What is energy?
Ability to do work
What is potential energy?
Stored energy, like the chemical bonds in carbs, lipids, proteins and ATP
What is kinetic energy?
Energy of movement used to synthesize chemical compounds, transport substances across a membrane, or enable movement
What is oxidation-reduction reaction?
One atom is oxidized (loses one or more e-) while another atom is reduced (gains these e-)
Redox reaction = oxidation reaction paired with a reduction reaction
Dehydrogenation = an oxidation reaction in which one proton AND one e- are lost
What is phosphorylation?
Adding a phosphate -> storing energy
What is dephosphorylation?
Removing a phosphate -> releasing energy
What is ATP?
ADP + P = ATP (energy)
What are the mechanisms of phosphorylation to generate ATP from ADP?
1. Substrate Level Phosphorylation
2. Oxidative Phosphorylation
3. Photophosphorylation
What is substrate level phosphorylation?
Production of ATP from ADP by a direct transfer of a high-energy phosphate group from a phosphorylated intermediate metabolic compount in an exergonic catabolic pathway.
-(HETC) High-energy transfer compounds = intermediates during glycolysis and aerobic
What is oxidative phosphorylation?
Electrons are transferred from organic compounds to one group of electron carriers, called an electron transport chain (NAD+ or FAD)
-Can be used to generate ATP by Chemiosmosis.
What is photophosphorylation?
Using light energy to phosphorylate ADP to ATP.
-Needs light-trapping pigments such as chlorophylls.
Explain glycolysis and the three main stages.
Glycolysis is breaking down glucose to be used as energy.
1. Preparatory - 2 ATP's to activate glucose to form fructose 1,6-diphosphate.
2. Splitting - Glucose is split to form two glyceraldehyde-3-phosphate molecules.
3. Energy Harvest or Conserving - 4
What are the alternative pathways to glycolysis?
1. Pentose Phosphate Pathway
2. Entner-Doudoroff Pathway
What is the Pentose Phosphate Pathway?
Uses pentoses and NADPH
Operates simultaneously with glycolysis
What is the Entner-Doudoroff Pathway?
Produces NADPH and ATP
Does not need glycolysis or Pentose Phosphate Pathway
Explain the differences between aerobic respiration, anaerobic respiration and fermentation.
1. Cellular respiration = Aerobic and anaerobic
-Aerobic respiration:
--Final electron acceptor = an inorganic molecule
--36 ATP's in eukaryotes
--38 ATP's in prokaryotes
--Glucose --> CO2
--O2 --> H2O
-Anaerobic respiration
--Final electron acceptor = in
What are the catabolic products of fat catabolism and protein catabolism?
Proteins <-- broken down by proteases --> into amino acids --> go into Kreb's Cycle
Triglycerides <-- hydrolyzed by lipase --> fatty acids + glycerol
How many calories are produced from one molecule of carbohydrate from aerobic, anaerobic respiration, and fermentation?
Aerobic - 688,000 calories
Anaerobic - 425,000 calories
Fermentation - 54,000 calories
What is genetics?
Study of what genes are, how they carry information, how information is expressed, and how genes are replicated.
What is a gene?
Segment of DNA that encodes a functional product, usually a protein.
What is a genome?
All of the genetic material in a cell.
What is a genotype?
Genetic composition of an organism; its entire complement of DNA
What is a phenotype?
The expression of the genes: the proteins of the cell and the properties they confer on the organism.
What are the two DNA sequence elements that control initiation?
Promoter sequences (they promote recognition of transcriptional start sites by RNA POLYMERASE.
1. -35 position (TTGACA)
2. -10 position (aka PRIBNOW-BOX - TATAAT)
They are recognized and contacted by RNA polymerase.
What is a promoter?
Upstream of the start site of gene --> RNA polymerase is going to recognize promoter and thus initiate mRNA synthesis
What is an operator?
Traffic light that acts as a stop and go signal for transcription of the structural genes
What is an operon?
