Download Lecture 17, Mar 3

BIO 311C
Spring 2010
Lecture 17 – Wednesday 3 Mar.
1
Review
ATP
acid anhydride
bonds
ester
bond
Ad
nitrogen base
nucleoside
A
Why is ATP often described as the “energy currency” of living cells?
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Table of Nucleosides and Nucleotides
that are of importance
in Living Cells
Review
You should be able to draw the abbreviated structure of a nucleotide (as
shown at right) from its name (as shown in the table).
You should also be able to write the abbreviated name of a nucleotide as
shown in the table from an illustration such as the one shown at right.
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Formation of a Dinucleotide from Two Nucleotides
5'
5'
3'
dehydration reaction
+
H2O
3'
ester bond
5'
5'
phosphodiester
bond
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3'
3'
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Two ends of a nucleotide or a dinucleotide can be distinguished, based
on the positions of the 3rd and 5th carbon atoms of the sugars
5‘ end of
nucleotide
5‘ end of
dinucleotide
5'
5'
3'
Formation of a Dinucleotide
3‘ end of
nucleotide
+
3'
H2O
5'
3'
3‘ end of
dinucleotide
5'
3'
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5’ end
nitrogen
base 1
Illustration of a trinucleotide
This trinucleotide can be
written as:
A
5’ – A – C – G – 3’
or:
5’ – A C G – 3’
nitrogen
base 2
If the sugars were known to be 2deoxyribose, then it could be written as:
5’ – d A – d C – d G – 3’
or:
5’ – dA dC dG – 3’
C
nitrogen
base 3
The alternating phosphate and sugar
components of this trinucleotide chain
are collectively called its “backbone”.
The nitrogen bases are not a
component of the backbone structure.
G
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3’ end
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Oligonucleotides and Polynucleotides
Dinucleotide: two nucleotides covalently bonded together
by a phosphodiester bond
Oligonucleotide:
less than 20
nucleotides covalently
bonded together by
phosphodiester bonds
Trinucleotide: three nucleotides covalently bonded
together by two phosphodiester bonds
Tetranucleotide: four nucleotides covalently bonded
together by three phosphodiester bonds
Polynucleotide (also called a polynucleotide chain):
Twenty or more nucleotides covalently bonded together by phosphodiester bonds.
Polynucleotide chains are linear polymers, meaning that they are not branched.
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Illustrations of Primary Structures of Polynucleotide Chains
5'
C
A
A
G
C
U
3'
A polyribonucleotide chain used for constructing RNA
This sequence may be shown as:
5'
dT
dG
5'
dC
3'
CAAG C U
dG
dA
dT
3'
A polydeoxyribonucleotide chain used for constructing DNA
This sequence may be shown as:
5'
dT dG dC dG dA dT
3'
Note: the “d” is generally not shown in front of the nucleosides if it is
understood that the molecule is a polydeoxyribonucleotide. Thus, this DNA
sequence could be shown as:
5'
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TGCGAT
3'
The primary (1°) structure of a polynucleotide chain is the sequence of
its nucleotides, starting at the 5’ end.
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Directionality of a Polynucleotide Chain
From textbook Fig. 5.27a, p. 87
3'
5' direction
5'
4’
1’
2’
phosphate
The "backbone" of a
polynucleotide chain
consists of alternating
sugar and phosphate.
3'
The nitrogen bases project
from the polynucleotide
chain backbone, much like
R-groups project from the
backbone of a polypeptide
chain.
3'
5' direction
5' end
Can you distinguish the
pyrimidine bases from the
purine bases in this
illustration?
5'
3'
sugar
3' end
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Abbreviated Structure of a Polynucleotide Chain
*
Consider a polynucleotide with a partial
nucleotide sequence of: 5'
AGCU
3'
5'
A
G
Would this molecule be a
component of DNA or would it
be a component of RNA?
Is this molecule expected to
contain ribose or is it expected
to contain 2-deoxyribose?
C
U
3'
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Consider a second polynucleotide chain with
an internal nucleotide sequence of: 5'
5'
AGCU
3'
3'
U
A
G
C
G
C
A
U
3'
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5'
Note: the 5’ end of the molecule is shown
at the bottom in this illustration.
*
When two polynucleotide chains, or two regions of the same
polynucleotide chain, align with each other as shown here, then they
are said to be antiparallel.
5'
3'
U
A
G
The two chains can lie next to
each other a uniform distance
apart if the nucleotide sequences
are such that a purine base is
always aligned directly across
from a pyrimidine base.
C
G
C
A
U
3'
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pyrimidine
base
5'
purine
base
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Two antiparallel chains of RNA are held together by extensive hydrogen
bonding when A is always adjacent to U, and G is always adjacent to C,
along the chains.
5'
3'
A
G
C
Two hydrogen bonds form
between each "A U" pair.
U
Three hydrogen bonds form
between each "G C" pair.
C
If each hydrogen bond has a
bond strength of 30 KJ/mole,
then what is the total
collective bonding strength of
the hydrogen bonds shown
here?
