Central Dogma of Molecular Biology - When nucleotides are incorporated, adjacent

nucleotides are linked by a phosphodiester bond: a

The central dogma of molecular biology describes the
covalent bond is formed between the 5' phosphate
flow of genetic information in cells from DNA to
group of one nucleotide and the 3'—OH group of
messenger RNA (mRNA) to protein. It states that
another
genes specify the sequence of mRNA molecules,
which in turn specify the sequence of proteins.

DNA double helix

- In 1953, James Watson and Francis Crick suggested a

model that DNA is composed of two nucleotide chains
that wrap around each other to form a double spiral
— like a spiral staircase. This shape is called a double
helix.

Hydrogen Bonds
DNA history:
- By facing towards the center, the bases on one chain
- Biologists did know that genes were located on of DNA face the bases on the other chain of DNA, with
chromosomes. The two chemical components of which they form bonds called hydrogen bonds.
chromosomes— DNA and protein—were therefore
the leading candidates to be the genetic material. - The hydrogen bonds help hold the two chains
together.
- In 1952, American biologists Alfred Hershey and
Martha Chase performed a very convincing set of DNA structure
experiments that showed DNA to be the genetic
- The alternating deoxyribose sugar and phosphate
material of T 2, a virus that infects the bacterium
molecules form a "backbone" to which the nitrogen
Escherichia coli (E. coli), a microbe normally found in
containing bases face toward the center of the helix
the intestines of mammals (including humans).
and that they are perpendicular to the sugar-
Viruses that exclusively infect bacteria are called
phosphate backbone.
bacteriophages ("bacteria—eaters"), or phages for
short. Chargaff Rule

DNA- Deoxyribonucleic acid, consisting of repeating - American biochemist Erwin Chargaff had discovered
called nucleotides. that the amount of adenine in the DNA of any one
species was equal to the amount of thymine and that
DNA: Structure
the amount of guanine was equal to that of cytosine.
Nucleotide
Complementary Base Pairing
Components: Nitrogenous base, A pentose sugar,
- A certain purine can only pair with a certain
Phosphate group
pyrimidine (Base complementary rule or Chargaff
•Deoxyribo refers to its form of the sugar, nucleic because DNA is rule)
in the nuclei of eukaryotic cells, and acid because the phosphate
group is in the ionized (negatively charged) form after donating a - Cytosine bonds with guanine and adenine bonds
hydrogen atom. with thymine

Complementary Base Pairing

- Recall that complementary base pairs are connected

to each other by hydrogen bonds

C-G: form 3
hydrogen bonds

A—T: form 2
hydrogen bonds

DNA replication- The process of copying and
duplicating DNA molecule.
This model for DNA
replication is known as
the semiconservative
model because half of
the parental molecule is
maintained (conserved)
in each daughter molecule.
- Watson and Crick proposed that the specific pairing
of complementary bases accounts for the ability of
DNA to be copied.
- Replication Of a chromosomal DNA molecule begins
at particular sites called origins of replication, short
stretches of DNA having a specific sequence of
nucleotides.
Replication
STEP 1: Initiation
- Before DNA can be replicated, the double stranded
molecule must be "unzipped" into two single strands.
- DNA helicase disrupts the hydrogen bonding
between base pairs to separate the strands into a Y
shape known as the replication fork. This area will be
the template for replication to begin.
- Once the DNA strands have been separated, a short
piece of RNA called a primer binds to the 3' end of the
strand. The primer always binds as the starting point
for replication. Primers are generated by the enzyme
DNA primase.
Notice that the sugar-phosphate
backbones run in opposite as a result each
strand has a 3' ("three-prime") end and a
5' ("five-prime") end.
The opposite orientation of the strands is
important in DNA replication.
- DNA is directional in both strands, signified by a 5'
and 3' end.
- This directionality is important for replication as it
only progresses in the 5' to 3' direction.
The replication fork is bi- directional
- During DNA replication, one new strand (the leading
strand) is made as a continuous piece. The other (the
lagging strand) is made in small pieces.
STEP 2: Elongation
- Enzymes known as DNA polymerases are responsible
creating the new strand by a process called
elongation.
- Because replication proceeds in the 5' to 3' direction
on the leading strand, the newly formed strand is
continuous.
- The lagging strand begins replication by binding with
multiple primers. Each primer is only several bases
apart. DNA polymerase then adds pieces of DNA,
called Okazaki fragments, to the strand between
primers.
STEP 3: Termination
- Rnase H removes the RNA primer.
- The gaps that remain are sealed by DNA ligase.
DNA: Other Functions
- In addition to their roles in adding nucleotides to a
DNA chain, DNA polymerases carry out a proofreading
step that quickly removes nucleotides that have base-
paired incorrectly during replication.
- DNA polymerases and DNA ligase are also involved in
repairing DNA damaged by harmful radiation, such as
ultraviolet light and X-rays, or toxic chemicals in the
environment, such as those found in tobacco smoke.
- Telomeres - The ends of linear chromosomes are
known as telomeres, which have repetitive sequences
that code for no particular gene in a way, these
telomeres protect the genes from getting deleted as
they divide.
Central Dogma of Molecular (part2)
A gene does not build a protein directly. Rather, a gene dispatches
instructions in the form of RNA, which in turn programs protein
synthesis.
The molecular "chain of command" is from DNA in the nucleus of
the cell to RNA to protein synthesis in the cytoplasm. The two
main stages are transcription, the synthesis of RNA under the
direction of DNA, and translation, the synthesis of protein under
the direction of RNA.
Gene
-A region of DNA that can be expressed to produce a
functional product that is either a polypeptide or an
RNA molecule.
-Simply put, genes provide the instructions for making
specific proteins.
-Specific sequences of bases, each with a beginning
and an end, make up the genes on a DNA strand. A
typical gene consists of hundreds or thousands of
nucleotides in a specific sequence.
Transcription- describes the process by which the
genetic information contained within DNA is rewritten
(transcribed) as a sequence of bases on RNA.
Transcription
STEP 1: Initiation
- Transcription is catalyzed by the enzyme RNA
polymerase. It attaches to and moves along the DNA
molecule until it recognizes a promoter sequence,
which indicates the starting point of transcription.
- Basically, the promoter tells the polymerase where
to "sit down" on the DNA and begin transcribing.
- Many eukaryotic promoters have a sequence called
a TATA box. It's recognized by one of the general
transcription factors, allowing other transcription
factors and eventually RNA polymerase to bind. It also
contains lots of As and Ts, which make it easy to pull
the strands of DNA apart.
- Once bound to the promotor sequence, RNA
polymerase unwinds a portion of the DNA double
helix, exposing the bases on each of the two DNA
strands.
Complementary Base pairing
Recall that complementary base pairs are connected
to each other by hydrogen bonds.
C-G: form 3 hydrogen bonds
A—T: form 2 hydrogen bonds
STEP 2: Elongation
- Incoming ribonucleotides are used by RNA
polymerase to from the mRNA strand. It does this
using complementary base pairing (A to U, T to A, C to
G and G to C)
- RNA polymerase then catalyzes the formation Of
phosphodiester bonds between adjacent
ribonucleotides. Bases can only be added to the 3'
(three-prime) end, so the strand elongates in a 5' to 3'
direction.
- One DNA strand (the template strand) is read in a 3'
to 5' direction and so provides the template for the
new mRNA molecule. The other DNA strand is
referred to as the coding strand. This is because the
base sequence of the new mRNA is identical to it,
except for the replacement of thiamine bases with
uracil.
STEP 3: Termination
- Elongation will continue until the RNA polymerase
encounters a stop sequence. At this point,
transcription stops, and the RNA polymerase releases
the DNA template.
- Elongation will continue until the RNA polymerase
encounters a stop sequence. At this point,
transcription stops, and the RNA polymerase releases
the DNA template.
Pre- translational mRNA processing
- The mRNA which has been transcribed up to this
point is referred to as pre-mRNA. Processing must
occur to convert this into mature mRNA.
- Remember that in eukaryotes, transcription happens
in the nucleus of human cells, while translation
happens in the cytosol