Promoter + Operator + Structural Gene
Where are the genes encoding enzymes that have a related function located?
Positioned in the same locus
What is polycistronic?
Bacteria
Multiple proteins coding on a single mRNA
A singly promoter is required to initiate transcription of all these genes
What is monocistronic?
Eukaryotes
One protein coding on one mRNA
What are the four major control points that result in regulated synthesis or activity of protein (enzyme)?
1. Transcriptional Regulation
2. RNA Processing
3. Translational Regulation
4. Protein Turnover
What happens during Transcriptional Regulation?
Activate or inactivate mRNA production
-In bacteria, the rate of Transcriptional Initiation is the predominant site for control of gene expression
What happens during RNA Processing?
Maturation or hydrolysis of RNA after production
What happens during Transitional Regulation?
Regulate the synthesis of proteins
What happens during Protein Turnover?
Hydrolyze protein after production
In bacteria, the rate of Transcriptional Initiation is the predominant site for what?
The control of gene expression
Are all genes in prokaryotes regulated?
No
What are Constitutive Genes?
Genes that are not regulated - always active
-Genes that are always turned on
-Genes are always needed
-Genes that code for enzymes of glycolytic pathway
Describe the regulated genes in prokaryotes.
#NAME?
What are Sigma Factors?
Bacterial cells use sigma factors, which help to control initiation of transcription.
-Sigma factor binds to RNA polymerase
-Sigma factor helps RNA polymerase find promoter
-Bacterial cells have different types of sigma factors specific for sets of genes
Besides the sigma factor of RNA polymerase, what else assists RNA polymerase in transcription of genes in prokaryotes and eukaryotes?
Regulatory proteins
What is Induction?
Turns ON a gene that is turned off
- Inducible genes are turned off unless a stimulus activates them
- Inducible genes are usually those used for catabolism (other than glucose catabolism)
- Example = Lac Operon
What is Repression?
Shuts OFF a gene that is turned on
- Repressible genes are normally on unless repressed
- Repressible genes are usually used for anabolism
- Example = Trp Operon
What is Catabolic Repression?
Genes that code for catabolic enzymes for substrates other than glucose are typically turned OFF when there is high glucose available.
- I.e., Lac Operon
- Low Glucose = high cAMP; cAMP binds to CRP (cAMP receptor protein); this complex stimulates RNA pol
Explain the Trp Operon.
Trp Operon = REPRESSIBLE gene
1. Anabolic pathway
2. Repressible because an overabundance of end product can repress the system (amount of enzyme varies inversely with amount of end-product)
3. E. coli naturally grows in your gut, and synthesizes Trp (Try
Explain the Lac operon.
Lac Operon = INDUCIBLE gene
1. Regulated catabolic pathway (i.e., lactose metabolism)
2. Inducible enzymes = synthesized in the presence of inducers
3. e.g., E. coli placed into a medium with lactose (inducer) -> B-galactosidase (inducible enzyme) is prod
How can bacteria change genetically?
Mutation
Transformation
Transduction
Conjugation
What is a mutation?
Change in the bacteria's chromosome
- Can be neutral, beneficial or harmful
What is a mutagen?
Agent that causes mutations
What can cause a mutation?
#NAME?
When can a mutation be lethal?
When there are irreversible changes to the cellular DNA
What can non-lethal mutation do?
Cause a heritable alteration of the genetic information
Are genetic changes more noticeable in germ line cells or somatic cells?
Germ line cells
What are the two main methods that DNA polymerases have for ensuring accuracy?
Base selection
Proofreading
What are the only base pairs that fit properly in the active site of the Polymerase?
AT and GC
What is a simple mutation?
Silent (neutral); the change in DNA base sequences causes no change in the activity of the product encoded by the gene.
What is a spontaneous mutation?
Occurs naturally (a normal mistake rate) about ONE IN EVERY MILLION TO ONE IN EVERY BILLION DIVISIONS and is probably due to a low level of natural mutagens normally present in the environment.
