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Bio.590-4.Metabolism

Integrative Physiology Ch. 4 - Energy and Cellular Metabolism

QuestionAnswer
Properties of life Basic unit is the cell; acquire/transform/store/use energy; sense/respond to environments; homeostasis; store/use/transmit info; reproduce/grow/die; emergent properties; adapt/evolve
Energy cycling in biology Energy cycling between environment and organisms is a fundamental concept in biology. Animal cells use energy from the environment provided by other animals or plants who obtained their energy from the sun.
What is the ultimate source of energy for all animals on earth? The sun
Respiration Animals extract energy from biomolecules through the process of respiration, which consumes oxygen and produces CO2 and H2O
The main energy stores in animals Glycogen and lipids
Energy The capacity to do work
What does work mean in the context of biological systems? One of three things: chemical work, transport work, or mechanical work
Chemical work The making and breaking of chemical bonds. This enables cells and organisms to grow, maintain a suitable internal environment, and store information needed for reproduction and other activities.
Transport work Enables cells to move ions, molecules, and larger particles through the cell membrane and organelles. It’s particularly useful for creating concentration gradients.
Mechanical work In animals is used for movement. This includes organelles moving around within the cell, cells changing shape, and the cilia and flagella beating. At the macroscopic level it includes muscle contraction.
Two forms of energy Kinetic and potential
Kinetic energy Energy of motion.
Potential energy Stored energy. In chemical bonds, for example, the potential energy is stored in the position of the electrons that form the bond
A key feature of all types of energy is… …the ability of potential energy to become kinetic energy and vice versa
The energy lost in the transformation from potential to kinetic energy depends on… …the efficiency of the process. Many physiological processes in the human body aren’t very efficient, e.g. 70% of the energy used in physical exercise is lost as heat rather than transformed into work
Two rules govern the transfer of energy in the universe The first and second laws of thermodynamics
The first law of thermodynamics AKA the law of conservation of energy, states that the total amount of energy in the universe is constant.
What type of system is the universe? What type of system is the human body? Universe: closed system – nothing enters, nothing leaves. Human body: open system: it exchanged materials and energy with its surroundings
Second law of thermodynamics Natural spontaneous processes move from a state of order (nonrandomness) to a condition of disorder (randomness), known as entropy.
Creating and maintaining order in an open system requires… …energy
Bioenergetics The study of energy flow through biological systems
Chemical reaction A substance becomes a different substance by the breaking and/or making of chemical bonds. A reaction begins with reactants and results in the products.
Reaction rate The disappearance rate of the reactants or the appearance rate of the products. It’s measured as change in concentration during a period of time and is often referred to as molarity per second (M/sec)
Free energy of a molecule The potential energy stored in the chemical bonds of a molecule. E.g. a large glycogen molecule has more free energy than a single glucose molecule
Displacement reaction L + MX -> LX + M
Double displacement reaction LX + MY -> LY + MX
Net free energy change of the reaction The difference in free energy between the reactants and products
Activation energy The initial input of energy required to bring reactants into a position that allows them to react with one another
Exergonic reaction If the free energy of the products is lower than the free energy of the reactants the reaction releases energy and is Exergonic
ATP -> ADP ATP + H2O -> ADP + P_i + H+ + energy. Exergonic.
Endergonic reaction The free energy of the products exceeds that of the reactants. A net input of energy is required and the reaction is endergonic.
If the activation energy is low then… …the reaction may be spontaneous
Synthesis reactions Complex molecules are made from smaller ones. Many of these reactions are endergonic
Energy coupling Using the energy released by an Exergonic reaction (e.g. ATP -> ADP) to overcome the energy required to drive an endergonic reaction. The two reactions take place simultaneously in the same location
Are all reactions in the body driven by energy coupling reactions occurring at the same time and location? No, that’s not always practical. In some instances high energy electrons are carried on nucleotides NADH FADH2 and NADPH and transferred to ATP later
Reversible reaction. Irreversible reaction Reversible: a chemical reaction that can proceed both ways. Irreversible: can only occur one way. Reactions that release huge amounts of energy are typically irreversible.
Are most biological reactions reversible or irreversible? Reversible due to the aid of enzymes
Enzymes Proteins that speed up the rate of chemical reactions. The enzymes are not changed in any way thus they’re biological catalysts. They help overcome activation energy.
What are enzymes comprised of? Most are large proteins but some RNA molecules can also function as catalysts
Isozymes A few enzymes come in a variety of related forms (isoforms) and are known as isozymes. Isozymes are enzymes that catalyze the same reaction but under different conditions or in different tissues.
Examples of isozymes Lactate dehydrogenase (LDH) has two types of subunits, H and M, which are assembled into tetramers (groups of 4). LDH isozymes include H4, H2M2, and M4. The different LDH enzymes are tissue specific.
Coenzymes Organic cofactors for enzymes. They don’t alter the enzyme’s binding site like cofactors do. Instead, they act as receptors and carriers for atoms or functional groups that are removed from substrates during reactions
Vitamins Many substances we call vitamins are the precursors of coenzymes. The water-soluble vitamins, such as B vitamins, vitamin-C, folic acid, biotin, and pantothenic acid, become coenzymes.
