The Central Dogma 9/17/2013 1:02:00 PM
Flow of Information in a Cell:
DNA (information storage)
->Transcription -> RNA (information carrier)
-> Translatio900n (by ribosomes) -> Proteins (polypeptide chain)
-> Phenotype (physical features of the genotype)
* proteins lead to and make up the phenotype
Phenotype: The observable physical or biochemical characteristics of an organism, as
determined by both genetic makeup and environmental influences.
Atom: most basic piece of matter (+proton, neutron and surrounded by - electrons);
smallest chemical unit of matter
Molecule: larger unit comprises of two or more atoms; atoms connected together by
DNA: molecule responsible for transmission of information from one generation to the next
in all forms of cellular life on this planet (mainly comprises of nitrogen bases)
The DNA structure contains linkages between sugars, phosphates and nitrogen bases.
Genome: complete set of genes
i) phosphate group
ii) sugar (deoxyribose in DNA & ribose in RNA)
*nucleotides are monomers
Nucleic Acid Structure- Nucleic acids are made up of nucleotides which are the building
blocks of DNA and RNA. The nucleotides are linked by covalent bonds between the
phosphate of one nucleotide and the sugar of the next. Polymerization results in a linear
spine which is composed of alternating sugars and phosphates, with bases extending from
them (Bauman, pp.49).
Phosphodiester Bond- Nucleotides polymerize to produce nucleic acids through formation
of a phosphodiester linkage between phosphate group on the 5' carbon of one nucleotide and the OH- group on the 3' carbon of another since phosphate binds with oxygen in a
- DNA has many nucleotides connected to each other by phosophodiester bonds.
DNA primary structure consist of sequence of nitrogen containing base which includes
information in the form of molecular code.
Deoxyribose – sugar back bone
*purine are double ringed molecules
*pyrimidines are single ringed molecules
- DNA are polymers of nucleotides consisting of a pentose sugar and a nitrogenous base
which is bound to a phosphate.
- In DNA base pairings consist of adenine and thymine, and guanine and cytosine
- In RNA base pairings consist of adenine and uracil, and guanine and cytosine
- There are 3 billion nitrogenous bases in human DNA and more than 99 % of these bases
are same in all human beings. Two strands of DNA run in opposite directions held together
by complementary base pairs with hydrogen bonds twisted into a double helix (Archaeal
DNA is separated and organized with histones, chromosomal DNA is folded into loops)
- Complement base pairs : A-T, G-C through hydrogen bonds. A-T are held together by two
hydrogen bonds. C-G are held together by three hydrogen bonds.
- base is the information in the form of a molecular code (on the inside/core)
- The backbone is the phosphate and sugars (outside) this creates a negative charge and
polar - Two grooves between backbones are called the major and minor groove. Most protein data
is made in the major groove because the minor groove is too narrow
- Bases are planar and perpendicular to the path of the backbone purine bases are
composed of two rings (A and G) and pyrimidine bases are composed of one ring (C, T, U).
Base stacking contributes to the stability of the double helix
- The complementary base pairing is important for DNA replication and transcription
- Moving toward medicine where DNA can be sequenced
Chargaff discovered the pairing rules of DNA letters, noticing A=T, C=G
DNA structure Summary:
- DNA structure is made of two stands ranging in opposite direction. the two strands are
antiparallel, one strand runs from 3' end to 5' end and the other from 5' to 3' end.
-The two strands have complementary base pairing; if base pair on one strand are
AATCGC then the base pair on other strand would be TTAGCG. The specificity of pairing of
A with T and C with G makes the two DNA strands complementary.
