IV.

Bacterial Biochemistry and Metabolism

a. Metabolism
o a type of bacteria uses to break down organic compounds.
o depends on the presence and activity of specific enzymes.
o Can be regulated by either regulating the production of the enzyme itself or regulating
the activity of the enzyme.
b. Fermentation and Respiration
 Bacteria use biochemical pathways to breakdown carbohydrates.
 produces energy by fermentation and oxidation.
 Fermentation, a chemical process by which molecules like glucose are broken down
anaerobically.
 Respiration, an efficient energy generating process in which molecular oxygen is the
final electron acceptor.

c. Biochemical Pathways from Glucose to Pyruvic Acid

 Glucose, the starting carbohydrate for bacterial fermentation.
 Pathways are designed to generate pyruvic acid
 Has 3 major biochemical pathways bacteria to break down glucose
1. Embden-Meyerhof-Parnas (EMP)
2. Pentese phosphate pathway
3. Entner-Doudoroff pathway

d. Anaerobic Utilization of Pyruvic Acid (Fermentation)

 A key metabolic intermediate
 pathways used by the microbes that inhabit the human body are:

1. Alcoholic fermentation: the end product is ethanol.

2. Homolactic fermentation: The end product is lactic acid.
3. Heterolactic fermentation: the end products include carbon dioxide, alcohols,
formic acid, and acetic acid.
4. Propionic acid fermentation: gram positive bacilli is the end product
5. Mixed acid fermentation: produce lactic, acetic, succinic, and formic acids as end
products.
6. Butanediol fermentation: The end products are acetoin (acetyl methyl carbinol) and
2,3-butanediol.

e. Aerobic Utilization of Pyruvate (Oxidation)

 pyruvate is oxidized
 carbon skeletons for biosynthetic reactions are created
 Pyruvate donates electron through an electron transport chain to form ATP.
 f. Carbohydrate Utilization and Lactose Fermentation
 fermentation of the sugar is detected by acid production and pH indicator.
 determination of the microorganism’s ability to ferment lactose.
 lactose fermenters or lactose nonfermenters.

V. Bacterial Genetics
a. Anatomy of a DNA and RNA Molecule

 DNA is a double helical chain of nucleotides twisted together like a spiral staircase
 Has a nucleotide with complex combinations of the following
1. A phosphate group (PO4)
2. A cyclic five-carbon pentose sugar
3. A nitrogen-containing base
 A purine consists of adenine & guanine
 A pyrimidine thymine & cytosine
 A nucleotide is a basic building block of nucleic acid
 Adenine of one chain always pairs with thymine of the other chain
 cytosine of one chain pairs with guanine of the other chain.
 The bases are held together by hydrogen bonds
 the two complementary sugar phosphate strands run antiparallel 3′ to 5′ and 5′ to 3′.
 RNA is single-stranded and short, contains sugar ribose
 In RNA, the nitrogenous base thymine is replaced by uracil
 Bacterial genome become a big part in microbiology
 Polymerase Chain Reaction or (PCR) technique amplifies specific DNA sequence to
detect bacteria present in the specimen.

b. Terminology

 Genotype, a genetic potential of the DNA of an organism

 protein synthesis is encoded in the bacterial DNA in the chromosome to each
generation of cells
 The general flow of information in a bacterial cell is from DNA to messenger RNA to the
actual protein itself.
 Replication is the duplication of chromosomal DNA for insertion into a daughter cell.
 Translation is the actual synthesis of a specific protein from the mRNA code.
 Proteins are polypeptide composed of amino acids
 Codons determines the number of sequences of amino acid in a polypeptide
 Ribosomes containing rRNA adds amino acids to the growing polypeptide chain and
brought back to ribosome by tRNA that translate the codons.
 tRNA molecules temporarily attach to mRNA using their complementary anticodon
regions
c. Genetic Elements and Alteration

Bacterial genome

 consists of a single, closed, circular piece of dsDNA that is supercoiled

 Genes are specific DNA sequences that code for the amino acid sequence in one protein

Extrachromosomal Elements

 bacteria contain extra information on small circular pieces of extrachromosomal, dsDNA

called plasmids
 plasmids are not essential for bacterial growth
 Genes that code for antibiotic resistance are often located on plasmids
 Plasmids are in the cytoplasm of the cell and are self-replicating just like DNA
 Antibiotic resistance genes are usually located in plasmids.

Mobile Genetic Elements

 Certain pieces of DNA are mobile also called as jumping genes

 simplest mobile piece of DNA is an insertion sequence (IS) element.
 Each IS element code for only one gene
 Bacterial genomes contain many IS elements.
 Transposons are related mobile elements that carry antibiotics

Mutations

 changes that occur in the DNA code and often result in a change in the coded protein or
in the prevention of its synthesis.
 Mutation can be result of a change in one nucleotide base
 Incomplete, inactive proteins are often the result of mutation
 Mutations also occur as the result of error during DNA replication

Mutations also occur as the result of error during DNA replication

 A method by which genes are transferred or exchanged between homologous regions

on 2 DNA molecules
 Provides the organisms to obtain new combinations

d. Mechanisms of Gene Transfer

can be transferred from one bacterium to another by

 Transformation
 Transduction
 Conjugation

Transformation
 the uptake and incorporation of naked DNA into a bacterial cell
 recombination takes plays by breaking down of DNA and recombined to produce new
combinations
 Cells that can take up naked DNA are referred to as being competent.
 Only a few bacterial species, such as Streptococcus pneumoniae, Neisseria gonorrhoeae, and H.
influenzae can do this naturally

Transduction
 transfer of bacterial genes by a bacteriophage from one cell to another

step by step on how Transduction occurs

1. Infection of the bacterial cell by bacteriophage.

2. the genome of the bacteriophage stably integrates into the chromosome of the host bacterium
and replicates in concert with it.

3. When these viruses infect another bacterial cell, they inject the viral DNA as well as donor DNA
into the host cell.
4. The bacterial DNA either forms plasmids or gets inserted into the recipient DNA if it is
homologous to the recipient genome.
 In the field of biotechnology, phages are often used to insert cloned genes into bacteria for
analysis.

Conjugation

 the transfer of genetic material from a donor bacterial strain to a recipient strain, Close contact
is required.
 In the E. coli system, the donor strain (F+) possesses a fertility factor (F factor) on a plasmid that
carries the genes for conjugative transfer.
 The first three letters in the restriction endonuclease name indicate the bacterial source of the
enzyme.