Download Unit 3: CHEMICAL PRINCIPLES:

Unit 3: CHEMICAL
PRINCIPLES:
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In the 17th century scientist discovered the
chemical and physical basis of living things,
and soon realized that the chemical
organization of all living things is
remarkably similar.
Microorganisms, as living things conform to
this principle and have chemical basis that
underlies their metabolism
Chemical Principles:
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All living things on earth, including
microorganisms, are composed
of fundamental building blocks called elements
Elements: over 100 known to exist, cannot be
decomposed by
chemical means. Ex Oxygen, Carbon
Each element is composed of one particular kind of
atom
Atom: smallest particle of an element that can
enter into
combination with atoms of other elements.
Atom
 Fundamental
unit of matter
 Discovered by Democritus
3000yrs ago
 Proved by John Daltons in
his Atomic theory
Components of Atom
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Proton :Positive charge ( in nucleus) ( id
Number of element)(atomic #)
Neutron: neutral charge ( in nucleus)
Electron :negative charge ( outside nucleus)
Protons + neutrons = atomic weight
Most of mass of atom is in nucleus
Most space of atom is electron cloud
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Center is Nucleus (makes up 90+ % of the weight
of atom)
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protons + neutrons — atomic weight of element
Surrounding the nucleus is electron cloud
(electrons negative charge)
Outer shell electrons (valence electrons) determine
the characteristics of elements.
Atoms tend to gain, lose or share electrons until
their outer shells are stable with 8 electrons in the
outer shell
This rearrangement of electrons is known as
chemical bonds
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Bonds:
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Chemical bonds : forces of
attraction due to outer shell electrons
Three important types of chemical bonds
are:
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Ionic bonds: (between a metal and nonmetal) involves a loss
or gain or electrons
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Covalent bonds: (between 2 nonmetals) involves a sharing
of
electrons
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Hydrogen bonds: exist when a hydrogen atom covalently
bonded to one oxygen or nitrogen atom is attracted to
another oxygen or nitrogen bond...it forms weak links
between different molecules or between part of the same
large molecule.
Ionic Bonds
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Gaining and losing electrons ( metal and
nonmetal)
Ionic compounds in water tend to dissociate
into free ions for other chemical reaction.
Dissolved ionic compounds are in all aqueous
solutions of living things, and are critical to normal
operation of body/cell systems
covalent bond
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The covalent bond involves a sharing of
electrons between two nonmetals.
The sharing of electrons can be an equal
sharing ( nonpolar), or an unequal sharing
(polar)
Hydrogen Bonding
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the type of bond attracting water molecules to
one another.
Weak bonds that gain strength in numbers
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Most microbial compounds of interest are
composed of molecules.
Molecule: a precise arrangement of atoms from
different elements (made up of 2 or more atoms)
Compound: a mass of molecules consisting of at
least 2 different kinds of atoms
Chemical reactions: The making and breaking of
chemical bonds (includes: synthesis,
decomposition, replacement
reactions)
Inorganic compounds:
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All living organisms require a wide variety of
inorganic compounds for growth, repair,
maintenance, and reproduction.
Water is one of the most important as well as
abundant of these compounds, and it is
particularly vital to microorganisms.
Water has structural and chemical properties
that make it particularly suitable for its role
in living cells.
Characteristics of water:
1.
2.
3.
4.
Water forms 4 hydrogen bonds
The polarity of water makes it an excellent
dissolving medium (solvent)
The polarity accounts for water's characteristic
role as a reactant or
product in many chemical reactions.
The relatively strong hydrogen bonding between
water molecules make water an excellent
temperature buffer.
Acid and Bases:
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The term pH refers to the concentration of
H+ in a solution.
A solution with a pH of 7 is neutral; a pH
less than 7 is acidic, and greater than 7 is
basic.
A pH buffer, which stabilizes the pH inside a
cell, can be used in culture media (most
microorganisms grow best at a pH of 6.58.5)
Acids and bases
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Acids:
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Base:
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substances which
when dissolved are
hydrogen donors
(proton donors)
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substances which
when dissolved are
hydrogen acceptors
(proton acceptors)
Also called alkaline
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PH Scale
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Ranges from 0 t0 14
Less than 7 = acid greater than 7= base
7= neutral
ORGANIC COMPOUNDS;
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1. carbohydrates; used by microorganisms as
source of energy. Also serves as a structural
component of microbial cell wall.
