Download Pentose sugars

DNA
2.6.1 The nucleic acids DNA and RNA
are polymers of nucleotides
Nucleic acids
 first discovered in material extracted from the
nucleus
 2 types
 DNA
 RNA
Nucleotides
 Monomers of nucleic acids
 Composed of 3 parts




5-Carbon sugars (pentose sugar)
Phosphate group (acidic, negatively
charged)
Nitrogen containing base (1 or 2
rings)
The nitrogen base and the phosphate
group are linked to the pentose sugar
by covalent bonds

Formation of nucleic acid
Covalent bonds are formed between
the phosphate of one nucleotide and
the sugar of the next (creating a
strong backbone of sugar and
phosphate group)
 There are 4 bases, so there are 4
different types of nucleotides that can
be linked in any sequence
 **Any sequence is possible in DNA
and RNA. This is the key to DNA
acting as a store for genetic
information.

2.6.2 DNA differs from RNA in the number of strands
present, the base composition, and the type of pentose
There are 3 major differences between DNA and
RNA
1.
Pentose sugars
DNA-deoxyribose sugar
RNA-ribose sugar
2.
Number of polymers of nucleotides
(strands)
DNA- 2 strands
RNA- 1 strand
3.
Nitrogen bases
DNA- A, T, G, C
RNA- A, U, G, C
S2.6.1 Drawing simple diagrams of the structure of the
single nucleotides of DNA and RNA, using circles,
pentagons, and rectangles to represent phosphates,
pentoses, and bases.
Covered in class; diagram should look like this.
2.6.3 DNA is a double helix made of 2 antiparallel
strands of nucleotides linked by hydrogen bonding
between complimentary base pairs




Each strand is a chain of nucleotides linked by covalent
bonds
The 2 strands are parallel, but run in opposite
directions: antiparallel (one runs 5’ to 3’, the other runs
3’ to 5’)
The two strands are wound together to form a double
helix
The strands are held together by hydrogen bonds
between their bases

Complimentary base pairing:
A-T (linked with 2 hydrogen bonds)
 G-C (linked with 3 hydrogen bonds)

A2.6.1 Crick and Watson’s discovery of the
structure of DNA using model making.


Watson and Crick used evidence to develop
possible structures for DNA and then tested their
theories by building models.
1st model- triple helix, bases on the outside,
magnesium holding the strands together. This was
falsified for 2 reasons.
 Ratio
of adenine to thymine was not 1:1 (as discovered
by Chargaff)
 It required too much magnesium as identified by
Franklin
2nd model Base Pairs



Watson and Crick had to take into account Chargaff’s findings that the
amount of adenine bases equal the amount of thymine bases, and the
amount of guanine equals the amount of cytosine.
They cut cardboard models of the nitrogen bases and showed that base
pairs could be formed, with hydrogen bonds linking them.
Antiparallel strands




Based on setbacks from first model and Xray diffraction patterns, they
knew DNA must be a double helix
They realized that the 2 strands had to run in opposite directions in
order to fit together (antiparallel)
They built a model to scale and quickly convinced all who saw it.
The model also suggested a mechanism for copying DNA and led to the
realization that the genetic code must consist of triplets of bases.
DNA Replication
2.7 and 7.1 (HL)
2.7.1 The replication of DNA is semi-conservative
and depends on complimentary base pairing.


As a cell prepares to divide,
the 2 strands of a DNA
double helix separate, each
serving as a template for a
new strand.
New strands are formed by
adding nucleotides, one by
one, resulting in 2 DNA
molecules each composed of
an original strand and a
newly synthesized strand 
semi-conservative
replication
2.7.2 Helicase unwinds the double helix and
separates the two strands by breaking hydrogen
bonds.
Helicase unwinds and separates the
DNA strands by breaking hydrogen
bonds.
Helicase consists of 6 globular
polypeptides arranged in a donut
shape. One strand goes through the
center and the other strand is on the
outside. Energy from ATP is used to
move helicase along the strand,
breaking hydrogen bonds.
2.7.3 DNA polymerase links nucleotides together to
form a new strand, using the pre-existing strand as a
template.
DNA polymerase moves along template
strand, adding complimentary base
pairs to form a new DNA strand.
-Adds one nucleotide at a time
-only adds nucleotides to the 3’ end of
the previous nucleotide
-hydrogen bonds form between the
complimentary bases
-covalent bonds form between the
phosphate group of the free nucleotide
and the C3 on the sugar at the existing
end of the new strand.
7.1.1 nucleosomes help to supercoil the
DNA.