What is induced mutation?
Caused by MUTAGENS, substances that cause a much higher rate of mutation.
What are the types of spontaneous mutation?
Point mutations
Frameshift mutations
What are point mutations?
Substitution of a nucleotide: substitution of one deoxyribonucleotide for another during DNA replication.
What are the types of point mutations?
Substitution
Insertion
Deletion
Duplication
Inversion
What are frameshift mutations?
Deletion or addition of a nucleotide: deletion or addition of a deoxyribonucleotide during DNA replication.
What are the results of mutation?
Missense mutation
Nonsense mutation
Sense mutation
Frameshift mutation
What happens when a missense mutation occurs?
RESULTS IN ONE WRONG CODON AND ONE WRONG AMINO ACID.
What happens when a nonsense mutation occurs?
RESULTS IN A "STOP" CODON AND PREMATURE TERMINATION OF THE PROTEIN.
What happens when a sense mutation occurs?
RESULTS IN A NEW CODON WHICH STILL CODES FOR THE SAME AMINO ACID.
What happens when a frameshift mutation occurs?
RESULTS IN A READING FRAME SHIFT. ALL CODONS AND ALL AMINO ACIDS AFTER THE SHIFT ARE USUALLY WRONG.
What causes induced mutation?
Mutagens - substances that cause a much higher rate of mutation.
How do chemical mutagens work?
As intercalating agents or BASE ANALOGS
CHEMICAL MODIFICATIONS OF PURINE AND PYRIMIDINE BASES THAT ALTER THEIR HYDROGEN-BONDING PROPERTIES.
What does the microbicidal activity of ultraviolet (UV) light depend on?
The length of exposure - the longer the exposure the greater the cidal activity.
Also depends on wavelength of UV used - most cidal wavelengths of UV light lie in the 260 nm - 270 nm range where it is absorbed by nucleic acid.
How does ionizing radiation result in mutation?
X-rays and gamma rays
Much more energy and penetrating power than UV rad.
Forms radicals -> Breaks DNA strands and alter purine and pyrimidine bases.
What are the DNA repair mechanisms?
1. Proofreading by DNA polymerases
2. If not proofreading, Mismatched (post-replication) repair followed by excision repair.
What is excision repair?
Base excision or nucleotide excision = repair mutations that occur spontaneously
1. Base Excision
-- Damaged base position = Abasic Site OR AP Site
-- AP endonuclease removes the AP site and neighboring nucleotides
-- Gap is filled by DNA Polymerase I and
Explain what spectrum of antibiotics means.
The spectrum of an antibiotic represents how many different kinds of organisms it is effective against fighting and treating.
What is the classification of antimicrobial drugs?
1. Inhibition of cell wall synthesis
2. Inhibition of protein synthesis
3. Disruption of cytoplasmic membrane
4. Inhibition of metabolism
5. Inhibition of DNA/RNA synthesis
6. Block attachment
How do antimicrobial drugs inhibit cell wall synthesis?
- Bacterial cell wall is composed of peptidoglycan composed of NAG-NAM chains
- B-lactams --> prevent cross linkage of NAM subunits
- PENICILLIN, Vancomycin, Bacitracin, Isoniazid
How do antimicrobial drugs inhibit protein synthesis?
- 30S subunit and 50S subunit --> read codons and initiate protein synthesis (50S forms peptide bonds between amino acids)
- Aminoglycosides:
---Streptomycin & Gentomycin = change shape of 30S subunit
---Tetracycline = prevent amino acids from entering th
How do antimicrobial drugs disrupt the cytoplasm membrane?
- Fungi contain a sterol in their membranes called ergosterol (cholesterol in humans)
- Anti fungal drugs:
---Polyenes = attach to ergosterol in the membrane
---Azoles = inhibit ergosterol synthesis
-Polymyxin = disturbs phospholipid bilayers, and effecti
How do antimicrobial drugs inhibit metabolism?
