Micro Exam 2- Ch. 5 Flashcards
Buildup and breakdown of nutrients within a cell to provide
energy and create substances that sustain life
Metabolism
breaks down complex molecules; provides
energy and building blocks for anabolism; exergonic
Catabolism
(of a metabolic or chemical process) accompanied by the release of energy.
Exceronic
uses energy and building blocks to build
complex molecules; endergonic
Anabolism
(of a metabolic or chemical process) accompanied by or requiring the absorption of energy, the products being of greater free energy than the reactants.
Endergonic
Catabolic and Anabolic Reactions
• Metabolic pathways are sequences of
enzymatically catalyzed chemical reactions in a
cell
• Enzymes are encoded by genes
Enzyme catalysis
is the increase in the rate of a process by a biological molecule, an “enzyme”.
states that chemical
reactions occur when atoms, ions, and molecules
collide
Collision Theory
is the collision energy required
for a chemical reaction to occur
Activation Energy
is the frequency of collisions
containing enough energy to bring about a
reaction
Reaction Rate
Reaction rate can be increased by
enzymes or by increasing temperature, pressure, or
concentration
speed up chemical reactions without
being altered
Catalysts
are biological catalysts
Enzymes
act on a specific substrate and lower
the activation energy
Enzymes
a molecule upon which an enzyme acts
substrate
Substrate contacts the enzyme’s active site to form an
enzyme-substrate complex
Substrate is transformed and rearranged into
products, which are released from the enzyme
Enzyme is unchanged and can react with
other substrates
Enzymes have specificity for
particular substrates
• Extremely efficient, under optimum conditions
▪ rate of reactions 108 to 1010 times higher than reactions without enzymes
Enzyme Efficiency
is the number of substrate molecules
an enzyme converts to a product per second
▪ Generally, 1 to 10,000 can be as high as 500,000
Turn over number
Names of enzymes usually end in
ase; grouped
based on the reaction they catalyze
Oxidoreductase
oxidation-reduction reactions
Transferase
transfer functional groups
Hydrolase
hydrolysis
Lyase
removal of atoms without hydrolysis
Isomerase
rearrangement of atoms within a
molecule
Ligase
joining of molecules; uses ATP
Factors Influencing Enzyme Activity
Temperature
• pH
• Substrate concentration
• Presence or absence of Inhibitors
Extreme temperatures denature
proteins
Denaturation of an enzyme changes
the arrangement of
amino acids in the active site
temperature alters enzyme shape and causing
to lose its catalytic activity
denaturation
partially or fully reversible
Catabolism & Anabolism
If the denaturation continues, enzyme loses
its solubility
and coagulates –original properties can not be regained
Enzymes include
Concentrated acids, bases, heavy metal ions, alcohol, UV
Enzyme activity
active at optimum pH
Enzyme activity declines as
above/below optimum pH
Increase in H+ and OH- ions concentration
changes 3-D
structure of proteins
Compete with hydrogen and ionic bonds in an enzyme resulting in
denaturation
Noncompetitive inhibitors
interact with another part of the enzyme
(allosteric site) rather than the active site in a process called
allosteric inhibition
fill the active site of an
enzyme and compete with the substrate
Competitive inhibitors
If the concentration of
substrate is high (saturation)
the enzyme
catalyzes at its maximum
rate
Substrate concentration
the amount of substrate present that can be turned into product
Competitive inhibitors
fill the active site of an enzyme and compete with the substrate
Noncompetitive inhibitors interact with another part of the enzyme (allosteric site) rather than the active site in a process called
allosteric inhibition
Ribozymes
• RNA that function as catalysts by cutting and splicing RNA
How is ATP an intermediate between catabolism and anabolism?
Energy is stored in the phosphate bonds of ATP and is produced in catabolism and used up in anabolic processes.
What is a coenzyme?
A cofactor that is an organic molecule
Why is enzyme specificity important?
Because the unique arrangement of each enzyme allows it to find the correct substrate from all the diverse molecules in a cell
What happens to an enzyme below its optimal temperature? Above its optimal temperature?
Below the temp molecules move slowly & don’t have enough energy to cause chemical reactions. Above this temp the protein is denatured and the reaction rate falls
Why is feedback inhibition noncompetitive inhibition?
Feedback inhibition stops a cell from making more of a substance than it needs. Frequently a substrate moves through an assembly line of enzymes to get to the end product. When it has enough, the end product can act as a allosteric inhibitor on the first enzyme in the assembly line - shutting it down.
