GENERAL BIOLOGY 2 - LECTURE 2
Central Dogma of Life
● Products are amino acids needed to make
proteins that are used in phenotypes (physical
structure)
● Chromosomes > Histones > DNA Strand [pic]
● DNA: double-helix, super coiled
Chromosomes
● In the nucleus of each cell, the DNA molecule is
packaged into thread-like structures called
chromosomes. Each chromosome is made up
of DNA tightly coiled many times around proteins
called histones that support its structure. DNA
and histone proteins are packaged into structures
called chromosomes.
● Chroma - colored
● Soma - body
● What is it for?
○ Organizes very long strands of DNA
○ Ensure DNA transfer is accurately copied
during cell division
● Humans: 46 chromosomes, 23 pairs
○ Dogs: 39 pairs
○ Plants: 12 pairs
○ Insects: 4 pairs
● Centromere: pulls the chromatid during cell
division
● Telomere: protects the ends
○ DNA is sticky
○ Structures the protect the ends of the
chromosomes
○ Like shoelace aglets
○ As the chromosomes undergo cell
division, telomeres tend to shorten
■ Length declines in dividing cells
as we age
○ Lifestyle changes may lengthen telomeres
○ Journal reading: doi:10.3390
○ Based on journal reading, telomeres are
■ Repetitive tandem DNA
sequences that cap chromosomal
ends protecting genomic DNA
from enzymatic degradation
■ Progressively shorten with cellular
replication and therefore assumed
to correlate with biological and
chronological age
■ Telomere length holds tantalizing
promise as a biomarker, however,
a host of evidential
inconsistencies and paradoxes
must be addressed.
■ Journal:
https://www.mdpi.com/1422-
0067/18/12/2573/htm
● Arms:
○ P arm = “petit”
○ Q arm
DNA REPLICATION, TRANSCRIPTION &
TRANSLATION
Genes: basic unit of heredity
● Sequence of nucleotides in a DNA molecule
Nucleotide Sequence
● Order of nucleotide in a gene
● Codes for a specific polypeptide chain
● Codons: groups of 3 nucleotides that code for
specific nucleic acid
DNA Replication > Transcription > RNA > Translation >
Proteins
I. DNA REPLICATION
● Goal: replicate, reproduce, duplicate, recreate
● Why is it important for DNA to be replicated?
Existing cells divide to produce cells, each of them
needs a full instruction manual to operate
properly. DNA needs to be copied before cell
division so the new cell could receive a full
instruction
● Parent DNA unzips in order to create new
daughter DNA
● A key feature of all nucleic acids is that they have
two distinctive ends: the 5' (5-prime) and 3' (3-
prime) ends. This terminology refers to the 5' and
3' carbons on the sugar. For both DNA and RNA,
the 5' end bears a phosphate, and the 3' end a
hydroxyl group.
 ● Semiconservative Replication: each DNA is ● RNA Primase
half-old and half-new ● Okazaki Fragments
○ First strand is from original parent DNA ● DNA Ligase
○ Second strand is freshly assembled
● Very crucial because wrong nucleotides can THE DNA REPLICATION PROCESS
cause mutations that can be inherited
● DNA REPAIR: during replication, 3 billion
nucleotides must be assembled properly and
rapidly
○ Sometimes errors occur
● GENE MUTATION:
○ DNA is altered in a way that changes the
whole gene
○ One base gets substituted for another
○ An extra base in inserted or deleted from
the sequence
○ Causes:
■ Radiation
● UV Radiation ● Helicase: enzyme that unzips the double strand
● X-rays by breaking the hydrogen bonds that bind
■ Chemicals complementary pairs or bases of nucleotides (A-T
● Cigarette smoke and C-G)
● Nitrate and nitrate ○ Separates double-stranded DNA into
preservatives single strands to allow strand to be copied
● Barbecuing ● Topoisomerase: ubiquitous enzyme whose
● Benzoyl peroxide function is to relieve the torsional strain in DNA,
■ Infectious Agents simply unwind the DNA
● HPV ○ Removes positive supercoils generated in
● Helicobac front of the replication fork and relieve
● When does it occur? negative supercoils occurring downstream
○ After the cell grows big enough to divide of RNA polymerase during transcription
during interphase, the “S” phase ○ DNA Gyrase is a type of a topoisomerase
that specifically relieves the negative
Where does it occur? supercoil of DNA
● In eukaryotes, the site of DNA replication is inside ● Single-stranded binding proteins: proteins that
the nucleus. bind to single-stranded regions of DNA
● Since prokaryotes does not have true nucleus, it ○ Produced during all aspects of DNA
happens in the cytoplasm metabolism: replication, recombination,
repair
Where does it initiate? ○ Stabilizes single-stranded regions of DNA
● DNA replication initiates at a single site in ○ Bind and modulate function of involved
prokaryotes proteins
● Multiple sites in eukaryotes

