Microbiology 2 Flashcards
Anabolism
biosynthesis reaction
taking smaller molecules and bringing them together with energy to create larger molecules
hydrolysis
Endergonic reaction
require more energy than they produce
Catabolism
break a large molecule down into smaller molecules to create a lot of energy
hydrolysis
an exergonic reaction
coupled to ATP synthesis
Enzyme characteristics
mostly proteins
catalysts(speed up a reaction)
not consumed by the reaction
lower activation energy
Components of holoenzyme (active enzyme)
Apoenzyme
Coenzymes
Cofactors
Apoenzyme
protein component of holoenzyme
Coenzymes
vitamin derived, organic, carbon containing
Accept electrons or donate electrons
Cofactors
low molecular weight
metal ions
Enzyme inhibition
both can bind reversibly or irreversibly (suicide inhibitor)
Competitive inhibition
occurs at the active site
sulfa drugs compete with PABA (para-aminobenzoic acid) at the active site of an enzyme that converts PABA to folic acid
Is a substrate analog (look a-like) that binds to the active site
Overcome by increasing substrate concentration
Non-competitive inhibitor
inhibits the reaction
do not compete with substrate at binding site
adheres to another binding site to distort the substrate binding site
Feedback inhibition or end product inhibition
Reversible, non-competitive inhibition
End product accumulates and inhibits the first enzyme of a metabolic pathway which shuts down the pathway
Reaction rate influences
temperature
pH
substrate concentration
Temperature effect on reaction rate
a catalyst up to a point then hinders the reaction by enzyme denaturation
pH effect on reaction rate
too high or too low causes denaturation of H+ compete with hydrogen and ionic bonds in an enzyme
Substrate concentration effect on reaction rate
saturation is when an active site of an enzyme always has a substrate bound
The more substrate there is, the faster the reaction until saturation occurs, and then there is a plateau
Oxidation
loss of electrons gains oxygen loses hydrogen loss of energy exothermic/exergonic reaction
Two key players to the oxidation of organic compounds
Dehydrogenases-enzymes
Coenzymes
Coenzymes
vitamin derived organic molecules
a. Nicotinamide adenine dinucleotide (NAD) b. Flavinadenine dinucleotide (FAD)
Reduction
gain of electrons loss of oxygen gain of hydrogen gain of energy endothermic/endergonic reaction
Redox
combination of oxidation and reduction reactions they are used simultaneously
Substrate level phosphorylation
ATP is generated when a phosphate is transferred from an organic compound to ADP
Oxidative phosphorylation
uses chemiosmosis and electron transport chain to phosphorylate ADP
Total ATP generated
38 ATP per glucose molecule
NAD produces more ATP than FAD
Fat catabolism
a fat is a lipid consisting of glycerol + 3 fatty acids-can be broken into this using a lipase
Krebs cycle is used
Protein catabolism
uses the Krebs cycle
proteins are too large to pass through plasma membranes and must be broken down first
Deamination
Used in protein catabolism
can use protease to break protein into individual amino acids that are able to enter the Krebs cycle
Metabolism
the sum of all chemical reactions occurring within an organism
balances energy
two classes of reactions, gaining or losing energy
Fermentation
an anaerobic pathway
generally does not use oxygen
does not use Krebs cycle
electron transport chain
cannot occur in presence of O2
can still perform glycolysis to get 2 ATP, 2 NADH NAD+
organic molecule is the final electron acceptor-is pyruvate or a derivative of pyruvate
Homeolactic acid fermentation
one glucose molecule is converted to two molecules of lactic acid
Alcohol fermentation/ethanol fermentation
sugars such as glucose, fructose, and sucrose are converted into cellular energy and produce ethanol and carbon dioxide as metabolic waste products
Lactic acid fermentation
glucose, fructose, and sucrose are converted into cellular energy and the metabolite lactate
Lactate dehydrogenase catalyzes the conversion of pyruvate and lactate with concomitant conversion of NADH and NAD+
Nutritional factors effecting the growth of bacteria
carbon energy sulfur nitrogen phosphorus trace elements oxygen
Carbon source
cell needs external carbon source
this makes up 50% of the cell’s dry weight
users can be heterotrophic or autotrophic bacteria
Heterotrophic bacteria carbon use
carbon comes from organic compounds like lipids, proteins and carbohydrates
Autotrophic bacteria carbon use
they can use inorganic carbon like from carbon dioxide
they can fix O2 from the atmosphere
Uses for carbon
required for all organic compounds
Categories of energy users
phototrophic bacteria
chemotrophic bacteria
Phototrophic bacteria
