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BIOL 228 > Module 02 - Microbial Biochemistry and Metabolism > Flashcards

Module 02 - Microbial Biochemistry and Metabolism Flashcards

1
Q

what are some reasons why the study of microbial physiology is often done using biochemistry?

A

allows of researchers to understand the biological processes of microbes and organisms

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2
Q

Common elements found in organic molecules

A

most abundant elements in cells are hydrogen, carbon, oxygen, nitrogen, and sulfur (macronutrients)

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3
Q

micronutrients/trace elements of a cell

A

Na, K, Mg, Z, Fe, Ca, Mo, Cu, Co, Mn, V

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4
Q

four most abundant elements in living matter

A

carbon, nitrogen, oxygen, and hydrogen, they have low atomic numbers, can form strong bonds with other atoms

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5
Q

biomolecules

A

part of living matter, contain C (C is unique, has 4 valence electrons)

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6
Q

carbon skeleton

A

(chain) carbon atoms bind together in large numbers
- shapes: straight, branched or ring-shaped (cyclic)
- many lengths but usually long

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7
Q

isomers

A

molecules with same atomic makeup but different structural arrangments of atoms
- important for chemistry because strucutre of molecule is directly related to its function

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8
Q

structural isomers

A

compounds that have identical molecular formulas but differ in the bonding sequence of atoms

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9
Q

stereoisomers

A

isomers that differ in spatial arrangements of atoms
- unique type - enantiomer, have characteristic of chirality

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10
Q

chirality

A

nonsuperimposable mirror images of each other in structures, important characteristic in biologically important molecule

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11
Q

functional group in organic molecules

A

atoms put into groups based on their chemical composition and chemical reactions they perform

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12
Q

explain the formation of biological macromolecules by dehydration synthesis

A

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.`

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13
Q

carbohydrates

A

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

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14
Q

examples of monosaccharides

A

aldose and ketose

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15
Q

examples of polysaccharides

A

starch, glycogen, and cellulose (fiber)

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16
Q

monosaccharides

A

they are building blocks (monomers), produce and store energy
- classified based on number of carbons in a molecule

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17
Q

polysaccharides

A

(not sweet) not soluble in water, key functions are energy storage or structural support

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18
Q

explain why molecules with extremely diverse chemical structures can still be classified as lipids

A

lipids with long chain hydrocarbons terminated with a carboxylic acid functional group
- lipid molecules can also contain oxygen, nitrogen, sulfur and phospholipids

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19
Q

triacylglycerides

A

is formed when 3 fatty acids are chemically linked to a glycerol molecule
- three fatty acid chains are bound to glycerol by dehydration synthesis

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20
Q

phospholipids

A

phosphate group, two fatty acid carbon chains may be both saturated, both unsaturated or one of each

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21
Q

describe how phospholipids are used to construct biological membranes

A

they are used to construct biological membranes by their hydrophilic heads (water loving) and fatty acid tails that are hydrophobic (water hating)

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22
Q

amino acid

A

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

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23
Q

side chain

A

fourth group thats bonded to the carbon varies among different amino acids.

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24
Q

primary structure

A

the sequence of amino acids that make up the polypeptide chain

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25
Q

secondary structures

A

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

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26
Q

alpha helix structure

A

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

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27
Q

beta-pleated sheet

A

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

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28
Q

tertiary structures

A

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)

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29
Q

quaternary structures

A

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

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30
Q

conjugated proteins

A

non protein portion, carbohydrate attached called a glycoprotein
- if a lipid is attached its called a lipoprotein

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31
Q

metabolism

A

description for all chemical reactions within a cell

32
Q

autotrophs

A

organisms that convert inorganic CO2 into organic carbon compounds
- ex. plants and cyanobacteria

33
Q

heterotrophs

A

rely on more complex organic carbon compounds as nutrients; provided to them intially by autotrophs

34
Q

phototrophs

A

gets energy for electron transfer from light
- ex. plants, algae, cyanobacteria, green and purple sulfur bacteria

35
Q

chemotrophs

A

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

36
Q

oxidation reactions

A

reactions that remove electrons from donor molecules - leaving them oxidized.