-The two strands are held together by base paring and they are also twisted into double
DNA Replication - this is also known as anabolic polymerization process
-it requires monomers (building blocks) and energy (in the form of triphosphate
Initial Process involves:
replication beginning at a nucleotide called the origin
A cell removes chromosomal proteins, exposing the DNA helix
DNA helix (enzyme) unzips the DNA by breaking the hydrogen and therefore leaving the
bases as a replication fork
Proteins then stabilize the strands to prevent them from rejoining
DNA polymerase then binds to each cell and synthesizes DNA by adding nucleotides only to
the hydroxyl group of the 3' end ** DNA polymerase replicates only from the 5' end to the
3' end DNA is antiparallel and therefore the replicated strands are synthesized in two ways:
-Helicase is responsible for "unzipping" the DNA. Helicase breaks the loose hydrogen bonds.
Free nucleotides floating in the cytoplasm are used to build new DNA, think of them like
loose bricks. DNA polymerase are responsible for constructing DNA strands. Bauman, p. 203
Leading Strand- synthesizes continuously as a single long chain of nucleotides
Lagging Strand- synthesizes in short segments that are later joined.
For a simpler understanding on DNA, please visit this link by Khan
Duplication/Replication:molecule replication and transmission in each cell division. It's
role is to replicate and transmit itself in each cellular division (almost always
identical) Bauman textbook chapter 7
Histones (stabilization proteins) are removed from the DNA, DNA Helicase unwinds the DNA
by breaking the hydrogen bonds between the complementary base pairs and essentially
unzipping it (this forms the replication fork), DNA is always replicated in the 5' end to 3'
end, therefore the leading strand (the strand which runs from 5' end to 3' end)synthesizes
uninterrupted or continuously by the DNA polymerase. However, the lagging strand
(complementary strand which runs from 3' end to 5' end) must be synthesized backwards
and in fragments because of the direction it runs. It is not continuous, but synthesized in
short segments (that are later joined) called Okazaki fragments. RNA Primase lays down
RNA primers, DNA Polymerase III lays down new DNA in between the primers. A different
polymerase (DNA polymerase I) replaces the RNA primers with DNA. Finally, DNA ligase
fuses the fragments together.
*at; 95 degrees the original DNA strand denatures
degrees primers finds its place
72 degrees DNA polymerase makes another copy of DNA
Information: information expression within molecule (sequence of nucleotides). DNA
expresses its information by transcription to RNA (m RNA) which is translated into proteins
by the ribosomes. Information is expressed into sequenced nucleotides. The sequences
transcribed into RNA in order to release their information.
DNA vs RNA
Contains a Deoxyribose
Contains a Ribose sugar.
Consists of A,T,C,G Consists of A,U,C,G Double-Stranded Single-Stranded
It's the genetic material of Is for protein synthesis in all cells and
all cells and DNA virus genetic material of RNA viruses
* DNA thymine (T) is replaced by uracil (U) in RNA *
DNA helix unwinds resulting in single DNA strand ; this is brought about by the enzyme
DNA polymerase attaches to DNA
DNA polymerase brings the correct nucleotides and also checks for errors in the
sequence before forming new DNA strands
After copied polymerase falls off
The cell divides, one set on DNA molecule goes to each cell
DNA replication is semi-conservative meaning out of the two DNA strands in daughter
cell one is the original strand from the parent cell and other is complementary replicated
copy of the parent strand.
DNA replication is also an anabolic polymerization process, and allows a cell to pass copies
of its genome to its descendants.
DNA Amplification: used for forensic analysis to identify pathogens. Creates multiple
copies of the original DNA sequence.
Polymerase Chain Reaction (PCR):
- Acts as a temperature regulating system.
- Quick amplification to detect specific DNA
sequence by altering temperature.
- PCR uses: used to detect specific genes for genetic research. Bauman (2012) says that
scientists used this method to study the genome of a previously unknown pathogen that
killed people in 2003 with SARS. PCR helped scientist determine the nucleotide sequence,
which was found to be similar to coronaviruses.
-PCR can also be a tool used for genetic mapping: provides information on organism's
metabolism and growth; locating genes; nucleotide sequencing of pathogens. Essentially,
PCR is used to create multiple copies of the DNA molecule, which is used for in various
applications for genetic research (Bauman, 2012).