mRNA Processing
- 5' Capping describes the addition of a methylated
guanine cap to the 5' end of mRNA. Its presence is
vital for the recognition of the molecule by ribosomes,
and to protect the immature molecule from
degradation.
mRNA Processing
- Polyadenylation describes the addition of a poly(A)
tail to the 3' end of mRNA. The poly(A) tail consists of
a string of approximately 200 adenosine
monophosphate molecules. This further protects the
mRNA from degradation.
- Pre-mRNA Splicing involves removing non-coding
regions called "introns", leaving only the protein
coding "exons”. The splicing of pre mRNAs is
conducted by complex proteins and RNA molecules
called spliceosomes.
Central Dogma of molecular (Part 3)
Translation
- a process by which the genetic code contained
within a messenger RNA (mRNA) molecule is decoded
to produce a specific sequence of amino acids in a
polypeptide chain
- mRNA to protein
- The key components required for translation are
mRNA, ribosomes, and transfer RNA (tRNA).
A codon is a trinucleotide sequence of DNA or RNA
that corresponds to a specific amino acid.
Stop codon- UAA, UAG, UGA
STEP 1: Initiation
- For translation to begin, the start codon AUG must
be recognized. This is a codon specific to the amino
acid methionine, which is nearly always the first
amino acid in a polypeptide chain.
- At the 5' cap of mRNA, the small 40s subunit of the
ribosome* binds. Subsequently, the larger 60s subunit
binds to complete the initiation complex. The next
step (elongation) can now commence.
Ribosomes are complexes of rRNA molecules and proteins.
STEP 2: Elongation
- The ribosome has two tRNA binding sites; the P site
which holds the peptide chain and the A site which
accepts the tRNA.
- The initiator tRNA resides in the P site, leaving the A
site, open. When a new tRNA molecule recognizes the
next codon sequence on the mRNA, it attaches to the
open A site. A peptide bond forms connecting the
amino acid of the tRNA in the P site to the amino acid
of the tRNA in the A binding site.
- As the ribosome moves along the mRNA molecule,
the tRNA in the P site is released and the tRNA in the
A site is translocated to the P site. The A binding site
becomes vacant again until another tRNA that
recognizes the new mRNA codon takes the open
position. This pattern continues as molecules of tRNA
are released from the complex, new tRNA molecules
attach, and the amino acid chain grows.
STEP 3: Termination
- One of the three stop codons enter the A site. No
tRNA molecules bind to these codons so the peptide
and tRNA in the P site become hydrolyzed releasing
the polypeptide into the cytoplasm.
- Stop Codons: UAG, UGA UAA (Huwag uga,
Waaahh!!)