Download Bis2A 3.4 Nucleic Acids

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Bis2A 3.4 Nucleic Acids
The BIS2A Team
This work is produced by OpenStax-CNX and licensed under the
Creative Commons Attribution License 4.0†
Abstract
This module will briey introduce the macromolecules with a Design Challenge Perspective.
Figure 1: The cheeseburger shown here contains nucleic acids, but where?
Source: mcdonalds.com.au/sites/mcdonalds.com.au/les/hero_pdt_cheeseburger.png
NUCLEIC ACIDS
Nucleic acids are molecules made up of nucleotides that carry the genetic blueprint of a cell and contain
instructions for the functioning of the cell such as directing cell division and protein synthesis. Each nucleotide
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is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic
acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to ospring
(in the form of chromosomes). Double stranded DNA (such as chromosomes) has a helical structure with the
two strands running in opposite directions (opposite polarity). The two strands are connected by hydrogen
bonds, and complementary to each other. RNA can either be single-stranded, or double-stranded. and is
made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein
synthesis, its regulation, regulatory processes and some catalytic activity. Messenger RNA (mRNA) is copied
from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction
of proteins.
Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas
transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. microRNA regulates the use
of mRNA for protein synthesis.
1 Nucleotide Structure
The two main types of nucleic acids are
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
The dierence being the presence or absence of a hydroxyl group at the C2 position, also called the 2'
position, of the ribose.
DNA, lacks the ribose and contains a hydrogen atom at that position, hence the
nucleotides. The
nucleic acid which is a polymer can be composed of DNA
name, "deoxy" ribonucleic acid. DNA and RNA are made up of monomers known as
nucleotides combine with each other to form a
nucleotides or RNA nucleotides.
Each nucleotide is made up of three components: a nitrogenous base (for which there are ve dierent types),
a pentose (ve-carbon) sugar, and a phosphate group. These are depicted in Figure 2 below.
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Figure 2: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and
one or more phosphate groups. Carbon residues in the pentose are numbered 10 through 50 (the prime
distinguishes these residues from those in the base, which are numbered without using a prime notation).
The base is attached to the 10 position of the ribose, and the phosphate is attached to the 50 position.
When a polynucleotide is formed, the 50 phosphate of the incoming nucleotide attaches to the 30 hydroxyl
group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found
in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead
of an OH at the 20 position. Bases can be divided into two categories: purines and pyrimidines. Purines
have a double ring structure, and pyrimidines have a single ring.
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The Nitrogenous Base
The nitrogenous bases of nucleotides are organic molecules and are so named because they contain carbon
and nitrogen.
They are bases because they contain an amino group that has the potential of binding an
extra hydrogen, and thus, decreases the hydrogen ion concentration in its environment, making it more basic
(review module 2.2). Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A),
guanine (G) cytosine (C), and thymine (T). RNA contains adenine (A), guanine (G) cytosine (C), and uracil
(U) instead of thymine (T).
Adenine and guanine are classied as
purines.
The primary structure of a purine is two carbon-nitrogen
rings. Cytosine, thymine, and uracil are classied as
pyrimidines which have a single carbon-nitrogen ring
as their primary structure (see gure 2). Each of these basic carbon-nitrogen rings has dierent functional
groups attached to it.
note:
Take a moment to review the gure above of the nitrogenous base:
Identify functional
groups as described in class. For each functional group identied, describe what type of chemistry
you expect it to be involved in. If hydrogen bonding, does the functional group act as a donor or
acceptor?
The Pentose Sugar
0
0
The pentose sugar contains 5 carbon atoms. Each carbon atom of the sugar molecule are numbered as 1 , 2 ,
0
0
0
0
3 , 4 , and 5 (1 is read as one prime). The two main functional groups that are attached to the sugar are
often refured to in reference to the carbon number they are bound to. For example, the phosphate residue
0
0
is attached to the 5 carbon of the sugar and the hydroxyl group is attached to the 3 carbon of the sugar.
We will often use the carbon number to refer to functional groups on nucleotides so be very familiar with
the structure of the pentose sugar.
The pentose sugar in DNA is called deoxyribose, and in RNA, the sugar is ribose. The dierence between
the sugars is the presence of the hydroxyl group on the 2' carbon of the ribose and its absence on the 2'
carbon of the deoxyribose. Hence you can determine if you are looking at a DNA or RNA nucleotide by the
presence or absence of the hydroxyl group on the 2' carbon atom.
The Phosphate Group
There can be anywhere between 1 and 3 phosphate groups bound to the 5' carbon of the sugar.
