Microbiology Exam 1

Microbiology

The study of microscopic organisms

What determines if an organism is a microorganism

size

Microorganism

• an organism whose size is measured in microns

• can be seen in detail only through a microscope

• include Bacteria, Archaea (prokaryotes), eukaryotes (and most parasites and viruses)

Characteristics of living organisms

• Metabolism - ALL

• Reproduction - ALL

• Differentiation - SOME

• Movement - SOME

• Communication - ALL

• Evolution - ALL

Metabolism

Done by all living organisms; uptake of nutrients from the environment, their transformation with in the cell, and elimination of wastes into the environment

Reproduction

Done by all living organisms; new cells from preexisting cells; growth

Differentiation

Done by some; some kind of change that can be detected as they grow; formation of a new cell structure

Movement

Done by some; motility; movement by self-propulsion

Communication

Done by all living organisms; interact primarily by means of chemicals that are released or taken up

Evolution

Done by all living organisms; all things evolve

Population

All organisms of the same species

Microbial ecology

The study of microorganisms in their natural environment and their relationships with one another

Antoni Van Leeuwenhoek

• first person to describe bacteria as individual cells

• developed the first high magnification lenses

• first person to view and report on bacteria

• developed the first simple microscope

Louis Pasteur

• pasteurization

• established the “germ theory of disease”: showed that infectious agents were living things for the first time

• Disproved “spontaneous generation” with swan neck experiment

Spontaneous Generation

People believed that if you had some sort of corrupted meat that flies just magically appeared

Swan neck experiment

• disproved spontaneous generation

• Contaminated flask neck does not contaminate the sterile liquid until the flask is tipped and the liquid mixes with the contaminated particles causing it to putrefy

Robert Koch

• first to demonstrate the role of bacteria in causing disease

• Germ theory of disease

• established four postulates

1st Kochs Postulates

The suspected pathogen must be present in all cases of the disease and absent from the healthy animals

2nd Kochs Postulates

The suspected pathogenic microorganism should be grown in pure culture - must be isolated

3rd Kochs Postulates

Cells of the pure culture of the suspected pathogen must cause disease in healthy animal; must have the same symptoms as animal with the original disease

4th Kochs postulate

The microorganism should be re-isolated and shown to be the same as the original in the culture

Elements of cell structure

• cell wall - In most bacteria, plants, archaea, and fungi

  • Outer membrane

  • Means no engulfment

  • Rigid structure outside cytoplasmic membrane

  • Provides support and protection from osmotic lysis (the cell bursting)

• Cytoplasmic membrane - in all cells

  • critical permeability barrier → separates inside from outside

Macromolecules

1. Proteins - amino acids

2. Nucleic acids - nucleocides

3. Lipids - fatty acids + glycerol

4. Polysaccharides - carbohydrates (a polymer of sugar)

Small organic molecules

1. Amino acids

2. Nucleotides

3. Fatty acids

4. Sugars

5. Communication molecules

Not typically found in high abundance inside the cell

Prokaryotes

• No nucleus

• smaller and less complex than eukaryotes but bigger and more complex than viruses

Eukaryotes

• Have a nucleus

• Larger and more complex than viruses and prokaryotes

• all multicellular life forms

Arrangement of DNA in Prokaryotes

• nucleoid - DNA just loosely in the cytoplasm; no real structure

• Single chromosome

  • singular circular DNA molecule that is usually a single protein

• Circular

• Haploid (one copy of each gene)

• Extra-chromosomal DNA - plasmid fission

• aprox. 1000 bases = 1 gene = 1 peptide = 300 amino acids

Arrangement of DNA in Eukaryotes

• nucleus

• linear

• diploid/haploid

• multiple chromosomes

• mitosis and meiosis

Viruses

• Not cellular

• obligate “parasites”: only way they can survive is by hijacking a cell

• Cannot reproduce themselves; synthesis is carried out by the host cell

• No growth (fixed size)