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a. glucose; (monosaccharide) is basic form of fuel
for many species of microorganisms
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b. lactose; (disaccharide) carbohydrate in milk
that is digested to acid by microorganisms when
they sour milk and form sour milk products such
as yogurt and sour cream.
2.
lipids; some microorganisms use fat as energy
source. They produce the enzyme lipase which
breaks down fats to fatty acids and glycerol
3.
Proteins; Major molecule from which
microorganisms are constructed, also reservoir
source of energy for microorganism.
4.
4. Nucleic acids; Microorganism contain 2
import types of nucleic acids: DNA, RNA
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GENETICS - Science of heredity.
CHROMOSOMES - Cellular structures
composed of DNA that carry hereditary
information
DNA
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The 5 carbon sugar
(PENTOSE) is
Deoxyribose
It is double stranded
DNA is found in the
nucleus of the cell
Composed of sugar,
phosphate and nitrogen
base pairs
DNA is a Double Helix
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Nucleotides
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A, G, T, C
Sugar and phosphate
form the backbone
Bases lie between the
backbone
Held together by
H-bonds between the
bases
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A-T – 2 H bonds
G-C – 3 H bonds
H - Bonds
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Base-pairing rules
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AT only (AU if DNARNA hybrid)
GC only
DNA strand has
directionality – one end is
different from the other end
2 strands are anti-parallel,
run in opposite directions
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Complementarily results
Important to replication
Helical Structure
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Nucleotide: The base unit of a DNA
molecule composed of the sugar
deoxyribose, a phosphate group and one of
the four nitrogen bases.
Bacteria; possess a single chromosome composed of
double stranded DNA.
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Many bacteria (some yeast/fungus) also possess
looped bits of DNA
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Bacteria have relatively few genes and are not
essential for bacteria to survive in host, but may
impart antibiotic resistance or increase the
pathogenicity of the host bacteria.
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Eukaryotes; have 2 or more chromosomes
composed of double stranded DNA.
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DNA: discovered 1953 by Watson and
Crick. Composed of 5 carbon sugar
(deoxyribose) nitrogen base pairs, and a
phosphate group
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The DNA"of E coli has about 4 million
base pairs and is about 1mm long - 1000
times longer than the entire cell.
Makes up about 10% of cell's volume.
DNA REPLICATION
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DNA REPLICATION - One "parental" double-stranded
DNA molecule is converted to two "daughter" molecules.
The Parental DNA unwinds and separates from each
other as the hydrogen bonds holding the nitrogen bases
together breaks apart.
Each side of the parental DNA joins with nucleotides
having the appropriate complementary nitrogen base,
thus 2 duplicate strands are formed.
An enzyme, •DNA polymerase) joins the nitrogen, bases to
the parental strands.
DNA synthesis is a surprisingly fast process: about 1000
nucleotides per second in E. coli growing at 37 Degrees C.
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After Synthesis has occurred, one old
strand of DNA unites with a new strand to
form the double helix.
Thus, the old strand of DNA directs the
synthesis of a new strand of DNA through
complementary base pairing.
This is the Semiconservative Model.
RNA:
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RNA: A single strand of nucleic acid composed of
the sugar-ribose, a phosphate group, and nitrogen
bases.
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Nitrogen Bases of RNA:
1. Adenine
2. Uracil
Adenine always, joins ,with uracil.
3. Cytosine .
4. Guanine
Guanine alwaysjoins,with_cytosine
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Three. types of RNA
1.
2.
3.
mRNA - messenger RNA - takes the
message from the chromosome to the
ribosome.
tRNA -transfer RNA - takes the
appropriate amino acid to the ribosome.
rRNA - the type of RNA found in the
ribosome.
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PROTEIN SYNTHESIS - The information
in DNA is used to make the proteins that
control the cell's activities.
TRANSCRIPTION-;- Genetic information
in DNA is copied, or transcribed, into a
complementary base sequence of mRNA.
TRANSLATION : The process by which
the message in mRNA is translated by "the
'ribosome to make the appropriate protein.