- Sulfonamides = shut down DNA/RNA synthesis -> and thus protein synthesis
- Sulfonamides are structural analogues to PABA (a chemical critical in synthesis of nucleotides for DNA and RNA synthesis)
How do antimicrobial drugs inhibit DNA/RNA synthesis?
- Nucleotide analogs mimic normal nucleotides used to build DNA/RNA
-- Quinolones = attack DNA replication specifically by attacking an enzyme associated with DNA uncoiling (DNA Gyrase) [Doesn't effect eukaryotes or virus]
-- Rifampin = binds to bacterial
How do antimicrobial drugs block attachment?
#NAME?
What are common antibiotics used in veterinary clinics?
Polymyxin
Tetracycline
Erythromycin
Streptomycin
Gentamicin
Penicillin
Arildone
Rifampin
What does the effectiveness of antimicrobial treatments depend on?
1. Number of microbes
--- The more microbes, the longer to eliminate population
2. Environment (organic matter, temp, biofilms)
--- Organic material tends to inhibit antimicrobials (blood, feces, saliva)
3. Time of exposure
--- More effective at longer ti
What are the common physical methods of microbial control?
Moist heat
Autoclave
Pasteurization
Dry heat
Filtration
Low temperature
Desiccation
Osmotic pressure
How does moist heat control microbes?
Denatures proteins
What is autoclaving?
Steam under pressure
What is TDP?
Thermal death point
Lowest temp at which all cells are killed in 10 minutes
What is TDT?
Thermal death time
Time to kill all cells in a culture
What is DRT?
Decimal reduction time
Minutes to kill 90% of a population at a given temp
What is pasteurization?
Reduces spoilage by organisms and pathogens
63 C for 30 min
High temp for short time = 72 C for 15 seconds
Ultra high temp = 140 C for < 1 sec
--- Only Thermoduric organisms can survive
How does dry heat sterilization kill microbes? And what are examples?
Kills by oxidation
1. Flaming
2. Incineration
3. Hot-air sterilization
What is filtration?
Removing microbes (small holes where microbes can't pass through)
What are methods of low temperature inhibition of microbial growth?
Refrigeration
Deep freezing
Lyophilization
How does high pressure control microbes?
Denatures proteins
How does desiccation control microbes?
Prevents metabolism
How does osmotic pressure control microbes?
Causes plasmolysis
What are the chemicals (disinfectants) used commonly in household and disinfect hospital instruments?
Alcohols
Aldehydes
Biguanides
Ethylene Oxide Gas
Halogens
Metals
Ozone
Peroxygens
Phenolic Compounds
Quaternary Ammonium Compounds
How do alcohols disinfect?
Antiseptics to degerm skin and as disinfectants for treating instruments.
--Ethanol and Isopropanol
How do aldehydes disinfect?
Capable of destroying all forms of microbial life
--Glutaraldehyde = sterilize medical instruments
--Formalin = vaccine preparation
How do biguanides disinfect?
Destroys a wide range of microbes
--Chlorhexidine = antiseptic in soaps and lotions
How does ethylene oxide gas disinfect?
Penetrates hard to reach places; toxic, explosive, carcinogenic
--Sterilize medical devices
How do halogens disinfect?
Chlorine - disinfects inanimate objects, surfaces, drinking water and waste water
Iodine - disinfectant or antiseptic
How do metals disinfect?
Silver sulfadiazine - topical dressings to prevent infection of burns
Drop to prevent eye infections in newborns
Prevent microbial growth in industrial processes
How does ozone disinfect?
Disinfects drinking water and waste water
How do peroxygens disinfect?
Hydrogen peroxide - sterilize containers for juices and milk; limited because enzyme catalase breaks it down
Peracetic acid - disinfect and sterilize medical devices
How do phenolic compounds disinfect?
Toothpastes, lotions and deodorant soaps
--Hexachlorophene - against Staphylococcus Aureus, but an cause neurological damage
How do quaternary ammonium compounds disinfect?
Disinfects inanimate objects and preserves non-food substances