Unit 3: CHEMICAL PRINCIPLES:

In the 17th century scientist discovered the chemical and physical basis of living things, and soon realized that the chemicalorganization 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:

All living things on earth, including microorganisms, are composedof fundamental building blocks called elements

Elements: over 100 known to exist, cannot be decomposed bychemical means. Ex Oxygen, Carbon

Each element is composed of one particular kind of atom

Atom: smallest particle of an element that can enter intocombination 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 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

Center is Nucleus (makes up 90+ % of the weight of atom)

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

Bonds: Chemical bonds : forces of

attraction due to outer shell electrons

Three important types of chemical bonds are:

Ionic bonds: (between a metal and nonmetal) involves a loss or gain or electrons

Covalent bonds: (between 2 nonmetals) involves a sharing ofelectrons

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

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 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 the type of bond attracting water molecules to

one another. Weak bonds that gain strength in numbers

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, replacementreactions)

Inorganic compounds: 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. Water forms 4 hydrogen bonds

2. The polarity of water makes it an excellent dissolving medium (solvent)

3. The polarity accounts for water's characteristic role as a reactant orproduct in many chemical reactions.

4. The relatively strong hydrogen bonding between water molecules make water an excellent temperature buffer.

Acid and Bases: 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 6.5-8.5)

Acids and bases

Acids: substances which

when dissolved are hydrogen donors (proton donors)

Base: substances which

when dissolved are hydrogen acceptors (proton acceptors)

Also called alkaline

PH Scale

Ranges from 0 t0 14 Less than 7 = acid greater than 7= base 7= neutral

ORGANIC COMPOUNDS; 1. carbohydrates; used by microorganisms as

source of energy. Also serves as a structural component of microbial cell wall.

a. glucose; (monosaccharide) is basic form of fuel for many species of microorganisms

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

GENETICS - Science of heredity. CHROMOSOMES - Cellular structures

composed of DNA that carry hereditary information

DNA

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 Nucleotides

A, G, T, C Sugar and phosphate

form the backbone Bases lie between the

backbone Held together by

H-bonds between the bases A-T – 2 H bonds G-C – 3 H bonds

H - Bonds Base-pairing rules

AT only (AU if DNA-RNA hybrid)

GC only DNA strand has

directionality – one end is different from the other end

2 strands are anti-parallel, run in opposite directions Complementarily results Important to replication

Helical Structure

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.

Many bacteria (some yeast/fungus) also possess looped bits of DNA

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.

Eukaryotes; have 2 or more chromosomes composed of double stranded DNA.

DNA: discovered 1953 by Watson and Crick. Composed of 5 carbon sugar (deoxyribose) nitrogen base pairs, and a phosphate group

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 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.

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: RNA: A single strand of nucleic acid composed

of the sugar-ribose, a phosphate group, and nitrogen bases.

Nitrogen Bases of RNA: 1. Adenine 2. Uracil Adenine always, joins ,with uracil. 3. Cytosine . 4. Guanine Guanine alwaysjoins,with_cytosine

Three. types of RNA1. mRNA - messenger RNA - takes the

message from the chromosome to the ribosome.

2. tRNA -transfer RNA - takes the appropriate amino acid to the ribosome.

3. rRNA - the type of RNA found in the ribosome.

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.

During transcription, a strand of mRNA is synthesized using a specific gene--a portion of the Cell's DNA--as a template.

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.

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.

The endpoint for transcription of the gene is signaled by a terminator region in the DNA. (UAA, UAG, UGA)

After transcription the message on the tnRNA is translated by a ribosome.

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

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. The ribosome attaches to the mRNA 'and reads the start Codon.

2. The first tRNA (with its amino acid) base pairs with mRNA at the start Codon.

3. As the ribosome moves to the second Codon, a second tRNA molecule (with its animo acid) moves into position on the second Codon.

4. 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. The ribosome moves along the mRNA to the next Codon.

6. As the proper amino acids are brought into position one by one, peptide bonds form the amino acids, and a polypeptide chain is formed.

7. 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.

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 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.

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 : 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. nitrous acid - converts adenine to a form that no longer pairs with thymine but instead pairs with cytosine.

2. 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 1.X- rays and gamma rays - have ability to ionize atoms

and molecules.

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.

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.

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.

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.

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.

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;1. 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.2. Site specific recombination; involves integration of viral

genome into bacterial chromosome.3. 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.

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.

TRANSFORMATION; 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.

A single stranded fragment then replaces a similar but not identical fragment in the recipient organism, and the transformation is complete

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 transformation1. requires direct cell-to-cell contact.

2. 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; 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. Phage attaches to bacterial cell wall and injects its DNA

into the cell.2. 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.

3. Occasionally during phage assembly, pieces of bacterial DNA are packaged in the phage capsid.

4. 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

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