UF MCB3020 Exam 1 - Asghari

Microbes

Photosynthetic microbes changed the Earths atmosphere by releasing oxygen as a byproduct of photosynthesis. Valuable ecosystem services and maintain livability of the Earth. Organism that cannot be seen by the naked eye. NOT ALL MICROBES CAUSE DISEASES!

Antimicrobial Agents

Chemicals that kill bacteria; naturally produced by bacteria and fungi as defense mechanisms

Chemotherapeutics

General category of chemicals that protect against diseases

Microbiology

branch of biology that deals with microbes

Infectious diseases

When microbes grow and multiply after entering the body

1900 top causes of death:

Tuberculosis, pneumonia, diarrhea, enteritis

Top causes of death today:

Heart Disease, Cancer, Stroke

Why a decrease in the role of infectious diseases?

Dr. Asghari attributes this decrease to the discovery of antibiotics, vaccines, & greater attention to sanitation. (U.S. Department of Health recognized the role of dirty water in spreading infectious diseases.- Recommended chlorination of drinking water to rid it of microbes.)

Aristotle

Spontaneous Generation: living things could spontaneously arise from non-living things.

Louis Pasteur (The Father of Microbiology)

Disproved spontaneous generation with the swan neck flask experiment. (Germ Theory of Disease).

Also known for his work on pasteurization (for eliminating unwanted organisms in wine), working with vaccines for rabies, and perfected fermentation showing that yeast can turn sugar to ethanol.

Robert Hooke

Coined the term "cell". All organisms are made of cells.

Antony Van Leeuwenhoek

Discovered the first microscope, first to visualize microbes.

Edward Jenner

Developed first vaccine (smallpox vaccine).

He noticed that milkmaids almost never got the disease and hypothesized that it was because they were already exposed to a similar diseases( cowpox), allowing them to develop immunity.

Tested this theory by having a young boy have cowpox and then injecting him with smallpox.

His theory was correct. Smallpox- first human disease to be eradicated, no need for any vaccines.

Ignaz Semmelweis

Advocated hand washing. Suggested that women were more likely to die during childbirth at a hospital than at home because of the spread of diseases.

John Snow

Began science of epidemiology how diseases spread). Showed how cholera spreads in a contaminated water supply.

Robert Koch (Koch's Postulate)

Relationship between a microbe and a disease. "One microbe, One disease". This theory does not always hold true.

Discovered Bacillus anthracis.

Paul Ehrlich

Mixed and matched chemicals to find magic bullets for a disease.

Developed a drug called Salvarsann- treats syphilis

Alexander Fleming

Discovered penicillin, first antibiotic.

Frederick Griffith

Discovered genetic transformation

James Watson & Francis Crick

Discovered structure of DNA

Basic Research Microbiology

study of the classification of microbes , microbial processes, relationships between microbes and diseases.

Impact of microbes on CO2 & CH4 levels

Impact global climate change. Greenhouses form a "blanket" that traps heat".

Need greenhouse gases, but too much in the atmosphere causes global temperatures to gradually increase.

Applied Microbiology

application of our basic understanding or microbial processes and interactions.

Three Domains of life

Bacteria, Archaea, ( Porkaryotes)

Eukarya (fungi, plants, animals, algae, protozoans)

Hallmarks of Cells (All cells, whether prokaryote or eukaryote have this)

-Cell Membrane (controls what comes in and out)

-Genetic material, DNA in chromosomes

*Cells can have extrachromosmal DNA*

*Plasmids: small pieces of DNA that exist outside of the chromosome*

-Self replication

-Regulation across membranes

-Similar macromolecules

-Energy use

Prokaryotes

- Less than 0.5 to 2 microns

-No nuclei, DNA integrated in a nucleoid region

-DNA is circular

-Have plasmids

-Ribosomes

-CAN have cells walls, but dont have to

-Have a more active cell membrane than eukaryotes (ATP produced along membrane)

-Faster gene expression

Larger SA to V ratio, allowing more efficient nutrient transport 3

-Binary Fission: division of cell into two

-Gas Vacuole: makes cells buoyant in an aquatic environment

-Inclusion bodies: used for storage of nutrients such as carbon and phosphate. (PHB: poly-b-hydroxybutyrate, a carbon and energy source often stored here)

-Capsules and slime layers

-Pili and Fimbriae

-Endospore

Eukaryotes

-More than 10 microns large

-DNA in a nucleus

-DNA is linear

-Membrane bound organelles (mitochondria, Golgi apparatus, chloroplasts in plant cells, lysosomes in animal cells , endoplasmic reticula)

Mitochondria & Chloroplasts are though to have been integrated through endosymbiosis.*

-Extrachromosomal DNA found in mitochondria and chlorplasts

-Ribosomes

-CAN have cells walls, but dont have to

-Less active cell membrane (ATP produced in mitochondria organelle

-Slower gene expression

Five-Kingdom system

Monera, Protista, Fungi, Plantae, Animalia

Prokaryotes grouped in Monera.

