Module 02 - Microbial Biochemistry and Metabolism Flashcards
what are some reasons why the study of microbial physiology is often done using biochemistry?
allows of researchers to understand the biological processes of microbes and organisms
Common elements found in organic molecules
most abundant elements in cells are hydrogen, carbon, oxygen, nitrogen, and sulfur (macronutrients)
micronutrients/trace elements of a cell
Na, K, Mg, Z, Fe, Ca, Mo, Cu, Co, Mn, V
four most abundant elements in living matter
carbon, nitrogen, oxygen, and hydrogen, they have low atomic numbers, can form strong bonds with other atoms
biomolecules
part of living matter, contain C (C is unique, has 4 valence electrons)
carbon skeleton
(chain) carbon atoms bind together in large numbers
- shapes: straight, branched or ring-shaped (cyclic)
- many lengths but usually long
isomers
molecules with same atomic makeup but different structural arrangments of atoms
- important for chemistry because strucutre of molecule is directly related to its function
structural isomers
compounds that have identical molecular formulas but differ in the bonding sequence of atoms
stereoisomers
isomers that differ in spatial arrangements of atoms
- unique type - enantiomer, have characteristic of chirality
chirality
nonsuperimposable mirror images of each other in structures, important characteristic in biologically important molecule
functional group in organic molecules
atoms put into groups based on their chemical composition and chemical reactions they perform
explain the formation of biological macromolecules by dehydration synthesis
Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts.`
carbohydrates
primarily a combination of carbon and water, they have empirical formula (CH2O)n, n=number of repeated units
- molecules are “hydrated” carbon atom chains and water molecules attach to each carbon atom
- ex. glucose/sugar
examples of monosaccharides
aldose and ketose
examples of polysaccharides
starch, glycogen, and cellulose (fiber)
monosaccharides
they are building blocks (monomers), produce and store energy
- classified based on number of carbons in a molecule
polysaccharides
(not sweet) not soluble in water, key functions are energy storage or structural support
explain why molecules with extremely diverse chemical structures can still be classified as lipids
lipids with long chain hydrocarbons terminated with a carboxylic acid functional group
- lipid molecules can also contain oxygen, nitrogen, sulfur and phospholipids
triacylglycerides
is formed when 3 fatty acids are chemically linked to a glycerol molecule
- three fatty acid chains are bound to glycerol by dehydration synthesis
phospholipids
phosphate group, two fatty acid carbon chains may be both saturated, both unsaturated or one of each
describe how phospholipids are used to construct biological membranes
they are used to construct biological membranes by their hydrophilic heads (water loving) and fatty acid tails that are hydrophobic (water hating)
amino acid
organic molecule in which a H atom, a carboxyl group (-COOH), and an amino group (-NH2) are all bonded to the same carbon atom, a carbon
side chain
fourth group thats bonded to the carbon varies among different amino acids.
primary structure
the sequence of amino acids that make up the polypeptide chain
secondary structures
chain is long, hydrogen bonding may occur between amine and carbonyl functional group within the peptide backbone (excluding R side group) which results in the localizing folding of a polypeptide chain into helices and sheets
alpha helix structure
held by H-bonds between the oxygen atom in carbonyl group of one amino acid and the hydrogen atoms of the amino group that is just 4 amino acid units farther along the chain
beta-pleated sheet
pleats are formed by similar H-bonds between continuous sequences of carbonyl and amino groups that are further seperated on the backbone of the polypeptide chain
tertiary structures
3D shape of a single polypeptide chain. the teritary structure is determined by interactions between amino acid residues that are far apart in the chain
- interactions give rise to protein tertiary structure (ex. disulfide bridges)
quaternary structures
proteins are assemblies known as protein subunits. proteins function well only when all subunits are present and appropriately configured
- protein consisting of more than one amino acid chain
- ex. hemoglobin has 4 globular protein subunits
conjugated proteins
non protein portion, carbohydrate attached called a glycoprotein
- if a lipid is attached its called a lipoprotein
metabolism
description for all chemical reactions within a cell
autotrophs
organisms that convert inorganic CO2 into organic carbon compounds
- ex. plants and cyanobacteria
heterotrophs
rely on more complex organic carbon compounds as nutrients; provided to them intially by autotrophs
phototrophs
gets energy for electron transfer from light
- ex. plants, algae, cyanobacteria, green and purple sulfur bacteria
chemotrophs
obtain energy for electron transfer by breaking chemical bonds
- 2 types: organotrophs and lithotrophs
- ex. hydrogen-, sulfur-, iron-, nitrogen-, and carbon monoxide-oxidizing bacteria, all animals, most fungi, protozoa and bacteria
oxidation reactions
reactions that remove electrons from donor molecules - leaving them oxidized.