- Denaturation: Alters temperature to 95 C, in which the heat denatures DNA, breaking
the hydrogen bonds that hold the strands together, exposing the bases (no need for
helicase). The DNA strand is now open to be replicated.
- Priming:Temperature is then reduced to 60 C so primers can anneal (form hydrogen
bonds) with complementary sequences.
- Extension: Then alters temperature to 72 C o
(allows for optimal functioning of DNA polymerase) to allow the enzyme DNA polymerase to
copy in both directions and attach nitrogen bases with the correct pairing to form new DNA strand.
- These 3 temperature changes repeat to amplify protein (i.e. cycle 3 has 8 copies,
cycle 4 has 16 etc.) By changing the temperature from to 95 then to 60 and to 72, the DNA
polymerase keeps duplicating the DNA.
- PCR is the DNA duplication that is done in a tube.
- What do we need for PCR? We need primers, DNA polymerase, nucleotides.
Transcription: (DNA -> mRNA) the enzyme complex called RNA polymerase causes the
DNA strands to separate over a short region (10-20 base pairs). The polymerase move
along the DNA, and as it does, it forms an RNA chain using free nucleotides. The order of
the nucleotides in RNA is determined by the order of the nucleotides in one of the DNA
strands through the complementary base-pairing rule. RNA is shorter than DNA and it
contains the base uracil (U) instead of Thymine (T). If the first letter RNA polymerase
encounters in DNA is a T, the enzyme will add an A to the chain and if the next DNA letter is
G, a C will be added to the new chain.
Translation: (mRNA -> polypeptide chain) ribosomes use the mRNA sequences to build
polypeptides with the help of transfer RNA (tRNA) which is responsible for identifying the
correct sequence of CODON (group of 3 nucleotides) so as to present complimentary amino
acid. Each ribosome contains 3 sites for tRNA to bind (A, P, and E). A site is where tRNA
initially binds, tRNA in the P site results in the amino acid binding to the growing
polypeptide chain, E site releases tRNA)
DNA (double stranded):
Is a double stranded molecule and it contains thousands of hydrogen molecules between the
bases making it a weak bond, but at a normal temperature they form a stable double
stranded DNA molecule.
DNA carries instructions (information) for the synthesis of RNA and proteins.
Cells replicate their DNA molecules and pass the copies on ensuring they are viable for life.
DNA is self replicating
Is made up of a deoxyribose sugar, phosphate backbone and complimentary bases of
Adenine-Thymine (A-T) and Cytosine-Guanine (C-T)
RNA (usually single stranded):
Acts as an enzyme and binds amino acids together to form polypeptides.
A monomer of nucleic acids is a nucleotide.
RNA is synthesized from DNA when needed.
RNA is made up of ribose, phosphate backbone and complimentary bases of Adenine-Uracil
(A-U) and Cytosine-Guanine (C-T)
Genotype: Is the actual set of genes in its genome. Phenotype: refers to the physical features and functional traits of an organism (i.e.
structures, morphology and metabolism).
In any circumstance genotype determines phenotype by specifying what kinds of RNA and
structural, enzymatic and regulatory protein molecules are produced.
The transfer of genetic information:
First: make an RNA copy of the gene = Transcription
This information is copied as RNA nucleotide sequences...
RNA molecules synthesize polypeptides = Translation
These processes make up the Central Dogma of genetics: DNA is transcribed to RNA,
which is translated to form polypeptides. (Analogy p. 206 Bauman). The flow of genetic
information in cells is therefore from DNA to RNA to protein. All cells, from single-celled
bacteria to humans, express their genetic information in this way - this principle is so
fundamental that it is termed the Central Dogma of molecular biology (Alberts, Johnson,
Lewis et al., Molecular Biology of the Cell, 4th ed., pp. 301).