What is a ribozyme?
RNA that cuts & splices RNA
Distinguish catabolism from anabolism
- Catabolism- the break down of complex organic molecules into simpler ones; releases energy
- Anabolism- the building of simpler organic molecules to build large molecules
removal of electrons from an atom or molecule;
Oxidation
What are the important enzymes in metabolic reactions?
- NAD+ (niacin)
- NADP+
- FAD (Riboflavin)
- Coenzyme A
gain of electrons
Reduction
Redox reaction
an oxidation reaction paired with a reduction reaction
In biological systems, electrons and protons are removed at the same time; equivalent to
to a hydrogen atom (1 proton, 1 electron)
Biological oxidations are often
dehydrogenations
Cells use redox reactions in catabolism to extract
energy from nutrient molecules
Example Cell oxidizes Glucose molecule ———to CO2+ H2O+ ATP
Hydrogenation
a chemical reaction between molecular hydrogen (H2) and another compound or element, usually in the presence of a catalyst such as nickel, palladium or platinum
ATP is generated by the
phosphorylation of ADP with the input of energy
Phosphorolation
the addition of a phosphoryl (PO3) group to a molecule
- Substrate-Level Phosphorylation
ATP generated when a high-energy P is directly transferred from phosphorylated compound (a substrate) to ADP
- Oxidative Phosphorylation
Electrons are transferred from organic compound to one group of electron carriers (NAD+ and FAD) to another along an electron transport chain (system) on a membrane that releases energy to generate ATP
- Photophosphorylation
- Occurs only in light-trapping photosynthetic cells
- Light energy is converted to ATP when the transfer of electrons (oxidation) from chlorophyll pass through a system of carrier molecules
Metabolic Pathways of Energy Production
- Series of enzymatically catalyzed chemical reactions
* Extracts energy from organic compounds and stores it in chemical form (ATP)
Why is glucose such an important molecule for organisms
Because it has many hydrogen atoms and is a highly reduced compound, containing large amounts of potential energy
Metabolic Pathways
Sequences of chemical reactions in a cell
Outline the three ways that ATP is generated.
- Substrate-Level Phosphorylation
- Oxidative Phosphorylation
- Photophosphorylation
What is the purpose of metabolic pathways?
To release & store energy from inorganic molecules by a series of controlled reactions rather then a single burst.
List the three processes that are required for the complete catabolism of glucose to carbon dioxide. (cellular respiration)
1) Glycolysis
2) Kreb Cycle
3) (Oxidative Phosphorylation) = Electron Transport Chain
Carbohydrate Catabolism
Preparatory stage
- 2 ATP are used
* Glucose is split to form two molecules of glyceraldehyde 3- phosphate
Energy-conserving stage
- The two glyceraldehyde 3- phosphate molecules are oxidized to 2 pyruvic acid molecules
- 4 ATP are produced
- 2 NADH are produced
The oxidation of glucose to pyruvic acid produces
ATP and NADH
Glycolysis
The oxidation of glucose to pyruvic acid produces ATP and NADH
- Glucose + 2 ATP + 2 ADP + 2 PO
- Overall net gain of two molecules of ATP for each molecule of glucose oxidized
What are the alternatives to Glycolysis?
1) Pentose phosphate pathway
2) Enter-Doudoroff pathway
Pentose phosphate pathway
- Uses pentoses and produces NADPH
- Operates simultaneously with glycolysis
- Eg: Bacillus subtilis, E.coli, Leuconostoc mesenteroids, E. faecalis
Entner-Doudoroff pathway
- Produces NADPH and ATP
- Does not involve glycolysis
- Occurs in Pseudomonas, Rhizobium, and Agrobacterium
Aerobic Respiration- Krebs cycle
(tricarboxylic acid cycle/TCA cycle/citirc acid cycle)
• Pyruvic acid (from glycolysis) is oxidized and decarboxylation (loss of CO2) occurs
• The resulting two-carbon compound attaches to coenzyme A, forming acetyl CoA and NADH
• Oxidation of acetyl CoA produces NADH, FADH2, and ATP, and liberates CO2 as waste
Cellular Respiration
- Oxidation of molecules liberates electrons to operate an electron transport chain
- Final electron acceptor comes from outside the cell and is inorganic
- ATP is generated by oxidative phosphorylation
Aerobic Respiration
Uses oxygen as the final electron acceptor
Electron transport chain (system)
• Occurs in the plasma membrane of prokaryotes; inner mitochondrial membrane of eukaryotes
• Series of carrier molecules (flavoproteins, cytochromes, and ubiquinones) are oxidized and reduced as electrons are passed down the chain
• Energy released is used to produce ATP by
chemiosmosis
Electron transport and the chemiosmotic generation of ATP.