reduction reaction
add electrons to accept molecules - leaving them reduced
redox reactions
electrons can move from one molecule to another, oxidation-reduction reactions occur
ATP
a cell must be able to handle energy release during catabolism that enables the cell to store energy safely and release it when needed (adenosine triphosphate)
- “energy currency” of cell
NAD+
(nicotinamide adenine dinucleotide) most common mobile electron carrier used in catabolism
- NAD+ is the oxidized form of the molecule, NADH is the reduced
NADP+
(nicotine adenine dinucleotide phosphate) oxidized form of an NAD+ vairant with an extra phosphate group, important electron carrier
FAD
oxidized form of flavin adenine dinucleotide
- important in cellular respirtaion - transfer of energy to the molecule FAD to covert it to FADH2 (reduction)
catalyst
substance that helps speed up reactions
- can be reused
enzymes
inorganic molecules that serve as catalyists for a wide range of chemical reactions (proteins), they serve as catalysts for biochemical reactions in a cell
activation energy
energy needed to form or break chemical bonds and convert reactants to products
substrates
chemical reactions where an enzyme binds to
active site
location of where the enzyme and substrate bind
glycolysis
is a cytoplasmic pathway which breaks down glucose into two three-carbon compounds and generates energy
- for bacteria, eukaryotes, most archaea, most common pathway for catabolism of glucose
- produces energy, reduced electron carrier, precursor molecules for cellular respiration
- universal metabolic mechanism
- anaerobic type of respiration
describe how the process of glycolysis produces three-carbon molecules, ATP, and NADH
glycolysis is the first step in breakdown of glucose, resulting in the formation of ATP, which is produced by a substrate-level phosphorylation; NADH; and two pyruvate molecules
Krebs cycle
The tricarboxylic acid (TCA) cycle, also known as citric acid cycle, is the main source of energy for cells and an important part of aerobic respiration.
products of Krebs cycle
3 NADH molecules, one FADH2, and one ATP by substrate-level phosphorylation, and releasing 2 CO2 molecules
electron transfer system (ETS)
last components in the process of cellular respiration, comprised of many membrane-associated protein complexes and associated mobile accessory electron carriers
- ETS is embedded into the cytoplasmic membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes
substrate-level phosphorylation
metabolism reaction that results in the production of ATP/GTp by the transfer of a phosphate group from a substrate directyl to ADP/GDP
oxidative phosphorylation
process of ATP synthesis is coupled to the movement of electrons through the mitochondrial electron transport chain and associated consumption of O2
chemiosmosis
flow of hydrogen ions across the membrane, must occur through a channel in the membrane via membrane-bound enzymes called ATP synthase
proton motive force
electrons are passed from NADH and FADH2 through ETS, the electrons lose energy, the energy is stored through the pumping of H+ across a membrane generating proton motive force
ATP synthase
complex protein that acts as a small generator, turning by the force of H+ diffusing through the enzyme, down their electrochemical gradient from many mutually repelling H+ to fewer H+
ATP synthase in prokaryotes
H+ flows from the outside of the cytoplasmic membrane into the cytoplasm
ATP synthase in eukaryotes
H+ flows from the intermembrane space to the mitochondrial matrix
aerobic respiration
the final electron acceptor at the end of the ETS is an oxygen molecule that becomes reduced to water by the final ETS
- A chemical process in which oxygen is used to make energy from carbohydrates (sugars)
anaerobic respiration
(alternate to aerobic respiration) using an inorganic molecules other than oxygen as a final electron acceptor