Cells transcribe four main types of RNA from DNA:
RNA primer- needed for DNA replication.
mRNA- carries genetic information from chromosomes to ribosomes.
rRNA- combine with polypeptides to form ribosomes.
tRNA-deliver the correct amount of amino acids to ribosomes based upon the sequence of
Events in transcription (3):
Initiation: RNA polymerases (the enzyme that synthesizes RNA) bind to specific DNA
molecules called promoters. In bacteria Sigma factor is necessary for recognition of a
promoter. RNA polymerase (once adhered to a promoter) unzips and unwinds the DNA
molecule. It forms a bubble.
Elongation: RNA transcription being 10 spots away from the promoter. RNA polymerase
links together DNA and RNA, synthesizing RNA. The enzyme moves down the DNA strand,
elongating the RNA strand. No primer needed. Triphosphate ribonucleotides is the energy
source for the transcription process.
Termination: Complicated. In bacteria there are two ways:
Self termination: Occurring when RNA polymerase transcribes a terminator sequence of
DNA is composed of two symmetrical series: 1 rich in guanine and Cytosine and the other
rich in adenine. When RNA polymerase transcribes the adenine rich portion of the
terminator, DNA and the uracil bases of RNA cannot withstand the tension, and the RNA
transcript breaks away form the DNA, releasing RNA polymerase. Rho-Dependent Termination: Rho, binds to a specific RNA sequence near the end of an
RNA transcript. Rho protein moves toward RNA polymerase at the 3' end of the growing
RNA molecule, pushing between RNA polymerase and the DNA stand... forcing them apart. Microbiology week 2 9/17/2013 1:02:00 PM
Amino acids are the building blocks of proteins
Proteins are made by the grouping of amino acids
The DNA and RNA help to make specific proteins
Process of converting info stored in nucleic acid sequences into proteins
Genetic code: the ribosomes read mRNA sequences in 3-base codons
Components of Translation
mRNA – the template is used to specify acid pattern
Ribosomes – a complex of proteins and rRNA molecules
Transfer RNA – small RNA molecules serve as adaptors between codons in mRNA and
amino acids. Transfer RNA anticodon recognize the codon in the mRNA
Universal code used in the nuclear genome
Complimentary anticodons are present in tRNA molecules, specifically linked to amino acids
With 4 bases in RNA and 3 base codons, there are 64 posible codons but only 20 amino
* Uracil – RNA instead of DNA (Thymine)*
Strings of ribosomes, assembled along an mRNA to increase rate of protein production
Ribosomes translate the MRNA (many at a time)
Ribosome reaches the stop protein and detaches from the protein molecule
Recombination of DNA
DNA of interest
Bacterial genome Section of DNA breaks/cut there are 2 sticky ends that meet
In the living cell, DNA undergoes frequent chemical changes, when it is being replicated
Most of these changes are quickly repaired
Those that are not result in a mutation
Thus, mutation is a failure of DNA repair
Molecular base of mutation
A mutation is any change in the organisms DNA
DNA mutations affect phenotype only when the mutation expresses (DNA – RNA – protein)
and the resulting protein functions abnormally.
Not all mutations affect the proteins function
Most common is a point mutation (change in a single nucleotide)
Non complimentary nucleotide is paired. (Change in the second triplet)
Insertions and deletions result in a shift change – drastically changing the protein
Function: separates the inside of a cell from the outside environment
Separate cells from one another
Provide a surface chemical reactions occur
Regulate the passage of material in and out of the cells (looks like a plastic bag)
Membrane structure Structure/Function of Bacteria 2013-09-25 3:58 PM 9/17/2013 1:02:00 PM
Prokaryotes Vs. Eukaryotes
All cell life have the same characteristics:
Cell membrane (regulates flow of nutrients and wastes that enter & leave cell)
DNA as its genetic material
Basic chemicals (carbs, fats, vitamins etc.)