Chemiosmosis.
Anaerobic Respiration
Formation of ATP without Oxygen.
Uses a INORGANIC MOLECULE, such as nitrogen ions or sulfate ions, as the final electron acceptor.
Anaerobic Respiration
Electron Acceptor Products
Nitrate: NO3– NO2–, N2 + H2O
Sulfate: SO4– H2S + H2O
Carbonate: CO32 – CH4 + H2O
Net ATP: Carbohydrate Catabolism
- Each NADH can be oxidized in the electron transport chain to produce 3 molecules of ATP
- Each FADH2 can produce 2 molecules of ATP
ATP Yield during Prokaryotic Aerobic Respiration of One Glucose Molecule
Fermentation
- Releases energy from the oxidation of organic molecules
- Does not require oxygen
- Does not use the Krebs cycle or ETC
- Uses an organic molecule as the final electron acceptor
- Produces only small amounts of ATP
Fermentation.
Lactic acid fermentation:
produces lactic acid
Homolactic fermentation
produces lactic acid only
Heterolactic fermentation
produces lactic acid and other compounds
Glucose is oxidized to pyruvic acid, which is then reduced by
NADH
Alcohol fermentation
: produces ethanol + CO2
Glucose is oxidized to pyruvic acid; pyruvic acid is converted to acetaldehyde and CO2; NADH reduces acetaldehyde to ethanol
Types of fermentation
Fermentation
Some Industrial Uses for Different Types of Fermentations*
An Overview of Respiration and Fermentation.
Lipid catabolism.
Lipid and Protein Catabolism
Protein—–Extracellular proteases—–Amino acids
Deamination, decarboxylation, dehydrogenation, desulfurizatio——Organic acid—–Krebs cycle
Catabolism of various organic food molecules.
What are the reactants of Cellular Respiration?
Glucose (C6H12O6) & Oxygen (O2)
C6H12O6 + O2 ———> CO2 + H20 + ATP
What are the products of Cellular Respiration?
ATP is the main product
What happens during the preparatory and energy-conserving stages of glycolysis?
Prep phase: 2 ATP used as 6 carbon glucose is broken down to form DHAP and GP which are readily converted to eachother.
Energy phase: DHAP and GP which are now 3 carbon molecules are OXIDIZED to 2 molecules of pyruvic acid, NAD+ REDUCED to NADH and 4 ATP are formed
What is the value of the pentose phosphate and Entner-Doudoroff pathways if they produce only one ATP molecule?
they both provide the sugars that help to form nucleotides. Pentose helps e.coli and bacillis. Doud can metablize GLUCOSE
What are the principal products of the Krebs cycle?
CO2, NAD+, NADH, acetyl group, FADH2 & ATP
How do carrier molecules function in the electron transport chain?
the carrier molecules Flavoprotein, cytochromes and Q help . Flavo is for oxi-redox. Q is a nonprotein carrier. They are used to help diffuse the protons across the plasma membrane bc protons are too big to pass alone.
Compare the energy yield (ATP) of aerobic and anaerobic respiration
Aerobic respiration is far more energy-efficient than anaerobic respiration. Aerobic processes produce up to 38 ATP per glucose. Anaerobic processes yield only 2 ATP per glucose.
List four compounds that can be made from pyruvic acid by an organism that uses fermentation.
1) Lactic Acid
2) Ethanol
3) Propionic acid
4) Butyric Acid
Biochemical tests identify bacteria by detecting
enzymes (e.g., those involved in decarboxylation and dehydrogenation)
• Fermentation test
bacteria that catabolize carbohydrate or protein produce acid, causing the pH indicator to change color
• Oxidase test
identifies bacteria that have cytochrome oxidase (e.g., Pseudomonas)
Detecting amino acid catabolizing enzymes in the lab.