- found in bacteria and archaea
- occurs without oxygen and releases less energy but more quickly than aerobic respiration
fermentation
some living systems use an organic molecule (pyruvate) as a final electron accept through a process
- doesnt involve an ETS, and doesnt directly produce any additional ATP beyond already produced from glycolysis by substrate-level phosphorylation
- doesnt require oxygen because it is using an anaerobic pathway (non-oxygen requiring) for breaking down glucose
compare and contrast fermentation and anaerobic respiration
fermentation doesnt undergo citric acid cycle (Krebs cycle) and electron transport chain whereas anaerobic respiration undergoes citric acid cycle and electron transport chain
how can lipids enter catabolic pathways of central metabolism
the reaction breaksdown triglycerides, they are catalyzed by lipase and those involving phospholipids are catalyzed by phospholipase
- microbes use phospholipase to destroy lipids and phospholipids in host cells and then use the catabolic products for energy
- resulting prodcuts of lipid catabolism: glycerol and fatty acids can further be degraded
how can proteins enter catabolic pathways of central metabolism
proteins are degraded through a concerted action of a variety of microbe protease enzymes, degraded large proteins into small peptides
photosynthesis
biochemical process by which phototrophic organisms convert solar energy (sunlight) into chemical energy
- two stages: light dependent and light independent reactions
Location of photosynthesis of eukaryotes
photosynthesis takes place in the chloroplast, chloroplast are enclosed by a double membrane with inner and outer layers, within the chloroplast there is a 3rd membrane that forms stakes, disc shaped photosynthetic structures called thylakoids
location of photosynthesis of prokaryotes
photosynthetic membranes are not organized into distinct membrane-closed organelles, they are infolded regions of plasma membrane
pigment examples in photosynthesis
different kinds of light-harvesting absorb unique patterns of wavelengths (colours) of visible light
- bacteriochlorophylls (green, purple, red)
- chlorophylls (green)
light-dependent reactions
energy from sunlight is absorbed by pigment molecules in photosynthetic membranes and converted into stored chemical energy
- they produce ATP and NADPH/NADH to temporarily store energy
light-independent reactions
chemical energy produced by the light-dependent reactions is used to drive assembly of sugar molecules using CO2
- energy carried used in light-independent reactions to drive the energetically unfavourable process by “fixing” inorganic CO2 in organic form, sugar
noncyclic photophosphorylation
used in oxygenic photosynthesis when there is a need for both ATP and NADPh production
cyclic photophosphorylation
is a cells need for ATP is outweigh its need for NADPH
biogeochemical cycles
the recycling of inorganic matter between living organisms and their non-living environment
- geology and chemistry have an important role in the study of this process
carbon cycle
heterotrophs degrade organic molecules to produce CO2, whereas autotrophs fix CO2 to produce organics.
- methanogens typically form methane by using CO2 as a final electron acceptor during anaerobic respiration, oxidizes methane, using it as a carbon source
nitrogen cycle
nitrogen-fixing bacteria convert atmospheric nitrogen into ammonia (ammonification), the ammonia can be oxidized to nitrate and nitrite, nitates can be assimilated by plants. soil bacteria convert nitrate back to nitrogenous gas
sulfur cycling
many anoxygenic photosynthesizers and chemoautotrophs using hydrogen sulfide as an electron donor, producing elemental sulfur and then sulfate; sulfate-reducing bacteria and archaea then use sulfate as a final electron acceptor in anaerobic respiration, converting back to hydrogen sulfide