• Particles: bits and pieces of other cells

• Small

• Unable to carry out independent metabolism

Three domains of life

1. Archaea

2. Bacteria

3. Eukarya

Most genetic diversity

Bacteria

Least genetic diversity

Eukarya

LUCA

Last Universal Common Ancestor

Evolutionary Chronometer

evolutionary distance measured by differences in nucleotide or amino acid sequences

• bacteria rRNA: 16s

• Eukaryote rRNA: 18s

Three sources of energy

1. organic chemicals (or carbon)

2. inorganic chemicals

3. light

Chemoorganotrophs

Get energy from organic chemicals

• bacteria, archaea, eukarya

Chemolithotrophs

Get energy from inorganic chemicals; strips electrons off of inorganic compounds

• Bacteria, Archaea

Phototrophs

Get energy from light; have chlorophyll that contains electrons that get excited from the sun

Heterotrophs

derive carbon from organic carbon

Autorophs

Derive carbon from inorganic carbon

Gram Negative

• Have a cytoplasmic membrane, periplasmic space, peptidoglycan, and lipopolysaccharides - essential difference is that it has an outermembrane

• proteobacteria (largest phylum)

• extreme metabolic diversity

• red to pink stain

• have lipopolysachharides

Gram-positive bacteria

• Have a cytoplasmic membrane and peptidoglycan (which is thick and heavily crossed making it hard to remove stain)

• second largest phylum

• has a purple stain

Mycoplasma

relate to gram-positive but lack a cell wall; still cannot engulf

Cyanobacteria

• first to carry out oxygenic photosynthesis

Methanogens

Unique metabolism; responsible for production of all natural gas

Total weight of bacteria

aprox. 1.0 × 10^12 grams

Cells are made up of mostly…

macromolecules - most of which are proteins

Carboxylic acid

• functional group

• Source: organic, amino, and fatty acids; lipids; proteins

Aldehyde

• functional group

• Source: functional groups of reducing sugars such as glucose; polysaccharides

Alcohol

• functional group

• Source: lipids; carbohydrates

Keto

• functional group

• Source: pyruvate, citric acid cycle intermediates

Ester

• functional group

• Source: lipids of bacteria and eukarya; amino acid attachment to tRNAs

Phosphate ester

• functional group

• Source: nucleic acids, DNA and RNA

Thioester

• functional group

• Source: energy metabolism; biosynthesis of fatty acids

Ether

• functional group

• Source: lipids of Archaea, sphingolipids

Acid anhydride

• functional group

• Source: energy metabolism; ex: acetylphosphate

Phosphoanhydride

• functional group

• Source: energy metabolism; ex: ATP

Proteins are measured in

kilodalton

DNA is measured in

megadalton

Covalent bonds

Strong bonds

Hydrogen bonds

• easily broken and easily formed

• In strands of DNA:

  • Guanine and cytosine - triple H bond

  • Adenine and thymine - double H bond

Nucleotide

phosphate at the base

Nucleocide

No phosphate at the base

Polysachharides

• Carbohydrate polymers

• organic compounds containing carbon hydrogen and oxygen in a ratio of 1:2:1

• Most are D-form sugars

D-form sugar

• “dextrorotary” → means if you shine a light through it bends right

• OH on the right means D form

Alpha-1,4-glycosidic bond

• will NOT give you a branch

• Both down

alpha-1,6-glycosidic bond

• will give you a branch

• left up

beta-glycosidic bond

• left down

Lipids - fats

• fatty acids bound to glycerol

  • eukarya and bacteria: fats are esther linked

  • Archaea: fats are ether linked

• Contain both hydrophilic and hydrophobic components

• principle component of membranes

Nucleic acids

• DNA and RNA

  • can only be polymerized if there is an existing free 3’ hydroxy → polynucleotides are linked together in a 3’ to 5’ configuration → polymerize happens backwards so 5’ comes first