Prokaryotic Cell Structure
(Inside – Out)
flagellum (tail – allows bacteria to move - way to sense chemicals) – also known as a little
motor for movement, similar to a propeller, can change direction and speeds. Structured
like a tail(s).
Function – rotation propels bacteria through the environment. Used in chemo taxis –
movement toward/away from substances based on gradient of concentration.
Axial Filaments: spirochete: cause leprosy
Similar to flagella
Snake like movement
Runs lengthwise along cell
Fimbria and Pilli
helps bacteria stay in the same place.
Sticky projections used to adhere one to another to hosts, and to environmental substances
Fimbriae can be distributed evenly or over the entire surface
May be hundreds per cell and are shorter than flagella
Long hollow tubules
Longer than fimbriae
Only one or two per cell Join bacteria and mediate transfer of one cell to another (conjunction)
Capsule & Slime layer structure
Sticky substances surrounding cell
Almost always observed on the surface
Composed of polysaccharides, polypeptides, or glycoproteins
Mediates adherence of cells
Protect bacterial cells from engulfment
Prevents cells from drying
Reserves of carbs
Complex aggregation of microorganisms growing on a solid substrate
Mediated by fimbria & capsules
More resistant than planktonic cells to antimicrobial agents, and host immune responses
In medicine, biofilms spreading along implanted tubes or wires can lead to severe infections
Allows bacteria to resist osmotic stress
Prokaryotic cell wall – provides structure & shape
Assists in some cells attaching to other cells
Not found in eukaryotic animal cells
We can target the cell wall of bacteria with antibiotics
Structure – chain, alternating sugar (NAM, NAG, NAM, NAG)
Cell Wall Made of Peptidoglycan
Cell wall structure based on 2 sugars
N-acytl glucosamine (NAG) N-acytl muramic acid Gram Positive & Gram negative Bacteria 9/17/2013 1:02:00 PM
Gram Positive & Gram negative Bacteria
The cell walls of certain bacteria (denoted Gram-positive) retain the first dye and appear
violet, while those that lose it (denoted Gram-negative) appear red. Also called Gram's
The periplasm is a space bordered by two selective permeable barriers, i.e., biological
membranes, which are the inner membrane (i.e., cytoplasmic membrane) and the outer
membrane in Gram-negative bacteria.
There is no periplasmic space in Gram-positive bacteria because there is only one biological
membrane, the cytoplasmic membrane. A region termed "inner wall zone" (IWZ) has been
observed between the cytoplasmic membrane and the mature cell wall.
Chemicals produced by the pathogen
Harm tissues or trigger host immune responses that cause damage:
Exotoxins (a toxin released by a living bacterial cell into its surroundings.)
Endotoxins (a toxin that is present inside a bacterial cell and is released when the cell
disintegrates. It is sometimes responsible for the characteristic symptoms of a disease).
secreted by live pathogen
abnormal signal to cells
destroy cellular and extracellular structures
Necrotizing Fasciitis *
* Pathogens are developing resistance to multiple drugs, some to nearly all. (MRSA). * Endotoxins:
Gram negative contains LPS (endotoxin)
LPS structure: O-side chain, Core polysaccharide, Lipid A
O-chain: chain varies depending on bacterium
Core-Polysaccharide: relatively constant composition
Lipid A: composed of glycolipids associated with toxic activity in gram negative bacterium
May play a role in infection by any gram negative bacteria
Released from dead cells when cell wall disintegrates
Activates macrophages, neutrophils
Produce pyrogens (may trigger fever)
LPS as an endotoxin
Release of too much LPS
Can be induced by antimicrobial drugs that kill bacteria
Systemic infection (sepsis)
Activates blood coagulation
Acute whole body inflammation
Drop of BP
Prokaryotic cell Organization and Structure
the material or protoplasm within a living cell, excluding the nucleus.
