CH. 35 DNA, RNA, REP

Each nucleotide contains
• a 5-carbon sugar called  
•   for DNA or   for RNA
• a  group
• one of 5  

Number of Rings:
A and G each have  -> Purines
T and C each have   -> Pyrimidine

Nucleotides are connected via a  
- Between  'phosphate group of 1 nucleotide and the  ' of a second nucleotide
->Each phosphate is connected to  

DNA is a double-stranded polynucleotide that adopts a  helix
- The two strands are  
- 5' end of one interacts with 3' of the other

Bases lie   in 3-D (  to axis)

The bases face the inside and form the   with the
bases from the opposite strand.
- Hydrogen bonds only form between   and  

Most common type of DNA found in most cells is  

**** Test Question
  – Observed when water is removed from the DNA
(dehydration/high-salt)
-It is more  that B DNA
-It is  -handed
-Bases are tilited  and grooves are   and  

Z-DNA – Observed when DNA is constructed to have mostly
 base pairs
- Has a spread-out,   shape
-  handed helix
- Major groove is  present

Test Question:
- is found in some bacteria species (Gram  ) form
protective  when environmental
conditions become too harsh
-It  the DNA and protects it from damaging agents (e.g.   light)

Z-DNA and the  that bind to them
- Scientists have discovered cellular and viral proteins that have the ability to
bind tightly to  (but not or  )

 : in single strands of nucleotides, when
sequences of nucleotides on the same strand are inverted
complements

When the complementary sequences are contiguous,
the hairpin has a stem but  

Where are hairpin structures most commonly found?

• RNA/DNA similarities
- Helical-shaped, polynucleotide chain that is composed of   of nucleotides
- Nucleotides are attached via  

RNA is mostly   (but can fold back on itself
and form double-stranded regions)

- RNA does not contain the base . Instead, it
contains a different pyrimidine called   (A-U hydrogen bond)

The sugar in the RNA nucleotides is
 (not deoxyribose)

Each chromosome is made up of DNA tightly
coiled many times around proteins called
  that support its structure

DNA ->   ->   ->  

Histone proteins:  Charged proteins that stick to 
charged DNA and form  

 : can be transcribed and cleaved
 : never gets transcribed or cleaved

  break the phosphodiester
bond in DNA or RNA
DNase-> cleaves  
RNase -> cleave  

Chromatin has   thought to represent transcription

  sensitivity correlates with gene activity

•  changes: methylation; capable of being reversed
and often due to environmental factors.

Telomeres protect the ends of the DNA from
degradation via   (from->  end).

Telomere sequences are rich in   and  

The   single-stranded overhang of telomeres inserts
itself into the double helix and forms a
  structure, stabilizing the DNA as
if it had a circular shape.

** TEST QUESTION
Nucleases are enzymes capable of cleaving the  between   of nucleic acids

Nucleases that exhibit specificity for   are
referred to as  

Those nucleases that specifically hydrolyze RNA are
 

Nucleases that cut at the end of NT chain:  
• Nucleases that cut in the middle of NT chain:  

Nucleases
• Cleave   or 
• Optimum activity is   dependent
• Yield different  

Phosphodiester bond is broken by hydrolysis using a nuclease to generate a  
and  . Corrdinated with  , ,  .

Enzyme amino acids are usually the 

TEST QUESTION
Topoisomerases are enzymes that participate in  

Topoisomerase I helps with  
movement and relaxes  associated with  

Topoisomerase

-They bind to DNA and cut the   of either one or both strands

-This intermediate break allows the DNA to be
 , and then the DNA backbone is
 .

TEST QUESTION
  are motor proteins that move directionally along a
nucleic acid phosphodiester backbone, separating two   by breaking the hydrogen bonds between
complementary bases (use   as energy source)

TEST QUESTION
 ( '- ') belong to the group of
helicases, which help to maintain  of the genome and
suppress inappropriate recombination

Clinical Correlation: X-linked-alpha-thalassaemia-mental retardation
•  (AKA XH2 and XNP) of the , is involved in
chromatin remodeling, gene regulation, and DNA methylation

•Structure of the bacterial chromosome
- Single,   chromosome
- Adopts a  state (which makes it more compact)

Bacterial DNA replication (also called   replication)

Initiation Steps of Prokaryotic DNA Replication
1. Bacteria have  origin of replication
2. A complex of  proteins bind to the chromosome at origin of replication
and causes a  ” to be introduced

Unwinding Steps of DNA replication
1. Bending of the DNA creates tension and causes a small
  to form -> small region of strand separation
2. The  serves as a binding site for 2 other proteins
called   and  
3. Proteins called  
bind to the individual strands and keep them apart.
4. Unwinding the strands at oriC produces 
supercoiling ahead of the replication fork

How is tension at the replication fork relived?

Enzyme called   binds ahead of the fork and makes small cuts in strands

Primer Synthesis Steps of Prokaryotic DNA replication
1. Nucelotides can only be added to   group
2. Once strands are separated, enzyme called   makes short RNA chains (  to the template)
3.   can then come in and create a
new strand by extending from the primer (called
elongation)

TEST QUESTION Elongation Steps of Prokaryotic DNA Division
1.   can only add nucelotides to   end and makes DNA in the  direction
2. IMPORTANTLY,  had   endonuclease activity which gives it the ability to  

TEST QUESTION
  – Sliding clamp ( charged) structure that locks the whole
complex onto the   strands
-> Prevents the above core enzyme from  
-> Increases the  of the  -subunit

One strand is being made continuously as DNA pol III moves
towards the replication fork (this is called the  

The other strand is made discontinuously (moving away from the replication
fork) and is initially composed of
small fragments called   (this is called the
 )

Another type of DNA polymerase (DNA ) comes in and removes the  from both the leading and lagging strands (it has   exonuclease activity) and fills in the gaps with   (it also has   polymerization ability)

  uses the end of each Okazaki fragment as a starting point

The enzyme   then seals the
spaces between each Okazaki fragment
on the lagging strand

Test Question
Bacteria:  ,   chromosome (Avg size: 4.6 x 106 base pairs)
Humans:  ,  chromosomes (Total size: 3.3 x 109 base pairs)

TEST QUESTION
Eukaryotic chromosomes have   of replication
a. origins must be approved for replication by
 

TEST QUESTION
Unreplicated DNA is coated with  (which are  )
- No   proteins, no  

Eukaryotes have  DNA polymerases that prokaryotes

Once   removes the
primer at the absolute end of the
chromosome on the lagging strand, there is
 ahead of it
- In theory, our chromosomes should
shorten each time they are replicated, which would lead to loss of gene and death (we need  !)

-An enzyme called  is activated and adds >1,000 copies of a
repeated sequence (e.g.  ) onto the ends of each chromosome
- It is only active in gametes, embryos, and stem cells
-It has an   in a pocket that binds to the
chromosome end

Mitochondria are passed from   to  

Mitochondrial have 2 origins of replication:   and  . The   functions to replicate  .

How do 2'deoxycytidine and cytarabine stop DNA replication?

How do guanosine and acyclovir inhibit DNA replication?

How does Foscarnet inhibit DNA replication?