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During transcription, a strand of mRNA is synthesized
using a specific gene--a portion of the Cell's DNA--as a
template.
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During this process the nitrogen bases join as they would
to make DNA with the exception of adenine which joins
with URACIL instead of thymine.
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The process of transcription requires both an enzyme
called RNA polymerase and a supply of RNA nucleotides.
Transcription begins after RNA polymerase binds to
DNA at a site called promoter.
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The endpoint for transcription of the gene is signaled by a
terminator region in the DNA. (UAA, UAG, UGA)
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After transcription the message on the tnRNA is
translated by a ribosome.
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At the start of translation, the two ribosomal
subunits come together with the mRNA.
In the cytoplasm are 20 different types of amino
acids that participate in protein synthesis.
Before the appropriate amino acids can be joined
together to form a protein, they must be activated
by attachment to transfer RNA.
For each different amino acid there is a specific
tRNA, and during amino acid activation each
amino acid attaches to its specific tRNA.
A specific enzyme and energy from ATP is
necessary for the attachment
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Codon-Set of three nucleotides on mRNA
that code for a particular amino acid.
Anticodon-set of three complementary
nucleotides on the tRNA,
During translation, the anticodon of a
molecule of tRNA hydrogen bonds to its
complementary Codon on mRNA.
Steps in Translation:
1.
2.
3.
4.
The ribosome attaches to the mRNA 'and reads
the start Codon.
The first tRNA (with its amino acid) base pairs
with mRNA at the start Codon.
As the ribosome moves to the second Codon, a
second tRNA molecule (with its animo acid)
moves into position on the second Codon.
The two amino acids are then joined by a peptide
bond, and the first tRNA molecule leaves the
ribosome and goes to pick up another amino
acid.
5.
6.
7.
The ribosome moves along the mRNA to the next
Codon.
As the proper amino acids are brought into
position one by one, peptide bonds form the
amino acids, and a polypeptide chain is formed.
One of three special stop colons in the mRNA
signals the end of the polypeptide chain, at
which time the chain is released from the
ribosome.
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The typical mRNA has about 300 codons and is
about 900 nucleotides long.
The DNA of E. coli contains about 4000 genes
and can specify about 4000 different kinds of
proteins.
Sense codons code for amino acids.
Nonsense codons (stop codons) - UAA, UAG,
UGA, - signal the end of a protein molecule's
synthesis.
Repression
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Repression: a regulatory mechanism that
inhibits gene expression and decreases the
synthesis of enzymes.
Repression is mediated by regulatory
proteins, called repressors, which block the
ability of RNA polymerase to initiate
transcription from the repressed genes.
Repression is usually the response to an
overabundance of an end-product.
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Induction: the process that turns on the
transcription of a gene.
A substance that acts to induce transcription of a
gene is called an inducer, and enzymes that are
synthesized in the presence of inducers are
inducible enzymes.
Mutation: Change in the base sequence of DNA.
Types of mutations :
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point mutations - single base at one point in the
DNA is replaced with a different base.frameshift mutations - one or a few nucleotide
pairs are deleted on inserted in the DNA. .
Mutagens - agents in the environment, such as
certain chemicals and radiation, that directly or
indirectly bring about mutations.
Chemical Mutagens - Examples
1.
2.
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nitrous acid - converts adenine to a form that no
longer pairs with thymine but instead pairs with
cytosine.
base analog - molecules that are structurally
similar to normal nitrogen bases, but have
slightly altered base-pairing properties.
Some antiviral and antitumor drugs are base
analogs.
frameshift mutagens - cause small deletions or
insertions in the
Radiation Mutagens : examples
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1.X- rays and gamma rays - have ability to ionize atoms
and molecules.
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Some of these ions can combine with bases in DNA,
resulting in errors in DNA replication and repair that
produce mutations.
Can break the covalent bonds between the sugars and
phosphates making the sides of the ladder.
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2 ultraviolet light '-"causes' the formation of covalent
bonds between adjacent thymines in a DNA strand.
The dimers of thymine keep the cell from properly
transcribing or replicating its DNA.
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The spontaneous rate of mutation is about
once in a million replicated genes
Mutagens increase the mutation rate to
once in 100,000 to once in 1,000.