Typically one large circular molecule of DNA With no nuclear membrane
May have plasmids (a genetic structure in a cell that can replicate independently of the
chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or
Main roles of bacterial DNA
Contain the genetic material
a minute particle consisting of RNA and associated proteins, found in large numbers in the
cytoplasm of living cells. They bind messenger RNA and transfer RNA to synthesize
polypeptides and proteins.
Some differences from eukaryotes
The ribosomes of prokaryotes (70S) are smaller then cytoplasmic ribosomes of eukaryotes
But 70S ribosomes can be found in eukaryotes
A resistant asexual spore that develops inside some bacteria cells.
the inner layer of the membrane or wall of some spores and pollen grains.
Formed by a few groups of gram positive bacteria as intracellular structures but ultimately
they are released as free spores
Formed by vegetative cells in response to environmental signals that indicate a limiting
factor for vegetative growth
E.g. exhaustion of an essential nutrient
Endospores exhibit no sings of life. Although, they retain viability indefinitely
Mature spores are Highly resistant to environmental stress such as:
High temperature, irradiation, strong acids, disinfectants etc.
Endospores germinate and become vegetative cells when the environment stress is relieved
Endospore – formation is a mechanism of survival rather than a mechanism of reproduction Genetic Changes in Bacteria
Mutations in Bacteria
Mutations arise in bacterial populations
Some chemotherapy agent
Rare Mutations are expressed as a phenotype however, bacteria are haploid. ((of a cell or
nucleus) having a single set of unpaired chromosomes. Compare with diploid. (of an
organism or part) composed of haploid cells)
Rapid growth rate
Selective advantage enriches for mutants
Exchange of Genetic Information in Bacteria
Horizontal gene transfer
Donor to Recipient (unidirectional) – Transfer only
Donor does not give an entire chromosome
Gene transfer can occur between species
DNA from dead bacteria
By a bacteriophage
Naturally competent bacteria are able to take up exogenous DNA and undergo genetic
Transduction Gene transfer from a donor to a recipient by way of a bacteriophage.
Head (capsid) – genetic material is here
Infection of Host Cells by Phages
Receptor is LPS for T4
Potentially any donor gene can be transferred
Infection of Donor
Phage replication and degradation of host DNA
Assembly of phages particles
Release of phage Infection of recipient
Recombination into host DNA
Gene transfer from a donor to a recipient by direct physical contact between cells
Mating types in bacteria
F-factor (Fertility factor)
Clinical Significance of Transformation Conjugation and Transduction
Rapid spread of harmful bacteria genes
121 degree c (heat/pressure)
Heat resistant materials
Non-heat resistant materials
Ultra violet light
E.g. surfaces (operating rooms)
Not totally effective
Disinfection Liquids that kill bacteria
E.g. Phenol based
Too toxic for the skin surfaces
Eg. Iodine or 70% alcohol or isopropanol
Reduce bacterial load
Natural “antibiotics” (primitive medicine – e.g. Honey for cough?)
Chicken soup cures a cold?
What are Antibiotics
Antibiotics are any natural substances secreted by one microorganism against another
Irreversible drug. The effected microbes are dead
Reversible growth inhibition
Treatment of both is sufficient if host defenses mechanisms can take care of the residual
Antibiotics work together with the immune system
No (or limited) harm to patient
Destroy structures/ stop functions present in bacteria
Not present in host Diversity of Prokaryotes 9/17/2013 1:02:00 PM
Diversity of Prokaryotes
Grows best below 20 degrees C (psychrophiles)
Grows best between 20 – 50 Degrees C (mesophiles)
Grows best above 50 degrees C (thermophiles)
pH (Acidic or Basic) Environments
Grows well at pH of 1 to 2 (Acidic) (Acidophiles)
Grows best near neutral pH (Neutrophile)
Grow well at pH as high as 9 (basic) (Alkaliphile)
Most bacteria require a minimum moisture
Spores: near absence of moisture
Most bacteria require a moderate level of salt
Some cells can exist in very high salt concentrations (halophiles)
Require O2 for growth (aerobic)
Require lack of O2 for growt