One
phosphate bound is referred to as NMP for (any Nucleotide Mono Phosphate). If 2 phosphates are bound it
is referred to as NDP (any Nucleotide Di Phosphate) and when 3 phosphates are bound NTP (any Nucleotide
Tri Phosphate). The bonds between the phosphate groups are considered high energy bonds. Because the
phosphate groups are negatively charged and packed tightly together results in unstable bonds that are ready
to break. The breaking of the bonds between the phosphate groups supply the energy to drive many reactions
forward in the cell. The gure below shows an example of the breaking (or hydrolysis) of the nucleotide ATP.
To carry out life processes, ATP is continuously broken down into ADP, and like a rechargeable battery,
ADP is continuously regenerated into ATP by the reattachment of a third phosphate group. You will learn
more about this process in the metabolism modules.
note: The term "high energy bond" is used A LOT in biology. It is, however, one of those shortcuts
we referred to in section 1. The term refers to the amount of negative free energy associated with
the HYDROLYSIS of that bond! The water is important. Keep this in mind when we go over this
in subsequent sections.
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Figure 3: ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis
to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).The negative charges on the
phosphate group naturally repel each other, requiring energy to bond them together and releasing energy
when these bonds are broken.
2 Double Helix Structure of DNA
DNA has a double-helix structure (shown below). The sugar and phosphate lie on the outside of the helix,
forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a
staircase, in pairs; the pairs are bound to each other by hydrogen bonds. Every base pair in the double helix
is separated from the next base pair by 0.34 nm. The two strands of the helix run in opposite directions,
meaning that the 5
0
0
carbon end of one strand will face the 3
is referred to as antiparallel orientation.
interactions.
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carbon end of its matching strand.
This
It is important to DNA replication and in many nucleic acid
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Figure 4: Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy
lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen
bonding with a base from the opposing strand. (credit: Jerome Walker/Dennis Myts)
Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain
pyrimidine.
This means A can pair with T, and G can pair with C, as shown below.
This is known as
the base complementary rule. In other words, the DNA strands are complementary to each other. If the
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sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG.
During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one
parental DNA strand and a newly synthesized strand.
Figure 5: In a double stranded DNA molecule, the two strands run antiparallel to one another so that
one strand runs 50 to 30 and the other 30 to 50 . The phosphate backbone is located on the outside, and
the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine
base pairs with cytosine.
Exercise 1
(Solution on p. 9.)
Using gure 5 above. What functional group is the 3' end of the nucleic acid referring to?
a. Phosphate group
b. the nitrogenous base
c. the ribose sugar
d. the hydroxyl (OH group)
Exercise 2
Using the gure 5 above, which functional group is the 5' referring to?
a. Phosphate group
b. the nitrogenous base
c. the ribose sugar
d. the hydroxyl (OH group)
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(Solution on p. 9.)
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Exercise 3
(Solution on p. 9.)
What are the structural dierences between RNA and DNA?
3 Functions and roles of nucleic acids and nucleotides
Nucleic acids play a variety of roles in in cellular process besides being the information storage molecule.
Nucliec acids, RNA in particular, is believed to be the rst biologically active molecules during a period
referred to as the "RNA world". RNA can have catalytic properties, an attribute often reserved mistakenly
riboproteins essential for life.
These are
RNA-Protein complexes where the RNA can serve both in a catalytic or structural capacity.
Examples
for proteins. Remnants of the RNA world can be seen in many
include, Ribosomes, RNases, splicesosome complexes and Telomerase.
Nucleotides also serve as energy
storage units for the cell, such as ATP, and GTP. And they play inportant roles as co-factors (in addition
to energy vehicles) to many enzymatic reactions. Like lipids, proteins and carbohydrates, nucleic acids and
nucleotides play a wide variety of roles in the cell.
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Solutions to Exercises in this Module
Solution to Exercise (p. 7)
D
Solution to Exercise (p. 7)
a
to Exercise (p. 8)
DNA has a double-helix structure. The sugar and the phosphate are on the outside of the helix and the
nitrogenous bases are in the interior. The monomers of DNA are nucleotides containing deoxyribose, one of
the four nitrogenous bases (A, T, G and C), and a phosphate group. RNA is usually single-stranded and
is made of ribonucleotides that are linked by phosphodiester linkages. A ribonucleotide contains ribose (the
pentose sugar), one of the four nitrogenous bases (A,U, G, and C), and the phosphate group.
Glossary
Denition 1: DNA:α
Deoxyribonucleic acid, polymer made from deoxynucleiotides.
Denition 2: RNA:
Ribonucleic acid, polymer made from nucleotide monomers
Denition 3: deoxyribose(β -pleated)
pentose, a 5-carbon sugar, lacking the hydroxyl group at the C2 (2') position which is found in
ribose.
Denition 4: nucleiotides and deoxynucleiotides
(NTP or dNTP) basic monomers or subunits that make up RNA and DNA. Each nucleotide consists
of a nitrogenous base, a ribose (deoxyribose for DNA)and a phosphate
Denition 5: nucleoside and deoxynucleoside
a nucleotide or deoxynucleiotide without the phosphate
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