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The probability of a mutation occurring during
cellular division is known as Mutation Rate.
In bacteria, spontaneous mutation rates are about
1 in 1 billion meaning that in every population of
a billion cells, there is at least one mutation,
which may never be expressed.
However if the mutation renders antibiotic
resistance, than the mutant will survive when
antibiotic s are applied to the population and new
colonies of antibiotic resistant bacteria will
emerge.
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Genetic recombination-the exchange of genes
between two DNA molecules to form new
combinations of genes on a chromosome..
Donor cell - gives a portion of its total DNA to
another cell.
Recipient cell - receives a portion of a donor cell's
DNA.
Recombinant - the recipient cell that incorporates
donor DNA into its own DNA.
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In recombination: a new chromosome with
a genotype different from that of the
parents results from the combination of
genetic material from 2 organisms.
There are several kinds of
recombination's;
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2.
3.
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General recombination: most common. Involves
reciprocal exchange of DNA between a pair of DNA
sequences.
Occurs anywhere on microbial chromosomes.
Typical of bacterial transformation and bacterial
recombination and bacterial transduction.
Site specific recombination; involves integration of viral
genome into bacterial chromosome.
Replicate recombination; due to movement of genetic
elements as they switch positions from one place to
another (on chromosome)
The principles of recombination apply to prokaryotic
microorganisms but not to Eukaryotic microorganisms
WAYS GENETIC RECOMBINATION
TAKES PLACE:
1.
Transformation - genes are transferred from one
bacterium to another as naked DNA solutions.
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Some bacteria, release their DNA into the environment.
Other bacteria can then encounter the DNA and,
depending on the particular species and growth
conditions, take up fragments of DNA and integrate them
into their own chromosomes by recombination.
Transformation occurs naturally among very few genera
of Bacteria. ex include Bacillus, Hemophilus, Neisseria/
Acinetobactor, and certain strains of the genera
Streptococcus and Staphylococcus .
Competence - The physiological state of the cell in which
it can take up donor DNA.
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TRANSFORMATION;
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Discoved in 1928 by Frederick Griffith (pneumococci
causes bacterial
pneumonia)
Discoved if he mixed fragments of dead pathogenic
pneumococci with
specimens of live harmless pneumococci they took on
genes of the bacterial fragments and became pathogenic.
Thus first demonstration that bacteria could undergo
genetic changes.
During transformation, competent cells take up DNA and
destroy one strand of double helix.
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A single stranded fragment then replaces a
similar but not identical fragment in the recipient
organism, and the transformation is complete
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This has been studied in detail in Streptococcus
pneumonia and Haemophilus influenza
2.
Conjugation - A mechanism by which
genetic material is transferred from one
bacterium to another using one kind of
plasmid"
2 Ways Conjugation differs from
transformation
1.
2.
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requires direct cell-to-cell contact.
conjugating cells must generally be of opposite
"mating type"; donor cells must carry the
plasmid and recipient cells do not.
During conjugation, the plasmid is replicated
during transfer of a single-stranded copy of the
plasmid DNA to the recipient where the
complementary strand is synthesized.
Conjugation;
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2 bacterial cells come together and mate
such that a gene transfer occurs between
them.
One cell, the Donor cell(F+) gives up DNA
and the other cell, the recipient (F-)
receives DNA.
Transfer is nonreciprocal
3.
. Transduction - Bacterial DNA is
transferred from a donor cell to a recipient
cell inside a virus that infects bacteria.
Steps in generalized transduction
1.
2.
3.
4.
Phage attaches to bacterial cell wall and injects its DNA
into the cell.
Phage DNA acts as a template for making new phage
DNA and directs the synthesis of phage protein coats.
The bacterial chromosome is broken apart by phage
enzymes.
Occasionally during phage assembly, pieces of bacterial
DNA are packaged in the phage capsid.
A phage carrying bacterial DNA infects a new host cell,
the recipient cell and bacterial genes will be transferred
to the newly infected recipient cell at low frequence
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Transposony small segments of DNA that
can move from one region of the DNA
molecule to another. (jumping genes)
TRANSDUCTION;
Bacteria virus (bacteriophage) transfer
DNA fragments from one bacteria to
another bacteria