37
Q

reduction reaction

A

add electrons to accept molecules - leaving them reduced

38
Q

redox reactions

A

electrons can move from one molecule to another, oxidation-reduction reactions occur

39
Q

ATP

A

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

40
Q

NAD+

A

(nicotinamide adenine dinucleotide) most common mobile electron carrier used in catabolism
- NAD+ is the oxidized form of the molecule, NADH is the reduced

41
Q

NADP+

A

(nicotine adenine dinucleotide phosphate) oxidized form of an NAD+ vairant with an extra phosphate group, important electron carrier

42
Q

FAD

A

oxidized form of flavin adenine dinucleotide
- important in cellular respirtaion - transfer of energy to the molecule FAD to covert it to FADH2 (reduction)

43
Q

catalyst

A

substance that helps speed up reactions
- can be reused

44
Q

enzymes

A

inorganic molecules that serve as catalyists for a wide range of chemical reactions (proteins), they serve as catalysts for biochemical reactions in a cell

45
Q

activation energy

A

energy needed to form or break chemical bonds and convert reactants to products

46
Q

substrates

A

chemical reactions where an enzyme binds to

47
Q

active site

A

location of where the enzyme and substrate bind

48
Q

glycolysis

A

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

49
Q

describe how the process of glycolysis produces three-carbon molecules, ATP, and NADH

A

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

50
Q

Krebs cycle

A

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.

51
Q

products of Krebs cycle

A

3 NADH molecules, one FADH2, and one ATP by substrate-level phosphorylation, and releasing 2 CO2 molecules

52
Q

electron transfer system (ETS)

A

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

53
Q

substrate-level phosphorylation

A

metabolism reaction that results in the production of ATP/GTp by the transfer of a phosphate group from a substrate directyl to ADP/GDP

54
Q

oxidative phosphorylation

A

process of ATP synthesis is coupled to the movement of electrons through the mitochondrial electron transport chain and associated consumption of O2

55
Q

chemiosmosis

A

flow of hydrogen ions across the membrane, must occur through a channel in the membrane via membrane-bound enzymes called ATP synthase

56
Q

proton motive force

A

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

57
Q

ATP synthase

A

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+

58
Q

ATP synthase in prokaryotes

A

H+ flows from the outside of the cytoplasmic membrane into the cytoplasm

59
Q

ATP synthase in eukaryotes

A

H+ flows from the intermembrane space to the mitochondrial matrix

60
Q

aerobic respiration

A

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)

61
Q

anaerobic respiration

A

(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

62
Q

fermentation

A

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

63
Q

compare and contrast fermentation and anaerobic respiration

A

fermentation doesnt undergo citric acid cycle (Krebs cycle) and electron transport chain whereas anaerobic respiration undergoes citric acid cycle and electron transport chain

64
Q

how can lipids enter catabolic pathways of central metabolism

A

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

65
Q

how can proteins enter catabolic pathways of central metabolism

A

proteins are degraded through a concerted action of a variety of microbe protease enzymes, degraded large proteins into small peptides

66
Q

photosynthesis

A

biochemical process by which phototrophic organisms convert solar energy (sunlight) into chemical energy
- two stages: light dependent and light independent reactions

67
Q

Location of photosynthesis of eukaryotes

A

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

68
Q

location of photosynthesis of prokaryotes

A

photosynthetic membranes are not organized into distinct membrane-closed organelles, they are infolded regions of plasma membrane

69
Q

pigment examples in photosynthesis

A

different kinds of light-harvesting absorb unique patterns of wavelengths (colours) of visible light
- bacteriochlorophylls (green, purple, red)
- chlorophylls (green)

70
Q

light-dependent reactions

A

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

71
Q

light-independent reactions

A

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

72
Q

noncyclic photophosphorylation

A

used in oxygenic photosynthesis when there is a need for both ATP and NADPh production

73
Q

cyclic photophosphorylation

A

is a cells need for ATP is outweigh its need for NADPH

74
Q

biogeochemical cycles

A

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

75
Q

carbon cycle

A

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

76
Q

nitrogen cycle

A

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

77
Q

sulfur cycling

A

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

BIOL 228 (3 decks)

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