Key Players/Terms
● Helicase
● Topoisomerase
● Single-stranded binding proteins
● Replication fork
● Leading Strand
● Lagging strand
● DNA Polymerase

● Replication fork: very active area where DNA
replication takes place
○ Created when DNA helicase unwinds the
double helix structure of DNA
○ Composed of leading and lagging strand
● Leading strand: synthesized in the 5’-’3’ direction
● Lagging strand: synthesized in 3’-5’ direction
● DNA Polymerase: enzyme that synthesizes DNA
molecules from deoxyribonucleotides (DNA
building blocks) ; it only works in the 5’-3’ direction
because it can only add nucleotides to the 3’ end.
○ Essential for DNA replication
○ Usually work in pairs
● RNA Primase: Synthesizes RNA Primers which
signal DNA polymerase, where it will start adding
nucleotides
● Okazaki Fragments: short sequences of DNA
nucleotides (approx 150 to 200 base pairs long in
eukaryotes)
○ Synthesized discontinuously and later
linked together by the enzyme DNA ligase
to create the lagging strand during DNA
replication
● DNA Ligase: After the strand is proofread, DNA
ligase seals up the sequence of DNA into two
continuous double strands. This enzyme can
connect two strands of DNA by forming a bond
between the phosphate group of one strand and
the deoxyribose group on another.
I. Helicase unzips DNA
A. Helicase unzips DNA by removing
hydrogen bonds
B. Topoisomerase unwinds and relaxes the
super coil of DNA
C. Single-strand binding proteins are used to
maintain the relaxed form of the DNA
II. DNA Polymerase: building enzyme
A. The one that adds nucleotides
B. Direction of the action of DNA
polymerase: 5’-3’ direction because it
can only add nucleotides to the 3’ end
1. Original strand: 3’-5’
2. Going to replication port
C. Leading strand: strand 3’-’5’
1. One primer created at the end of
DNA original strand
D. Lagging strand:
III. Primase: create primer that will signal the start of
replication
A. Initiate start of replication of new strand
B. Causes the
C. Okazaki Fragments: short synthesized
DNA fragments
1.
2. Reiji Okazaki (1930-1985):
Japanese molecular biologist
IV. Ligase: Glueing enzyme
A. Glues Okazaki fragments
RESULT: “Semi-conservative” strands
SUMMARY
 that is complementary to a strand of template
DNA. . It is carried out by an enzyme called RNA
polymerase and a number of accessory proteins
called transcription factors. DNA safely and stably
stores genetic material in the nuclei of cells as a
reference, or template. Meanwhile, mRNA is
comparable to a copy from a reference book
because it carries the same information as DNA
but is not used for long-term storage and can
freely exit the nucleus.

○ Both DNAs
○ Coding strand: matches the mRNA
sequence
DNA replication is the process by which DNA makes a ■ Replicated strand “blueprint”
copy of itself during cell division. strand
The first step in DNA replication is to ‘unzip’ the double ○ Template strand: complementary of
helix structure of the DNA molecule. mRNA
■ Original strand
This is carried out by an enzyme called helicase which
breaks the hydrogen bonds holding the complementary
bases of DNA together (A with T, C with G).
The separation of the two single strands of DNA creates a
‘Y’ shape called a replication ‘fork’. The two separated
strands will act as templates for making the new strands of
DNA.
One of the strands is oriented in the 3’ to 5’ direction
(towards the replication fork), this is the leading strand.
The other strand is oriented in the 5’ to 3’ direction (away
from the replication fork), this is the lagging strand. As a
result of their different orientations, the two strands are
replicated differently.

TRANSCRIPTION AND TRANSLATION

Initiation, Elongation and Termination of Transcription
Protein Synthesis
Common proteins of the body:
● Antibody: body’s protection against foreign
elements
● Enzyme: catalyzes reaction
● Messenger: transmits signals
● Structural: structure and support for cells
● Transport or storage: binds and carries atoms
and small molecule

