Biology 107
Macromolecules III
September 7, 2005
Proteins May Be Denatured and Renatured.
When proteins are changed from one environment to another
they usually change shape (denature). Return to the original
environment commonly results in folding that is different than
normally found under that condition.
Protein
“Partners”
(Chaperones)
Influence
Folding
Protein Chaperones Influence “Correct” Folding
Macromolecules III
Student Objectives: As a result of this lecture and the assigned
reading, you should understand the following:
1. Nucleic Acids are polymers of nucleotides. There are two types of
nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA).
2. Nucleic acids function in information coding, storage and transfer.
DNA does not directly control protein synthesis, instead it works
through intermediates, RNA molecules.
Macromolecules III
3.
Each nucleotide monomer has three (3) parts:
five carbon sugar
phosphate group
nitrogenous base
Nucleic acids contain one of two 5-carbon sugars, either
deoxyribose (in DNA) or ribose (in RNA). Linked to the one end
of the sugar is a phosphate group, and linked to the other end of
the pentose is one of the nitrogenous bases. DNA has the
nitrogenous bases adenine (A), guanine (G), thymine (T), and
cytosine (C). RNA has A, G, C and uracil (U) (instead of thymine).
Macromolecules III
4.
A nucleic acid polymer, a polynucleotide, forms from monomers
covalently linked by dehydration synthesis. The phosphate group
of one nucleotide bonds to the sugar of the next nucleotide, with
the result a repeating sugar-phosphate backbone.
5.
RNA is normally a single polynucleotide strand, while DNA is a
double-stranded molecule.
6.
Nucleic acids form complementary base pairs stabilized by
hydrogen bonds, with guanine pairing with cytosine and adenine
pairing with thymine or uracil.
Functions of
Nucleic Acids
Information coding,
storage, and transfer
Synthesis of other nucleic
acids or proteins
Central Dogma
DNA
↓
RNA
↓
Protein
The Flow of Genetic Information
(The Central Dogma)
Mass Storage of
Information
We store lots of information using
simple linear codes
CTGGGTTCTGTTCGGGATCCCAGTCACAGGGACAATGGCGCATTCATATGTCACTTCCTTTACC
TGCCTGGAGGAGGTGTGGCCACAGACTCTGGTGGCTGCGAACGGGGACTCTGACCCAGTCG
ACTTTATCGCCTTGACGAAGGGTTGGTTAATCCGTGCATGTGAGCTCCTCAGGGTGGAATCCAG
GAGGATCCACGAGGGTGAATTGGCGGCATTCTTGTCTTACGCCATCGCCTACCCCCAAAACTTC
CTGTCTGTGATTGACAGCTACAGCGTAGGATGCGGTCTGTTGAACTTCTGCGCGGTGGCTCTG
GCTCTCTGTGAACTGGGCTACAGGCCTGTGGGGGTGCGTTTGGACAGCGGTGACCTCTGCAG
CCTGTCGGTGGATGTCCGCCAGGTCTTCAGACGCTGCAGCGAGCATTTCTCCGTCCCTGCCTT
TGATTCGTTGATCATCGTCGGGACGAATAACATCTCAGAGAAAAGCTTGACGGAGCTCAGCCTG
AAGGAGAACCAGATTGACGTTGTCGGAGTCGGAACTCACCTGGTCACCTGTACGACTCAGCCG
TCGCTGGGTTGCGTTTACAAGCTGGTGGAGGTGAGGGGGAGGCCCCGGATGAAGATCAGCGA
GGATCCGGAAAAGAGCACCGTTCCCGGGAGGAAGCAGGTGTACCGCCTGATGGACACTGATG
CTCCTCCAGAACCTGGAGTCCCTCTGAGCTGCTTCCCTCTGTGCTCCGATCGCTCCTCCGTCT
CCGTCACCCCGGCGCAGGTTCACCGTCTGCGGCAGGAAGTCTTTGTTGATGGACAGGTCACA
GCCCGTCTGTGCAGCGCCACAGAGACCAGAACGGAGGTCCAGACCGCTCTCAAGACCCTCCA
CCCTCGACACCAGAGGCTGCAGGAGCCAGACTCGTACACGGTGATTCACATTCTGAAGAAAAC
AACATTGGATCGCGCTTTTCCGCTCTCTTCCCTTAGTTTCCCCTCCGAACTCCGCCGCTGGGCC
GGAGGACTGAACCGGCCCCCGACGGTGTCCCAGCGGCGGTGCAATGTGGCCCGGGTCCGG
GAGGAGTGCGTGACGCCAGAGCAGAATGGTTCGGTGGACGGGGGCGCACACGCTTCTCGCC
GCGGCCGCTCCCCGCGGCCCACGGAACCGCGGGATCGGAGCTGTTTTGTGCCGCCTGAAGG
ACTCGAAGGGGGACGGATAAATGCTGGATCCCCGAGTCCAGATCTGACCGTCTGCATTCCGCT
GGTGAGCTGCCAGACGCATCTGGAAACGAGCGCCGACAGAAGCAGCTCCGGACCATGTCGCC
GTCCGCGCACACAGGTCGCGTGTAAAGGGGACTTGGTCAGATCATCTTGCACCGGAACCAGG
TCTCCCCTGGAGATGGGGACGGTCATGACCGTCTTCTACCAGAAGAAGTCCCAGCGGCCGGA
GAGGAGAACCTTCCAGATCAAGCCTGACACGCGGCTCCTCGTGTGGAGCCGAAACCCCGACA
AAAGCGAAGGAGAGAGTGAGTATGAGCAGGCGGGCCGTGCCGGGACCGGGCCCACGCCGC
CCAGAACCTCATGTTCCTGGTGTTCCAGCACCGACCGGCCAGTTCTGGCTCAGCTCCACACAA
CATCTGACAAACCCTCGTGGTTCCTGGTGGTCGACCACACGGCTGGTGAGGCGGCCTCAGGT
AGCTCAGGTAGCTCAGGTTAGCGTAAAGGGAGTTTTAAGCATCACCTGGTGACGGGGCAGGTG
Mass Storage of
Information
Another simple linear code, the DNA
sequence, is the basis of life
Dense Information Storage
This image shows 1 gram of
DNA on a CD that can hold
800 MB of data.
The 1 gram of DNA can hold
about 1x1014 MB of data.