• Tubes contained bacteria, glucose, pH indicator, and a specific amino acid
pH indicator turns yellow when bacteria produce
acid from glucose
pH indicator turns purple when bacteria produce
produce alkaline products from decarboxylation
Tubes contained protein, carbohydrate, pH indicator, and an inverted Durham tube
pH indicator changes color if the carbohydrate catabolized and produced acid
Some bacteria produce acid as well as gas
Eg: E.coli ferments carbohydrate sorbitol but not pathogenic E.coli O157:H7 strains
E.coli produce gas from lactose but not Shigella
Salmonella produce H2S when
sulfur is removed from amino acids
Peptone agar
H2S produced in the tube precipitates with Fe in the medium as ferrous sulfide
On what biochemical basis are Pseudomonas and
Escherichia differentiated
Pseudomonas: oxidative- POSITIVE
Escherichia is oxidative- NEGATIVE
Photosynthesis
(uses light energy to convert chemical energy and synthesize organic compounds)
• Some organisms obtain energy by oxidizing organic compounds (eg:
(eg: dead plants, animals, living host, etc…)
Photosynthesis
• Oxygenic:
Photosynthesis
• Anoxygenic:
Two stages in Photosynthesis
• Light-dependent (light) reactions
conversion of light energy into chemical energy (ATP and NADPH)
Two stages in Photosynthesis
• Light-independent (dark) reactions
ATP and NADPH are used to reduce CO2 to sugar (carbon fixation) via the Calvin-Benson cycle
Photosynthesis Summary
Photophosphorylation
Photophosphorylation. Noncyclic
Cyclic Vs Non cylic
How is photosynthesis important to catabolism?
It is the synthesis of complex organic compounds from simple inorganic substances that can later be used for catabolism in cellular respiration
What is made during the light-dependent reactions?
collect energy from the sun and break down water molecules to produce ATP and NADPH.
How are oxidative phosphorylation and photophosphorylation similar?
a membrane associated electron transport chain. creation of a proton gradient. harvesting energy of the proton gradient by making ATP with the help of an ATP synthase
Summarize energy production in cells in a single sentence.
Cells use oxidation and reduction reactions in catabolism to extract energy from nutrient molecules.
Requirements of ATP production.
A nutritional classification of organisms.
Phototrophs use
light energy
Photoautotrophs
use energy in the Calvin-Benson cycle to fix CO2 to sugar
• Oxygenic
produces O2
• Anoxygenic
does not produce O2
Photoheterotrophs
use organic compounds as sources of carbon; anoxygenic
Photosynthesis: eukaryotes vs. prokaryotes
Chemoautotrophs
- Use energy from inorganic chemicals; CO2 as carbon source
* Energy is used in the Calvin-Benson cycle to fix CO2
Chemoheterotrophs
- Use energy and carbon from organic chemicals
* Medically and economically important
The biosynthesis of polysaccharides.
The biosynthesis of simple lipids.
The biosynthesis of amino acids
The biosynthesis of purine and pyrimidine nucleotide
The Integration of Metabolism
• Amphibolic pathways
- metabolic pathways that function in both anabolism and catabolism
- Many pathways function simultaneously with common intermediates
Summarize how oxidation enables organisms to get energy from glucose, sulfur, or sunlight.
Organisms get energy from oxidation, Cell must have an electron (or hydrogen) DONOR, which is the INITIAL energy source. The electrons removed from chemcal energy sources are transferred to electron CARRIERS (NAD+,NADP+,FAD) which is the redox reaction. INITIAL energy source is OXIDIZED & 1st electron CARRIER is REDUCED. ATP is produced HERE. Next stage, electrons are transfered from Electron CARRIERS to FINAL electron ACCEPTOR which makes MORE ATP.
- AEROBIC: O2 final electron acceptor
- ANAEROBIC: INORGANIC molecules OTHER then O2 is final acceptor (ex: Nitrate,sulfate)
- FERMENTATION: ORGANIC compounds are final acceptor
Almost all medically important microbes belong to which of the four aforementioned groups?
Chemoheterotrophs
Where do amino acids required for protein synthesis come from?
carbon sources like glucose. Not all amino acids are produced by the body; other amino acids are obtained from diet. Within the cells, proteins are generated involving transcription and translation processes.
Summarize the integration of metabolic pathways using peptidoglycan synthesis as an example.
Amphibolic pathway are metabloc pathways that function in BOTH cat. & ana. They help bridge reactions for BREAKDOWN and syn of carbs, lipids, proteins &nucleotides. Breakdown is used from one into another.
-Peptidoglycan forms bacterial cell walls. This forms from the energy use of ATP. UTP is the energy source which is a nucleotide & together with glucose 6-phosphate are synthesized from UDPG. UDPNac is what begins the synth. of pepti.