II. DNA TRANSCRIPTION

First step of Gene Expression
○ Gene expression: process wherein
genetic information is utilized to create
functional genetic products
Goal: transcribe, write out, copy
Site of Transcription: Nucleus
During transcription, a strand of mRNA is made
 ■ Proofreading
■ Coding
■ Termination recognition
3. TERMINATION
○ Termination is the ending of
transcription, and occurs when RNA
polymerase crosses a stop (termination)
sequence in the gene. The mRNA strand
is ready to detach from DNA.
○ Prokaryotes:
■ Rho-dependent termination:
protein “Rho” disrupts the
complex involving the template
strand, RNA pol and RNA
● A hexameric protein
called Rho factor attaches
to the DNA strand and
RNAP can not move
further and dissociates
from DNA strand and
moves it off of the
template, terminating the
1. INITIATION transcription
DNA molecules unwind and separate forming a ■ Rho-independent termination
small open complex. Initiation is the beginning of or Intrinsic termination: RNA
transcription. It occurs when the enzyme RNA forms a hairpin loop structure
polymerase binds to a region of a gene called the which displaces RNA polymerase
promoter. This signals the DNA to unwind so the and stop transcription, causing
enzyme can ‘‘read’’ the bases in one of the DNA the detachment
strands. The enzyme is now ready to make a ● Palindromic /palindrome-
strand of mRNA with a complementary sequence like bases occur at end
of bases. sequence of DNA. Due to
○ Promoter: initiator these sequences, the
■ Upstream 5’-3’ newly synthesized RNA
○ Tata Box: in eukaryotic; a promoter folds on itself to form
sequence that indicates where a genetic hairpin loop (due to
sequence can be decoded complementary base
■ In prokaryotes; Pribnow Box pairing) which terminates
2. ELONGATION the movement of RNA
○ Elongation is the addition of nucleotides to Polymerase.
the mRNA strand. RNA polymerase reads ● Palindrome - word or
the unwound DNA strand and builds the phrases that read alike
mRNA molecule, using complementary backwards and forwards
base pairs. There is a brief time during ○ Eukaryotes: RNA pol termination
this process when the newly formed RNA recognition sites
is bound to the unwound DNA. During this
process, an adenine (A) in the DNA binds
to an uracil (U) in the RNA. MAIN PRODUCT: Pre-mRNA sequence
○ RNA polymerase (RNA Pol) skills:
■ Initiates transcription PROCESSING mRNA - important before it will undergo
■ Helicase and DNA polymerase in translation
one Pre-mRNA -------------------------------------> Mature mRNA
 ● Splicing
○ Introns (noncoding) are removed
○ Exons (coding) are joined together
○ Spliceosome: large complex of snRNPs
which assemble with pre-mRNA to
achieve RNA splicing
■ Removes introns
■ snRNP: small ribonuclear proteins
● Editing
○ Changes some of the nucleotides in the
mRNA
○ Any process, other than splicing, that
results in a change in the sequence of a
RNA transcript such that it differs from the
sequence of the DNA template and may
generate precise point mutations is RNA
editing
○ Types
■ Base modification (deaminase)
or substitution: A to I, C to U, U
to C etc.
■ Insertion or deletion: U insertion
or deletion
Journal reading in Editing:
https://www.annualreviews.org/doi/abs/10.1146/annurev.n
utr.20.1.169
● Apolipoprotein (apo) B circulates in 2 distinct
forms because of editing One form is smaller than
the other because editing adds a premature stop
signal in the mRNA. This process has significant
effects on the metabolism of lipoproteins, and it
necessitates a single-strand template with clear-
cut characteristics in the vicinity of the edited
base. This kind of RNA editing in mammals relies
on base modification (C-to-U RNA editing).
○ ApoB100, ApoB48
○ apoB100: secreted by human liver
■ Product of a large mRNA
encoding 4536 residues
○ apoB48: secreted by small intestine of all
mammals
■ Arises following C-to-U
deamination of a single cytidine
base in the nuclear apoB
transcript, introducing a
translational stop codon-- also
called apoB RNA editing
○ apoB RNA editing: operates through a
multicomponent enzyme complex that
contains a single catalytic subunit,
apobec-1, in addition to other protein
factors that have yet to be cloned
■ Exhibits stringent cis-acting
requirements that include both
structural and sequence-specific
elemets, specifically efficiency
elements that flank the minimal
cassette, an AU-rich RNA context
& an 11-nucleotide mooring
sequence
● Polyadenylation
○ A 5' cap is added to the beginning of the
RNA transcript, and a 3' poly-A tail is
added to the end.
○ Polyadenylation specifically adds a “tail”
to the mRNA. The tail consists of a string
of As (adenine bases).
○ “Poly A tail”: around 250 as strings of
adenine bases
○ Signals the end of mRNA
○ Exports mRNA out of the nucleus
○ Protects mRNA from enzymes that might
break it down
○ Addition of adenine bases at the end of
the sequence to stabilize transcript
■ Assists exporting mRNA
DNA TRANSCRIPTION PRODUCTS
● CODING
○ mRNA: template for the synthesis of
proteins by ribosomes
● NON- CODING RNA
○ Transfer RNA (tRNA): transfers specific
amino acids to growing polypeptide
chains at the ribosomal site of protein
synthesis during translation
○ Ribosomal RNA (rRNA): a component
of ribosomes
○ Micro RNA: regulates gene activity
○ Catalytic RNA (Ribozyme): economically
active RNA molecules
III. TRANSLATION

