Fig 7-32
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Atomic-scale Structures
H3CH 2C
N
morphine
procaine
nicotine
CH 3
N
N
CH 2CH 3
H2C
botulinum
toxin
HO
O
CH 2
N CH
3
O
C O
HO
morphine
NH 2
(Download to your computer;
Then open with Swiss-prot pdb viewer)
http://www.its.caltech.edu/~lester/Bi-1/morphine.pdb
http://www.its.caltech.edu/~lester/Bi-1/procaine.pdb
http://www.its.caltech.edu/~lester/Bi-1/nicotine.pdb
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