Nucleosomes are formed by wrapping
DNA around 8 different histone
proteins.
Each nucleosome is composed of eight
histone proteins bundled tightly
together at the center (in purple) and
encircled by two loops of DNA (in
orange)
Nucleosomes are coiled together and
then stacked on top of each other,
forming chromatin.
Nucleosomes protect DNA and allow it
to be packaged in the nucleus.
http://www.hhmi.org/biointeractive/d
na-packaging

Nucleosomes help to supercoil the DNA


Supercoiling- when a DNA strand has been wound back on
itself multiple times so that the molecule becomes compacted
DNA needs to be supercoiled because
Cells need to package 6 ft (2 m) of DNA (nucleus is about
10 µm wide. It is essential to pack genetic material into the
nucleus.
 To organize DNA
 To control DNA expression (supercoiled DNA can’t be
transcribed)
 To protect DNA

S7.1.1 Utilization of molecular visualization software to
analyze the association between protein and DNA
within the nucleosome.




Use the link provided to use the Jmol visualization
and answer the following questions.
1. Identify the 2 copies of each histone protein. This
can be done by locating the tail of each protein.
2. Suggest how the positive charges help to form
the nucleosome (with the negatively charged DNA
molecule)
http://www.rcsb.org/pdb/explore/jmol.do?structur
eId=1AOI&bionumber=1
7.1.2 DNA structure suggested a
mechanism for DNA replication

Complimentary base pairing imply a
method for replication. Evidence that
supports complimentary base pairing:



X-ray diffraction- helix is tightly packed
and regular, so purines (A & G) must pair
with pyrimidines (C & T)
Electrical charges of adenine and thymine
are compatible and opposite, allowing 2
hydrogen bonds to form between them
Pairing of cytosine and guanine allows for
3 hydrogen bonds to form between them.
7.1.3 DNA polymerase can only add
nucleotides to the 3’ end of a primer.
7.1.4 DNA replication is continuous on the leading
strand and discontinuous on the lagging strand.

Refer to in-class notes and previous slide for further
explanation.
7.1.5 DNA replication is carried out by
a complex system of enzymes

Know the function of:
 Helicase
 DNA
gyrase
 Single stranded binding proteins
 DNA primase (primase)
 DNA polymerase III
 DNA polymerase I
7.1.6 Some regions of DNA do not
code for proteins but have other
important functions.


DNA is the blue print for the production of
polypeptides. However, only some of the DNA
sequences code for the production of polypeptides.
These are called coding sequences (genes)
The non-coding DNA is still important to organisms
for many reasons
 Some
serve as a guide in producing tRNA and rRNA
 Some regulate gene expression, such as enhancers or
silencers
 Introns are segments of DNA within a gene, but not included
in the final polypeptide product

Repetitive sequences are common within
the genome (nearly 60% of human
DNA consists of repetitive sequences)

Ex. telomeres, found on the ends of
chromosomes. During replication, DNA
polymerase can’t continue all the way to
the end of the chromosome. The telomeres
provide a buffer region so that no
essential DNA is left off during
replication. This non-coding, repetitive
region gets shorter with each DNA
replication, but sacrificing the repetitive
sequence serves a protective function.
A7.1.2 Use of nucleotides containing dideoxyribonucleic
acid to stop DNA replication in preparation of samples
for base sequencing.


Watch the following video for a brief overview.
https://www.dnalc.org/view/15479-Sangermethod-of-DNA-sequencing-3D-animation-withnarration.html