Download Biol 205 S08 Week 2 Lecture 1

Biol 205 S08
Week 2 Lecture 1
1. Intro to proteins
2. Basic carbon chemistry
3. Functional groups
4. Macromolecules in cells
In Alberts:
Chapter 2 pp. 50-52, 55-56
Panels 2-1 (chemical bonds), 2-2 (water) 2-5 (amino acids)
Chapter 4 - start reading
Reading Assignment for next lecture:
Text: Chapter 2 pp. 58-65, 74-75, Chapter 4 pp 119-- 143
Panels 2-2 (on water) and 2-7 (on noncovalent bonds)
Panel 4-2 on pg 132: Four ways of depicting protein structure
Recall that the SRY gene codes for a regulatory protein
that orchestrates the production of a testes
during the development of a mammalian embryo
The SRY protein controls the transcription of specific genes
required to build a testes from an “indifferent” gonad
>gi|17488858|ref|XM_010627.4|
Homo sapiens SRY (sex determining region Y chromosome)
Shorthand abbreviation of part of the DNA sequence of the SRY gene
GGCATGTGAGCGGGAAGCCTAGGCTGCCAGCCGCGAGGACCGCACGGAGGAGGAG
CAGGAGCGCGGAGCCGCGAGCCCCGAGCCCCGAGCCCGGCGCCTGGCTGAGTAGAT
GTCCATGAGGAGCCCCATCTCTGCCCAGCTGGCCCTGGATGGCGTTGGCACCATGGT
GAACTGCACCATCAAGTCAGAGGAGAAGAAAGAGCCTTGCCACGAGGCCCCCCAGG
GCTCAGCCACTGCCGCTGAACCTCAGCCTGGAGACCCAGCCCGGGCCTCCCAGGAT
AGTGCTGACCCCCAAGCTCCAGCCCAGGGGAATTTCAGGGGCTCCTGGGACTGTAGCTCTCCAG
AGGGTAATGGGTCCCCAGAACCCAAGAGACCAGGAGTGTCGGAGGCTGCCTCTGGAAGCCAGGA
GAAGCTGGACTTCAACCGAAATTTGAAAGAAGTGGTGCCAGCCATAGAGAAGCTGTTGTCCAGT
GACTGGAAGGAGAGGTTTCTAGGAAGGAACTCTATGGAAGCCAAAGATGTCAAAGGGACCCAAG
AGAGCCTAGCAGAGAAGGAGCTCCAGCTTCTGGTCATGATTCACCAGCTGTCCACCCTGCGGGA
CCAGCTCCTGACAGCC
Proteins are polymers of L amino acids
http://www.clunet.edu/BioDev/omm/aa/aa.htm
Shorthand abbreviation of the protein sequence coded for by the SRY
gene
>gi|17384045|emb|CAD13147.1|
sex determining region Y [Homo sapiens]
MQSYASAMLSVFNSDDYSPAVQENIPALRRSSSFLCTESCNSKYQCET
GENSKGNVQDGVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY
QWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPKNCSL
LPADPASVLCSEVQLDNRLYRDDCTKATHSRMEHQLGHLPPINAASSP
QQRDRY
This week we will explore the general
structure and function of proteins
First we will review some basic
chemistry
02_02_atomic number.jpg
• The electron configuration of carbon
– Gives it covalent compatibility with many
different elements
Hydrogen
Oxygen
Nitrogen
Carbon
(valence = 1)
(valence = 2)
(valence = 3)
(valence = 4)
N
C
H
O
Figure 4.4
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Molecular Diversity Arising from Carbon Skeleton
Variation
• Carbon chains
– Form the skeletons of most organic molecules
– Vary in length and shape
H H H
H C C C H
H H H
Propane
H
H C H
H
H
H H H H
(b) Branching
H C C C C H
H C C C H
H H H
H H H H
2-methylpropane
Butane
(commonly called isobutane)
H H H H
H H H H
(c) Double bonds H
H C C C C H
C C C C H
H H
H
H
1-Butene
2-Butene
H
H
H
H
C
H
H
C C H
C H
(d) Rings
H C
C
H
H C
C
H
H
C
C
C
(a) Length
Figure 4.5 A-D
H H
H C C H
H H
Ethane
Cyclohexane
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Benzene
The Functional Groups Most Important in the
Chemistry of Life
• Functional groups
– Are the chemically reactive groups of atoms
within an organic molecule
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
– Give organic molecules distinctive chemical
properties
Estradiol
OH
CH3
HO
Female lion
OH
CH3
CH3
O
Figure 4.9
Male lion
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Testosterone
• Six functional groups are important in the
chemistry of life
– Hydroxyl
– Carbonyl
– Carboxyl
– Amino
– Sulfhydryl
– Phosphate
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Some important functional groups of organic
compounds
FUNCTIONAL
GROUP
HYDROXYL
CARBONYL
CARBOXYL
O
OH
(may be written HO
C
C
OH
)
STRUCTURE In a hydroxyl group (—OH),
a hydrogen atom is bonded
to an oxygen atom, which in
turn is bonded to the carbon
skeleton of the organic
molecule. (Do not confuse
this functional group with the
hydroxide ion, OH–.)
Figure 4.10
O
The carbonyl group
( CO) consists of a
carbon atom joined to
an oxygen atom by a
double bond.
>
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
When an oxygen atom is doublebonded to a carbon atom that is
also bonded to a hydroxyl group,
the entire assembly of atoms is
called a carboxyl group
(—COOH).
• Some important functional groups of organic
compounds
AMINO
SULFHYDRYL
H
O
SH
N
(may be written HS
H
The amino group (—NH2)
consists of a nitrogen atom
bonded to two hydrogen
atoms and to the carbon
skeleton.
PHOSPHATE
)
O P OH
OH
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
Figure 4.10
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
In a phosphate group, a
phosphorus atom is bonded to four
oxygen atoms; one oxygen is
bonded to the carbon skeleton; two
oxygens carry negative charges;
abbreviated P . The phosphate
group (—OPO32–) is an ionized
form of a phosphoric acid group
(—OPO3H2; note the two
hydrogens).
02_15_organic molecules.jpg
02_26_Macromolecules.jpg
02_12_polar covalent.jpg
02_14_Protons on move.jpg
02_21_Alanine.jpg
A protein is a polymer of amino acids connected by
peptide bonds -- also called polypeptides
04_01_peptide bonds.jpg
04_02_polypeptide back.jpg
Decoding the SRY sequence: