Biology past and present

• In the past, biology was descriptive: e.g. classified

animals and plants into families, groups, species
• It was recognized that from one organism, e.g. a
dog, only the same organism, dog, emerges – dogs
don’t have cats or human babies. Why?
• Microscope, discussed later, did not help in defining
the information carrying material
• Once the components discussed this morning were
recognized biochemically, scientists tried to
determine which material passes on the information
 What is the molecule that
stores information?
• In the 1920s, it was concluded that chromosomes
were the carriers of information
• Chromosomes contain both proteins and nucleic
acids, which both were ordered and considered
good candidates to be the carriers of information.
• Since there are 20 different amino acids and only 4
different nucleotides, DNA was considered too
simple, proteins were considered more likely
carriers of information.
• The critical experiments were done by Griffith and
followed up by Avery in 1944.
 S bacteria contain
something that R are
lacking. Infectivity of S
bacteria can be killed
by heat.

(S colonies appear
smooth on plates, R
colonies appear rough
on plates)

Conclusion:
Smooth (S) bacteria
contain something that
is not destroyed by
heat that can be
passed to R bacteria
to make them more
like S bacteria, i.e. kill,
and that property can
be passed on to the
next generation.
Figure 5-3 Essential Cell Biology (© Garland Science 2010)
Figure 5-4 Essential Cell Biology (© Garland Science 2010)
 Hershey and Chase: Virus
• Viruses infect and kill bacteria
• Viruses consist of both DNA and proteins
• Hershey and Chase labeled* the DNA with
P, and the proteins with 35S.
32

• They asked: When a virus infects a

bacterium, what gets inside?

• * the idea of labeling a “tracer” or a “probe” to

follow a substance is commonly used in biology.
We will have more examples in later lectures
Figure 5-5a Essential Cell Biology (© Garland Science 2010)
Figure 5-5b Essential Cell Biology (© Garland Science 2010)
 Chargaff’s rules –
before the actual DNA structure
• Chargaff worked with Avery on discovering that
DNA, not proteins was the heritable material
• Looked at the chemical composition of all kinds
of species DNA and found that the molar A:T
ratio was always 1, the G:C ratio was always 1
• But the A/T:G/C ratio was variable from species
to species but constant within each species
• Even before Watson and Crick discovered the
structure of DNA, this pairing was recognized
 1953 – Structure of DNA
R. Franklin and M. Wilkens
show that DNA is a
double helix using x-ray
crystallography

Watson and Crick built

a model of the structure
of DNA
Figure 5-2a Essential Cell Biology (© Garland Science 2010)
Figure 5-2b Essential Cell Biology (© Garland Science 2010)
Figure 5-2c Essential Cell Biology (© Garland Science 2010)
Figure 5-6a Essential Cell Biology (© Garland Science 2010)
 Important features of DNA
• There is a direction: 5’ to 3’, defined by the
sugar phosphate backbone
• 5’ ends usually contain a phosphate
• DNA is double stranded
• the two strands are anti-parallel (5’-3’,
usually written on top)
5’ –CTATAG – 3’
||| || || || || |||
3 ’–GATATC – 5’
Figure 5-6b Essential Cell Biology (© Garland Science 2010)
 How is the information that is
stored in DNA used?
• Transmission through generations – more later
• DNA is stored in the nucleus, the design and
management center of the cell. Proteins are made in
the cytoplasm, the production site of the cell.
• Messenger RNA (mRNA) is used to transmit the
information from the nucleus to the cytoplasm
• Transfer RNAs (tRNAs) are adaptors: from the 4
base DNA code to the 20 amino acid protein code
• Ribosomes make the proteins using the mRNA as
template, and amino acids as the building blocks
Figure 7-1 Essential Cell Biology (© Garland Science 2010)
 “Central Dogma”
known by 1958:
• Protein synthesis is in cytoplasm, DNA in nucleus (in
eukaryotic cells)
– Need intermediate to carry the information

• Mutations could result in a change in a protein’s amino

acid sequence
– Sickle cell disease – single amino acid change
– Valine  Glutamine
– If an inherited mutation resulted in a change in a protein
sequence and DNA sequence was the genetic material, then a
change in DNA sequence must be able to lead to a change in a
protein sequence

• Put this all together -> The Central Dogma

Central Dogma Proposed by Francis
Crick in 1958
– DNA, RNA, and proteins are linear, sequential polymers

– Each position in a sequence is drawn from a fixed set of

residues, the alphabet
• Nucleotides for RNA and DNA (alphabet of 4)
• Amino acids for proteins (alphabet of 20)

– The central dogma concerns the flow of primary sequence

information between the three types of polymers
• Implies conversions between alphabets (translation!)
• The Central Dogma says that there is no way to convert information
in the protein alphabet back to information in a nucleic acid alphabet
• Also need some kind of adaptor to convert nucleic acid sequence
information to protein sequence information
Graphic Representation of the Central Dogma
Replication

Bold arrows – known transfers

Dotted arrows – possible transfers
DNA (we will discuss some later!)
n Note: No arrows out of proteins!
tio

No
n o
rip

pti

to
cri
sc

bs
ns

erv
an

Tra
Tr

ed
rse
ve
Re

Translation
RNA Protein

Replication (viral) Discussed in: F. Crick (1970) Nature 227: 561-563.

Figure 7-2 Essential Cell Biology (© Garland Science 2010)
 Major differences between
RNA and DNA
• Uracil (U) is used instead of Thymidine (T)
• 5-ribose is used instead of 5-deoxyribose
• RNA is single stranded, whereas DNA is an
antiparallel double stranded helix
– RNA can have partial pairings of bases
causing structure – see tRNA later
• Amount of RNA of a gene varies from cell
to cell and developmental stage, whereas
each cell has the same amount of DNA
 Gene expression
transcription regulation
• When mRNA is made from DNA, the genetic code
is utilized: genes are expressed.
• Regulation of gene expression is an important
feature of cellular functions: it determines whether
a cell is a liver, muscle or nerve cell
• Transcript or gene expression levels vary from cell
to cell in the same organism, at different times of
development, and in response to outside signals.
 RNA polymerases
• The enzymes that carry out transcription are
called RNA polymerases
• Synthesis of RNA happens always 5’ to 3’ – true
for all synthesis of RNA or DNA
• more than one RNA polymerase can transcribe
a single DNA molecule at a time
• There are signals on the DNA that tell RNA
polymerases where to start and where to stop
• Some of these signals are subject to regulation.
 Minimal Gene Structure
Promoter – Defines where
Signal to end the transcript
transcription should begin,
(terminator in bacteria)
RNA Pol binding site

5’ Coding Region 3’
DNA
3’ 5’
Transcription by RNA Polymerase
Synthesis of messenger RNA

Translation Translation
Initiation Site Termination Site
mRNA 5’ 3’
5’ UTR 3’ UTR
(untranslated region)
Translation by the Ribosome

N-terminus C-terminus
Peptide Chain
 Prokaryotes*
• Have no nucleus
• single cellular, although
they may join together in
chains or clusters
• can live in diverse
temperatures – from ice
to boiling vulcanoes
• can grow and evolve
quickly
ECB3 spells it Procaryotes and Eucaryotes – both spellings are customary
Eukaryotes *
• Have a nucleus
• are multicellular
• have other intracellular
organelles
• some organelles
(mitochondria and
chloroplasts) are thought
to have evolved from
invading bacteria
 Prokaryotic Genes
• Minimal gene
– Promoter – binding site for RNA Polymerase
– Ribosome binding site (Initiate protein synthesis on mRNA)
– Coding sequence – encodes protein sequence
– Stop codon (terminate protein synthesis)
– Transcriptional terminator (stop mRNA synthesis)
 Polycistronic mRNAs in
Prokaryotes
• Prokaryotes often have multiple protein coding regions
controlled by a single promoter
– Allows simple coordinate regulation
– Referred to as an operon
– The mRNA is polycistronic – more than one protein encoded
on a single mRNA molecule
Figure 8-7 Essential Cell Biology (© Garland Science 2010)
 Prokaryotes use polycistronic mRNAs when the multiple
proteins are regulated in a coordinated fashion.
Figure 8-8 Essential Cell Biology (© Garland Science 2010)
 Gene transcription
can happen on both DNA
strands in opposite directions
Eukaryotic genes have 5’ caps
and 3’ poly-A-tails
Eukaryotic transcription requires
general transcription factors
Gene regulatory elements can be located near the
promoter, far upstream or downstream, or within introns.
Looping of the DNA can bring regions closer together.
Multiple elements (enhancers and repressors) influence a
gene’s activity, either working together in concert or
responding to different conditions and cell state.
Enhancers can act over
distances of 1000s of bp

Changes local
structure of
chromosome

Regulation acts at many levels

and can involve interactions
over long distances
Figure 8-12 Essential Cell Biology (© Garland Science 2010)
Most Eukaryotic genes have
introns that are spliced
 Eukaryotic genes can be quite simple or very large, with >25 exons
Figure 7-18 Essential Cell Biology (© Garland Science 2010)
 Splicing requires intronic
signal sequences

Y stands for Pyrimidines, which are C and T – so the YYYYYY region is C/T rich
(Purines, G and A, are summarized similarly as R)

Figure 7-19 Essential Cell Biology (© Garland Science 2010)

Figure 7-20 Essential Cell Biology (© Garland Science 2010)
 Alternative Splicing can be
differentially regulated

Figure 7-21 Essential Cell Biology (© Garland Science 2010)

Figure 7-6 Essential Cell Biology (© Garland Science 2010)
Figure 7-7 Essential Cell Biology (© Garland Science 2010)
Figure 7-9 Essential Cell Biology (© Garland Science 2010)
Figure 7-1 Essential Cell Biology (© Garland Science 2010)
 Transferring Information from
One Alphabet to Another

• DNA -> DNA, 1:1 alphabet correspondence

– Base pair complementarity transfers sequence info
• DNA -> RNA, 1:1 alphabet correspondence
– Base pair complementarity transfers sequence info

• The problem:
• RNA -> Protein, Not a 1:1 relationship
– 4 Bases : 20 amino acids

• How could amino acid sequences be represented in

RNA or DNA sequences?
 What’s the code for converting DNA/RNA
sequence to protein sequence information?