organisms that use light
Chemotrophic bacteria
organisms that get energy from the oxidation of organic compounds and inorganic chemicals
Energy uses
metabolism, all cellular processes
Sulfur sources
sulfate ion (inorganic) proteins that have sulfur containing amino acids (organic)
Sulfur uses
sulfur containing amino acids for protein synthesis
thymine and biotin synthesis
Nitrogen sources
organic: proteins (contain amino acids), amino acid is denatured into NH2
inorganic: nitrogen gas (N2), NH4+, NO3
Nitrogen uses
required for synthesis of amino acids
synthesis of nitrogenous bases in DNA
synthesis of amino sugars—NAN, NAG
Phosphorus source
inorganic only—PO4 3-
Phosphorus uses
make ATP
nucleic acid backbone—synthesis of nucleotides
synthesis of phospholipids
Trace elements sources
inorganic only
ex: iron, copper, zinc, magnesium
Trace elements uses
cofactor for enzymatic reaction
required for synthesis of B12
bacteria have iron containing cytochrome in the electron transport chain
Superoxide dismutase
works of superoxide free radical to eliminate toxic forms of oxygen
Catalase
breaks down hydrogen peroxide to water and hydrogen gas
if bubbles form, catalase is present
2H2O2 2H2O + O2
Peroxidase
breaks down hydrogen peroxide
no O2 gas is produced
H2O2 + 2H+ 2H2O
Obligate anerobe
does not have superoxide dismutase, catalase or peroxidase
Facultative anerobe or aerobe
have superoxide dismutase, catalase and peroxidase
Physical factors affecting bacterial growth
some enzymes can adapt to be able to live in extreme environments like high salt, high heat and high or low pH temperature pH oxygen requirements osmotic pressure
Temperature affect on bacterial growth
there is an ideal temperature with steep drops on either end
Psychophile
optimal growth at 15C
ex: organisms that grow deep in the ocean
Mesophile
optimal temp = 37C (25-40 is ok too)
is most common type of microbe
Thermophile
heat loving microbes
optimal temp=50-60C
ex: microbes that grow in a compost heap
Neutrophiles
like a neutral pH
most bacteria like pH 6.5-7.5
Acidophiles
like pH 6 and below
ex: helicobacter pylori can grow at pH 2
Alkeliphiles
can grow at pH 7-11.5
Non-halophiles
grow at normal sodium levels
cannot survive high salt concentrations
Moderate/facultative halophiles
will grow at concentrations of 2-15% salt
doesn’t require high salt but can grow at high salt
Ex: pseudomonas, organisms involved in bioremediation (cleaning oil spills)
Obligate halophiles
require high salt concentration for growth
Extreme halophiles
require even higher salt concentration, > 15%
Ex: organisms from the dead sea grow at salt concentrations of 30%
Defined culture media
when we need to know everything that is in the growth media
we don’t use this in our labs
chemically defined is for research purposes only
Glucose culture media
carbon and energy source
Ammonium phosphate
nitrogen source and phosphate source
MgCl2
magnesium chloride provides trace metals
Sodium chloride
provides osmotic balance
K2HPO4
a buffer
can accept or donate protons to keep pH neutral
Fastidious
an organism that requires one or more growth factors (an essential organic compound that the bacterium cannot synthesize)
Complex culture media
chemically undefined
easier to grow than defined media
chemical compound of soy, beef, peptones or yeast extract-can vary
Agar
isolated from seaweed which can vary from batch to batch
any solid media is chemically undefined
Peptones
partially digested proteins that are easier for the bacteria to take up
if we add peptones, we add lots of different amino acids
TSA
tryptic digest of soy
trypsin is a protease, cleaves/digests soy proteins
Beef extract
adding this adds amino acids and vitamins
Selective media
ex: PEA will suppress the growth of certain microbes
suppresses growth of G- and gives G+ a chance to grow
Differential media
ex: Chrom agar E, causes pathogens to have different colors allowing for identification
ex: MSA, manitol salt agar, is also a selective media, has a pH indicator in it (phenol red), media is red at pH>6.8, media is yellow at pH <6.8, manitol ferments to change pH
Enrichment media
gives extra nutrition to fastidious organisms
ex: blood agar, does not suppress growth
Gas pak
has packet that when activated removes all O2 and creates H2 with it
Candle jar method
reduces O2 concentration
increases CO2 concentration
Binary fission
bacteria double in size before they split
is cell division in prokaryotes
is analogous to mitosis in eukaryotes
is asexual
Binary fission steps
i. DNA synthesis and elongation of the cell
ii. Cell begins to elongate
iii. Cross wall forms –> separates the 2 sets of chromosomes
iv. Binary fission/cell separates into 2 cells, all cells are clones of each other