The number of CDs required
to hold this amount of
information, lined up edge to
edge, would circle the Earth
375 times, and would take
163,000 centuries to listen to.
DNA as Mass Storage Device
If the DNA sequence from a single human sperm cell were
typed on a continuous ribbon in ten-pitch type, that ribbon
could be stretched from San Francisco to Chicago to
Washington to Houston to Los Angeles, and back to San
Francisco, with about 60 miles of ribbon left over.
Structure of Nucleotides
Structure of
Nucleotides
Pentose sugar
Phosphate group
Nitrogenous base
Nitrogenous Bases
Chargaff’s Rules
Erwin Chargaff’s data indicated that in DNA the amount of
adenine nearly always equaled the amount of thymine and the
amount of cytosine nearly always equaled the amount of
guanine.
mol % of bases
Ratios
Source
%GC
A
G
C
T
A/T
G/C
Octopus
33.2
17.6
17.6
31.6
1.05
1.00
35.2
Chicken
28.0
22.0
21.6
28.4
0.99
1.02
43.7
Rat
28.6
21.4
20.5
28.4
1.01
1.00
42.9
Human
29.3
20.7
20.0
30.0
0.98
1.04
40.7
Double Helix Structure of DNA
1953
2003
Original
Nature paper
by Watson
and Crick –
1953
Click to Open
Thread of History
Back in my rooms I lit the coal fire, knowing there was no
chance that the sight of my breath would disappear before I
was ready for bed. With my fingers too cold to write legibly
I huddled next to the fireplace, daydreaming about how
several DNA chains could fold together in a pretty and
hopefully scientific way. Soon, however, I abandoned
thinking at the molecular level and turned to the much
easier job of reading biochemical papers on the
interrelations of DNA, RNA and protein synthesis.
from
Chapter 21 of The Double Helix by James Dewey Watson.
Thread of History
Virtually all the evidence then available made me believe
that DNA was the template upon which RNA chains were
made. In turn, RNA chains were the likely candidates for
the templates for protein synthesis. There was some fuzzy
data using sea urchins, interpreted as a transformation of
DNA into RNA, but I preferred to trust other experiments
showing that DNA molecules, once synthesized, are very
very stable. The idea of the genes' being immortal smelled
right, and so on the wall above my desk I taped up a paper
sheet saying DNA -> RNA -> protein. The arrows did not
signify chemical transformations, but instead expressed the
transfer of genetic information from the sequences of
nucleotides in DNA molecules to the sequences of amino
acids in proteins.
from
Chapter 21 of The Double Helix by James Dewey Watson.
The Eagle
Questions to Consider For Watson
and Crick Paper
1.
What was one of the reasons Watson and Crick did not expect the
phosphate groups in DNA to be aligned along the axis of the DNA
molecule?
2.
What is the means by which the individual strands in DNA are joined
together?
3.
What is the consequence of knowing the base sequence of one strand?
What is the implication for copying the genetic material?
DNA Is Normally
Double-Stranded
Each strand has polarity (5’
and 3’ ends).
In double-stranded DNA
each strand is oriented
“anti-parallel” to the other
strand.
The strands are normally
held together by hydrogen
bonds.
The optimal hydrogen
bonding is when A bonds
with T and G bonds with C.
Base Pairing in DNA
G/C pairs have
three hydrogen
bonds
A/T pairs have
two hydrogen
bonds
Double Helix
Nucleic Acid Gel Electrophoresis
The Sequence of Nucleotides
Encodes Information
_
+
The Double Helix
Structure of
Complementary
Strands Explains
The Mechanism
of DNA
Replication
ATP Is a Nucleotide
ATP Structure and Hydrolysis
Summary of Adenine Phosphates
1. ATP (adenosine triphosphate) = 3 phosphate groups +
adenine + ribose sugar
a. This is the high energy form
b. The energy is greatest in the bond holding the third phosphate - that
bond is easily broken.
2. ADP (adenosine diphosphate) = 2 phosphate groups +
adenine + ribose sugar
a. This is the low energy form
b. ADP can be recharged into ATP by addition of phosphate, if a
phosphate source and enough energy are available.
3. AMP (adenosine monophosphate) = 1 phosphate group +
adenine + ribose sugar
a. Intracellular activator of processes
Additional Resources
http://www.nature.com/nature/dna50/ - Anniversary issue of Nature
celebrating the 50th year following the original DNA structure
articles. Interesting links. Article about Rosalind Franklin.
http://www.genome.gov/10001772 - Federal Human Genome Project
website.
http://www.time.com/time/time100/scientist/profile/watsoncrick.html short recount of Watson and Crick at Cambridge.
http://www.dnai.org/index.htm - Home page for DNA Interactive. Time
lines and interesting historical information. Photos at:
http://www.dnai.org/album/6/album.html.