● Goal: translate codons into amino acid sequence
● Second step in gene expression
● tRNA is a side product which is a complementary
to the mRNA sequence
● Occurs in the cytoplasm
○ Ribosome plays a sub function-- has
small subunit and a large subunit
■ Where the peptide bonds are
created
Initiation, Elongation and Termination
1. INITIATION: A particular initiator tRNA binds to
the smaller of two ribosome subunits and to the
mRNA molecule. The tRNA and the ribosome
subunit move along the mRNA until they
encounter a “start” (AUG) codon. At this point,
they are joined by a larger ribosomal subunit to
form the intact ribosome, which holds the mRNA
in place while the tRNAs bring amino acids to it.
2. ELONGATION: The chain of amino acids
lengthens one amino acid at a time. A tRNA
molecule carrying the next appropriate amino acid
binds to the ribosome and to mRNA. As the
mRNA passes between the two ribosomal
subunits, the ribosome catalyzes the formation of
the bond between the newest amino acid and the
previous amino acid in the growing chain. The
tRNA molecule is then released to find another
amino acid.
3. TERMINATION: There is no tRNA anticodon
corresponding to a “stop” codon on mRNA. When
a “stop” mRNA codon is encountered, the
ribosomal subunits and the newly formed peptide
chain detach from the mRNA.
Codons
● Codon: sequence of the 3 DNA or RNA
nucleotides that corresponds with a specific amino
acid
● Triplet Nature: A triplet code could make a
genetic code for 64 different combinations (4 X 4
X 4) genetic code and provide plenty of
information in the DNA molecule to specify the
placement of all 20 amino acids.
● Start codon: marks the start the site at which
translation into protein sequence begins
○ Stop codon: UAG, UAA, UGA -- marks the
site at which translation ends
Properties of Genetic Code
1. Unambiguous
a. In any organism each codon corresponds
to only one amino acid
2. Code is degenerate
a. There are multiple codons for most amino
acids
3. Universal
a. Codons are the same for all organism
4. Without punctuation
a. There are no punctuations between
trinucleotides
5. Nonoverlapping
a. Codons do not overlap each other
REVIEW
SUMMARY/GLOSSARY OF KEY TERMS
REPLICATION
● Helicase
● Replication Fork
● Leading Strand
● Lagging Strand
● DNA Polymerase
● RNA Primase
● Okazaki Fragments
TRANSCRIPTION
● UPSTREAM: toward the 5’ end of the RNA
molecule
● DOWNSTREAM: toward the 3’ end of the RNA
molecule
● TATA BOX: DNA sequence that indicates where
a genetic sequence can be read and decoded
○ Type of promoter sequence; specifies to
other molecules where transcription
begins
● RNA POL: RNA polymerase
○ Enzyme that synthesizes RNA from DNA
template
○ Locally opens the double-stranded DNA
so that one strand of the exposed
nucleotides can be used as a template for
the synthesis of RNA (aka transcription)
 ● TERMINATION SIGNALS : found at the end of
the part of the chromosome being transcribed
during transcription of mRNA
○ Needed because only parts of the
chromosome are transcribed
● POLY-A TAIL: long chain of adenine nucleotides
that is added to a mRNA molecule during RNA
processing to increase stability of molecule
● 5’ CAP AND POLY-A TAIL: A 5' cap is added to
the beginning of the RNA transcript, and a 3' poly-
A tail is added to the end.
● SPLICEOSOME: large and complex molecular
machine found primarily within the nucleus of
eukaryotic cells
○ Assembled from small nuclear RNAs and
approximately 80 proteins
○ Removes introns from transcribed pre-
mRNA
● EXONS: any part of a gene that will encode a part
of the final mature RNA produced by that gene
after introns have been removed by RNA splicing
● INTRONS: any nucleotide sequence within a gene
that is removed by RNA splicing during maturation
of the final RNA product
○ Non-coding regions of an RNA transcript

TRANSLATION
● Nuclear envelope
● Ribosome
● tRNA
● rRNA
● Codon
● Anticodon
● Start codon
● Stop codons
● Polypeptide chain .
 Edited and updated by:
Ms. Lorraine Joyce M. Del Rosario
(February 18, 2020)