Eukaryotes grouped in the rest.

Viruses are acellular & non-living, therefore not grouped into any group

Plasmids

-Small pieces of DNA that exist outside of the chromosome.

-Can contain bacterial-resistance genes or disease causing genes.

-Can be transferred from one bacterium to another.

Most of what we know about the function of human genes comes from our understanding of:

E.coli Bacteria

Micrometer =

Micron

Domain: Bacteria

Cell wall made up of peptidoglycan (or murein)

Only bacteria have endospores

Domain: Archaea

Cell wall made up pseudopeptidoglycan (or pseudomurein)

*Archaea do not cause diseases!! They are all "good" useful organisms. Sometimes called extremophiles*

Viruses (Acellular & Non-living)

-Lack cell membranes

-Genetic material is often RNA

-Cannot self-replicate

-Cannot regulate flow of materials

-Cannot use or produce energy

-Smaller than prokaryotes & eukaryotes

-Measured in nanometers

-Only visualized with electron microscopes

Other non-living & acellular infectious agents

-Prions (infectious proteins)

-Viroids (plant pathogens composed of infectious RNA)

Six major elements:

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur

Lipids

-C, H, O

-Polymers of fatty acids

-Hydrocarbons, insoluble

-Hydrophobic & do not interact with water

-Linkage: Ester Linkage

Two types of lipids:

Triglyceride and Phospholipids

Triglyceride

1 Glycerol + 3 Fatty Acids

Glycerol: An alcohol with hydroxyl groups attached to each of its three carbons

Fatty Acids: non-polar hydrocarbon chain. The carboxyl group is polar.

-All triglycerides are hydrophobic

Fat (triglyceride)

Solid at room temperature (saturated)

Oil (triglyceride)

Liquid at room temperature (unsaturated)

Saturated Fatty acids

-No double bonds

-Solid at room temperature

-No kinks

Unsaturated Fatty Acids

-Double bonds

-Liquid at room temperature

-Kinks

Phospholipids (primary building blocks of the plasma membrane)

Hydrophilic phosphate head + 2 Hydrophobic fatty acid tails

Hydrophilic Phosphate head

-Faces out towards the cytosol and extracellular fluid

-Interacts with the watery exterior and interior of the cell

Hydrophobic fatty acid tails

Face inward, facing each other within the cell membrane

Amphipathic Molecules

the dual hydrophilic/hydrophobic nature of phospholipids

Micelle

Forms when phospholipids clump together to form a ball

Polysaccharides (Carbohydrates)

-C,H,O

-Made of monomer subunits

-Linkage: Glycosidic Linkage

-Found in linear and ring structures. Ring structures give them more versatility & functionality.

Functions of Carbohydrates

-Structural support

-Nutrient and energy stores

-Cell membrane components (Glycoprotein & Glycolipid)

-Cell wall components

-Adhesion & formation of BioFilms

-Endotoxins

Monosaccaride

Carbohydrate monomers.

Ex. Glucose, fructose, galactose, ribose, deoxyribose

Disaccharide

Combination of two monosaccharides linked together

Polysaccharide

Many monosaccharides linked together

Starch is a polysaccharide of:

Glucose (*Monosaccharide*)

Starch

-Found in plants

-Digestible by humans

Cellulose

-Found in plants

-Not digestible by humans

Glycogen

Found in animals

Glycogen, chitin, cellulose, and starch are all made up of:

Glucose

Glucose

Found in most organisms and is the most important monosaccharide for the purpose of energy storage

Proteins

-C,H,O,N, and sometimes S

-Long chains of amino acids

-Linkage: Peptide Bonds

Amino Acids

1) Amino Group (NH2)

2) R Group (Determines polarity and acidity/basicity)

3) Carboxyl Group (COOH)

Functions of Proteins

-Enzymes being able to catalyze reactions

-Regulate cellular processes by turning metabolic activity on or off

-Provide structural support to cell

Shape of the protein determines its:

Function

Primary Structure

Amino acid sequence that makes up the backbone of the protein. This is crucial to protein structure and function)

Secondary Structure

-Alpha Helix and Beta-Pleated Sheet

Hydrogen Bonding plays a role in these

Tertiary Structure

-Refers to the bonds between the variable R groups of amino acids

Ex. Disulfide bridge

-Most proteins become functional once tertiary structure is achieved.