• Nucleotide sequence is like a base 4 number

system
– 1 nucleotide  4 words or values (1:1)
– 2 nucleotides  16 words or values (2:1)
– 3 nucleotides  64 words or values (3:1)

• There are 20 standard amino acids

– 2 nucleotides per amino acid not enough
– 3 nucleotides per amino acid more than enough
– What’s are possible solutions for this?
• Use only a subset
• Use multiple triplets to mean the same amino acid
 Translation
• Once the mRNA gets out of the nucleus, it
is translated into proteins. Nucleotides
and proteins use a different alphabet and
a different language – like translating
English into Chinese.
• How is the code of 4 bases translated into
20 amino acids (plus at least one “stop”)?
A commonly used alternative
way to show the genetic code
A second alternative way to
show the genetic code
 How did scientists find this
genetic code?

Nirenberg et al.: Synthetic mRNA with specific

sequence was mixed in a cell free system of ribosomes
and tRNA. The protein then was analyzed: Poly UUU
resulted in poly Phenylalanine
Figure 7-27 Essential Cell Biology (© Garland Science 2010)
The genetic code
is directional:
5’ to 3’ mRNA
encodes N-
terminal to C-
terminal proteins.

Like Chinese, the

genetic code has
no spaces to
indicate the 下雨天留客天留人不留
beginnings and
ends of “words”. 下雨天留客 , 天留人不留
下雨天 , 留客天 , 留人不 ?
留
 6 different reading frames
from DNA to proteins

Like Chinese, the DNA strand can be read from left to right, or right to left.
However, unlike Chinese, 5’-3’ gives you the direction in which to read:
you can only read the top strand left to right, and the bottom strand right to left
 Beginnings and Ends
• All proteins start with the amino acid methionine
• Sequence around is important to recognize “start”:
A/GccAUGG/A (so not any Met can be start)
This is called the Kozak sequence, and the purine at
position -3 and +1 are very important.
• Sometimes proteins will cleave off part of their
amino acids (post-translational processing)
• TGA, TAA, TAC (UGA, UAA, UAC) signal: STOP
• Next week we will discuss regulation of
transcription with features of mRNA that are not
relevant for protein encoding
 t-RNA is an adaptor molecule
INPUT OUTPUT

220 V 6V
2 prongs 1 prong

1 amino
3 bases
acid
Nucleotide
peptide
chain
chain
 Based on the predicted secondary structure of t-RNA, it
was usually shown as a cloverleaf structure. But in 3D,
t-RNAs usually adopt more an L-shape structure.
E shows the schematic shown in the book/my slides
Figure 7-28 Essential Cell Biology (© Garland Science 2010)
 t-RNA synthetases charge t-RNA with amino acids
t-RNAs anticodons then base pair with the correct codon
on the mRNA. Both adaptors are necessary to decode
the bases on the mRNA strand into a amino acids
Figure 7-29 Essential Cell Biology (© Garland Science 2010)
 Ribosomes are large
multimeric
complex molecules
consisting of both
proteins and rRNA –
ribosomal RNA

rRNA is the most

abundant RNA in most
cells.

The Nobel Prize in

Chemistry in 2009 was
awarded for the
discovery of Ribosome
Structure and function
Figure 7-31 Essential Cell Biology (© Garland Science 2010)
Figure 7-35 (part 1 of 5) Essential Cell Biology (© Garland Science 2010)
Figure 7-35 (part 2 of 5) Essential Cell Biology (© Garland Science 2010)
Figure 7-35 (part 3 of 5) Essential Cell Biology (© Garland Science 2010)
Figure 7-35 (part 4 of 5) Essential Cell Biology (© Garland Science 2010)
Figure 7-35 (part 5 of 5) Essential Cell Biology (© Garland Science 2010)
There are several different
types of RNA in cells
 Summary
• DNA is stored in the nucleus, the command center of the cell.
• DNA is read into mRNA. The amount and timing of mRNA is
regulated and makes the difference between types of cells
• Messenger RNA (mRNA) is used to transmit the information
from the nucleus to the cytoplasm
• Initial RNA has exons and introns and needs to be spliced
into mature mRNA, of which there may be several types
• Proteins are made in the cytoplasm, the cell’s production site
• Transfer RNAs (tRNAs) and t-RNA synthetases are adaptors:
from the 4 base DNA code to the 20 amino acid protein code,
including start and stop codons
• Ribosomes are complex, multimeric complexes made of
ribosomal RNA and proteins. They make proteins using the
mRNA as template, and amino acids as the building blocks