• Bases of nucleic acids are either purines or pyrimidines

Pyrimidine

• base of nucleic acids

• have one ring

• cytosine, thymine and uracil

Purine

• have two rings

• longer

• adenine and guanine

Three rules of biochemistry

1. biochem is backwards

2. biochem does not exist in the absence of water

3. biochem is stupid

Amino Acids

• monomeric units of proteins and polypeptides

• joined together by peptide linkage

• Has 4 groups

Ionizable acidic amino acid

• one of four groups of amino acids

  1. aspartate

  2. glutamate

Ionizable basic amino acid

• one of four groups of amino acids

  1. lysine

  2. arginine

  3. Histidine

Nonionizable polar amino acid

• one of four groups of amino acids

  1. serine

  2. cysteine

  3. theoronine

  4. asparagine

  5. Glutamine

  6. selenocysteine

  7. tyrosine

Nonpolar (hydrophobic) amino acid

• one of four groups of amino acids

  1. alanine

  2. valine

  3. leucine

  4. isoleucine

  5. methionine

  6. phenylaline

  7. tryptophan

  8. proline

L-form

• in amino acids - commonly used in biology

Primary structure

• the juxtaposition of alpha-carbon R groups dictates the primary structure of a protein (the amino acid sequence)

Secondary Structure

• determined by intramolecular hydrogen bonds

  1. alpha - helix

  2. beta - pleated sheets

  • Both in all proteins

Tertiary structure

• folding of the secondary structure and is “cemented” by the covalent bridging (which takes a lot to break) by Disulfide Linkages

Quaternary structure

• when one or more peptide chains interact via strong or weak molecular bonds

• separate peptide chains bonding together

Denaturation

• cannot be (in most cases) fixed

• occurs when secondary, tertiary, or quaternary structures are broken chemically or by heat or radiation

Parts of a microscope

1. ocular (lense)

2. objective (lense)

3. stage

4. condenser

5. focusing knobs

6. light

Limit of resolution

• 0.2 micrometers

  • anything smaller, you wont be able to see

• wavelength determines if you can see something → to increase resolution decrease amplitude

Staining

increases contrast for bright-field microscopy

Gram-staining

• shows phylogenic differences

  • gram negative are all genetically related to each other and gram positive are all genetically related to each other

• Gram-positive → purple

• Gram-negative → pink to red

Ribosomes

• responsible for synthesis of proteins

• composed of protein and ribonucleic acids

Inclusions

• NOT universal

• aggregates of storage compounds containing carbon (eg. starch), nitrogen, sulfur, or phosphorus

Coccus

• 1 of the 6 basic morphological structures of bacteria

• round

Rod (bacillus)

• 1 of the 6 basic morphological structures of bacteria

• Staff - long shaped

Spirillum

• 1 of the 6 basic morphological structures of bacteria

• Corkscrew

Spirochete

• 1 of the 6 basic morphological structures of bacteria

• wave

Appendaged

• 1 of the 6 basic morphological structures of bacteria

• has a thing sticking out

Filamentous

• 1 of the 6 basic morphological structures of bacteria

• long rod

Importance of smallness

• transport is a function of size

• sa/v ration decreases as size increases

• want a bigger sa/v ratio (meaning being smaller)

• being small means more nutrients it can take in and less to feed - less surface area to bring nutrients throughout the cell and get waste out

Size of bacteria in based on environment

• nutrient poor - get smaller

• nutrient rich (theres food for them) - get bigger

Reductive cell division

• divide in half without growing

• parent is larger than daughter cells

Structure of cytoplasmic membrane in eubacteria

1. phospholipid bilayer: fatty acid, glycerol, phosphate

2. integral membrane proteins: anchored proteins in the membrane;

   1. membrane strengthening proteins

      • eukaryotes and methanotrophs: use sterols (cholesterol)

      • bacteria: use hopanoids

• phospholipid bilayer formed from glycerol components esther linked to fatty acids