-Remember that peptide bonds, hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions all play a role in proper protein folding.

Quaternary Structure

Highest level of protein structure , formed by the combination of multiple polypeptides into functional units

Ex. Hemoglobin (carries oxygen in the blood, consists of four polypeptide components)

Denatured

-When the folding and conformation are changed, due to heat or other chemicals.

-Occurs under harsh conditions, such as high temperatures, extreme pH, and high salinity

-A denatured protein may maintain its primary structure by retaining its peptide bonds

-Once its denatured, it can sometimes return to normal

Fluid-Mosaic Model

The cell membrane consists of proteins floating in a sea of phospholipids

Transmembrane Proteins

Cross the entire cell membrane and interact with the intracellular and extracellular fluid

Signal Transduction

Process by which a signal is conveyed from the signal molecule to target molecules inside the cell with the help of proteins

Glycoproteins

-Protein with a sugar molecule attached to it.

-Act as signal receptors

-The signal molecule does not have to cross the cell membrane to have an effect within the cell.

Cells are mostly made of:

Protein

Nucleic Acids

-C,H,O,N,P

-Polymers of nucleotide bases

-Function to store, transmit, and use hereditary information

-Linkage: Phosphodiester Bonds

Nucleotide

1) 5-carbon sugar

2) Phosphate group

3) Nitrogenous Bases

Phosphodiester Linkage

Occurs between the hydroxyl group on 3' carbon of the pentose sugar on one nucleotide and the phosphate group on 5' carbon pentose sugar on another nucleotide, forming the "backbone"

DNA

-Deoxyribose sugar

-Adenine, Guanine, Cytosine, Thymine

-Store genetic information

-Double stranded

-Nucleotides are connected via. Hydrogen Bonds

-A + T : 2 hydrogens bonds

-C + G : 3 hydrogen bonds

RNA

-Ribose sugar

-Adenine, Guanine, Cytosine, Uracil

*Used for both storing information and structural support* (greater diversity in functions)

-Store genetic information

-mRNA (during transcription), tRNA (in translation), rRNA(structural role in ribosomes)

-Single stranded

Valence Electrons

Electrons in the outer orbital

Ionic Bonds

Electrons are transferred

Covalent Bonds

Electrons are shared

Hydrogen Bonds

-Weak bonds! "FON" (This weak nature is important because it means that the strands can easily be pulled for transcription and DNA replication)

-Plays a role in protein and DNA structures

-Plays a role in giving water its unique properties

Unique Properties of Water

-High boiling point (100 C) Hydrogen bonding raises the boiling point

-Temperature Buffer

-Excellent Solvent (because of polar nature). Water dissolves hydrophilic molecules, but no good interactions with hydrophobic.

Not "true bonds" but still hold molecules together and contribute to their 3-dimensional shapes

Hydrophobic interactions & Van der Waals Forces

Hydrophobic

Water-afraid

Hydrophilic

Water-loving

van der Waals forces

Weak attractions created when positive and negative charges come close to one another

Exergonic Reaction

Releases energy, forming bonds, energy stored by ATP.

Many exergonic reactions require an activation energy.

Endergonic Reaction

Absorbs energy, breaking bonds

Spontaneous

Releases free energy

Nonspontaneous

Absorbs free energy

Activation energy

Gets the reaction started. Puts the reactants into a transition state.

A barrier that inhibits the transition from reactants to products.

Transition state

Reaction will not start until it goes through the transition state, where the activation energy is added.

Catalysts (Enzymes)

-Speed up the reaction by lowering the activation energy

-Helps the system overcome the transition state

-Does not change the energy of reactants and products nor the energy released.

Condensation Reaction (dehydration synthesis)

Release water molecule, forming bond, anabolic pathway

Hydrolysis

Adds water molecule, breaking bonds, catabolic pathway

Functional Groups

Determine the unique properties of each molecule

Biofilm

-Complex of slime-enclosed colonies that stick to each other on a surface

-Can form on both living AND non living surfaces

Protects some of the bacteria from the effects of UV light, antibiotics , and desiccation (drying out)

-May engage in Quorum Sensing

Quorum Sensing

Strategy in which bacteria coordinate the expression of certain genes based on population density

Ex. Acylhomoserine lactone (AHL) Auto inducer molecule produced by Gram Negative organisms; induces the expression of virulence genes

Millimeter (mm)

10^-3, one-thousandth of a meter