G
A
U
3'
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5'
*
Two antiparallel chains of DNA are held together by extensive hydrogen
bonding exactly as in RNA, except that in DNA an A is always adjacent
to a T (instead of a U), and the sugar is always 2’-deoxyribose (instead
of ribose).
5'
3'
dA
dG
dT
Two hydrogen bonds form
between each "dA dT" pair.
dC
Three hydrogen bonds form
between each "dG dC" pair.
dG
dC
dA
dT
3'
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5'
*
The secondary structure of a polynucleotide chain is the alignment of
nucleotide-pairs imposed by hydrogen bonding between complementary bases.
From textbook Fig. 17.14, p. 338
3'
For simplicity in this illustration,
only one hydrogen bond is shown
between each pair of aligned
bases.
5'
The secondary structure of RNA
often occurs as stem-loop regions
of the polynucleotide chain.
stem-loop
The nucleotides of a few positions
along this molecule (for example,
position 10) are not shown
because the nitrogen bases of the
nucleotides in those positions are
slightly changed after the
molecules is synthesized in order
for it to function properly.
Secondary Structure of a molecule of t-RNA
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The tertiary structure of a polynucleotide chain is the 3-dimensional
shape (conformation) of the polynucleotide chain.
backbone of alternating ribose and phosphate
(grey)
loop
nitrogen bases of loop; they are not
hydrogen bonded
nitrogen bases of stem; they are
hydrogen bonded
stem
The two segments of nucleotide chain that are
hydrogen-bonded together also twist around
each other in a "double-helix" conformation.
The tertiary structure of a stem-loop
region of a polynucleotide chain
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The tertiary Structure of a Molecule of t-RNA
From textbook Fig. 17.14, p. 338
5'
3'
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Colors identify loops of stem-loop
regions in this t-RNA molecule,
corresponding to the loops seen
in the secondary structure of
t-RNA (shown below).
The tertiary structure of a polynucleotide chain is its 3-dimensional shape.
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The secondary structure of DNA
5'
end
3'
end
5'
3'
3'
5'
3'
end
5'
end
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The secondary structure of
DNA consists of two separate
polynucleotide chains that are
hydrogen-bonded to each
other in an antiparallel
conformation. In this
illustration each set of red
hash-lines represent a single
hydrogen bond.
The nucleosides of this portion
of a DNA molecule are shown
by single capital letters
(G, T, C, A), rather than as
(dG, dT, dC, dA).
*
Illustration of the Secondary Structure of DNA
From textbook Fig 16.7b, p. 309
This abbreviated illustration of
a segment of DNA shows the
backbone structure and its
relationship to the bases.
Nitrogen bases are flat
molecules. In a double helix
they rotated such that the flat
faces are perpendicular to the
direction of the backbone.
abbreviated structural formula
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Illustration of the Structure of DNA
From textbook Fig 16.7a, p. 309
This ribbon model of a segment of DNA
shows the helical shape and the
dimensions of the double-helix.
The double helix is approximately 20 Å in
diameter. The total linear distance of one
complete rotation is 34 Å and there are 10
base pairs for each complete rotation.
ribbon model
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Illustration of the Structure of DNA
From textbook Fig 16.7c, p. 309
This space-filling model of DNA shows
the physical shape of the double helix,
including groves along the chain.
groove
space-filling model
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The tertiary structure of DNA typically is determined by its
binding to specific proteins
The black line represents a double helix
of DNA.
The colored balls (red, blue, green,
yellow) and rods (lighter blue) represent
histones, which are globular proteins
around which the DNA in eukaryotic cell
nuclei wraps.
nucleosomes of a
eukaryotic cell
A segment of DNA plus the 9
polypeptide chains around which it is
wrapped is called a nucleosome.
Many RNA molecules also tightly bind to specific proteins, which
greatly influences their tertiary structures.
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As with proteins, the tertiary structures of nucleic acids and their
binding to other molecules are directly related to their functions.
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Some General Functions Performed by Nucleotides,
Oligonucleotides and Polynucleotides in Cells
They are information storage molecules.
DNA
They convey information to the site of protein synthesis.
mRNA
They are major structural components of ribosomes
rRNA
They activate amino acids and carry them to the site of
protein synthesis.
tRNA
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cont.
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Some General Functions Performed by Nucleotides,
Oligonucleotides and Polynucleotides in Cells (cont. 1)
They serve as carriers of hydrogen atoms, thereby
undergoing reversible oxidation and reduction.
dinucleotides
They are the energy currency of cells.
ATP
They covalently bond to some proteins, and transfer phosphoric
acid functional groups to others, thereby activating the protein's
function.
nucleoside triphosphates
They covalently bond to some sugars in order to activate the
sugar.
nucleotides
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Some General Functions Performed by Nucleotides,
Oligonucleotides and Polynucleotides in Cells (cont. 2)
They serve as "second messengers" by responding to signals
external to a cell and eliciting responses within the cell.
nucleotides
Cyclic AMP contains a phosphodiester
bond, but no "high-energy" phosphate
bonds.
Cyclic AMP, a "second messenger"
in many kinds of cells
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