E.g. vitamin C is needed for… …adequate collagen synthesis
How are enzymes inactivated By inhibitors or by becoming denatured. This can occur because of temperature or pH. Most enzymes have optimum pH at about 7.4
How do enzymes decrease activation energy? They bind to substrates and bring them closer together
Equilibrium constant Keq ([C][D])/([A][B])
Law of mass action AKA LeChatelier’s principle When a reaction is at equilibrium, the ratio of the products to the substrates is always the same
Most reactions catalyzed by enzymes can be classified into four categories: Oxidation-reduction, hydrolysis-dehydration, exchange-addition-subtraction, and ligation reactions
Kinase An enzyme with the name “kinase” in it indicates that it will phosphorylate the substrate
Phosphorylation To add a phosphate group
Oxidation-reduction reactions To add or subtract electrons. The molecule that gives is oxidized and the one that gains is reduced.
Hydrolysis-dehydration reactions In dehydration reactions water is one of the products. Most of the time two molecules combine into one, losing a water molecule. In hydrolysis water is added to a substrate. Covalent bonds are usually broken (“lysed”)
Addition-subtraction-exchange reactions Addition: adds a functional group to a substrate. Subtraction: removes a functional group from the substrate. Exchange: functional groups are exchanged among substrates.
Deamination reaction Removal of an amino group from an amino acid or peptide.
Amination reaction Addition of an amino group
Transamination The transfer of an amino group from one molecule to another
Ligation reactions Joins two molecules together using enzymes known as synthetases and energy from ATP. E.g. the synth. Of acetyl CoA from fatty acids and coenzyme A.
Metabolism Refers to all chemical reactions that occur in an organism
Metabolism is often divided into Catabolism (release energy through the breakdown of biomolecules) and anabolism (energy-utilizing reactions that synthesize biomolecules.
Kilocalorie (kcal) The amount of energy needed to raise the temperature of 1 liter of water by 1 degree C. One kcal = one Calorie (with a capital C) in the context of nutrition and = 1000 calories
The molecules in a long pathway are known as Intermediates
Key intermediates They participate in more than one pathway and act as branch points for channeling substrate in one direction or another. E.g. glucose is a key intermediate in many pathways
How do cells regulate the flow of molecules through their metabolic pathways? 5 ways Enzyme concentrations; Allosteric and covalent modulators; using two different enzymes to catalyze reversible reactions; isolating enzymes in organelles; maintaining optimum ratio of ATP to ADP
Feedback inhibition The end product of a pathway acts as an inhibitory modulator of the pathway
Why is the ratio of ATP to ADP important Through complex regulation, the ratio of ATP to ADP determines whether pathways that result in ATP synthesis are turned on or off. When ATP is high, production of ATP drops. When ATP is low, production increases.
The metabolic pathways that yield the most ATP are… …Aerobic, or oxidative, pathways. That is, they require oxygen. Anaerobic pathways produce ATP, but not enough for humans to live off of
Two pathways of aerobic respiration to produce ATP from glucose Glycolysis and citric acid cycle
Do glycolysis and the citric acid cycle produce the bulk of the ATP? No they only produce a small portion. Their most important contributions are the high-energy electrons carried by NADH and FADH2 to the electron transport system in the mitochondria which ultimately creates the most ATP
At various points what are the byproducts of respiration? CO2 and H2O. H2O can be used by CO2 must be removed
How do carbohydrates (glucose), lipids, and proteins enter the pathways of respiration? Glucose enters at the very start and runs through both pathways in their entirety. Lipids are broken down to glycerol which feeds into glycolysis and fatty acids which are metabolized to acetyl CoA. Proteins enter at various points
Summary of glycolysis One molecule of glucose is converted by a series of enzymes into two pyruvate molecules, producing a net release of energy. Overall it’s exergonic. Oxygen is not required (anaerobic).
Chemical equation for glycolysis Glucose + 2 NAD+ + 2 ADP + 2P -> 2 Pyruvate + 2 ATP + 2 NADH + 2H+ + 2H2O
Glycolysis: step 1 Glucose is phosphorylated (with the aid of ATP) to glucose-6 phosphate.
Glycolysis: step 2 Glucose-6 phosphate is rearranged to fructose-6 phosphate
Glycolysis: step 3 With the aid of ATP, fructose-6 phosphate becomes fructose 1,6 bisphosphate
Glycolysis: step 4 Fructose 1,6 bisphosphate is split into two glyceraldehyde 3-phosphate molecules
Glycolysis: step 5 Each glyceraldehyde 3-phosphate donates an electron to NAD+ to yield two NADHs. Each glyceraldehyde 3-phosphate is also phosphorylated in the process and becomes two 1,3-bisphosphoglycerate molecules
Glycolysis: step 6 Each 1,3-bisphosphoglycerate phosphorylates an ADP molecule to create two ATPs and become two 3-phosphoglycerate molecules
Glycolysis: step 7 Each 3-phosphoglycerate is rearranged to become two 2-phosphoglycerate molecules
Glycolysis: step 8 Each 2-phosphoglycerate undergoes dehydration and become two phosphoenol pyruvate molecules
Glycolysis: step 9 The phosphoenol pyruvate molecules each phosphorylate an ADP to yield two ATPs and become two pyruvate molecules
NET energy yield from glycolysis From each glucose the net energy yield is two ATP and two NADH
What does the cell do with pyruvate Two pathways depending on the needs of the cell. If the cell contains adequate oxygen it’s shuttled to the citric acid cycle. If not, it’s reduced by NADH and converted to 2 lactates.
Net energy yield for anaerobic respiration Anaerobic respiration is the pathway the cell takes when lacking oxygen. In this case two NADH’s are used to reduce pyruvate to lactate thus the net yield is two ATPs and zero NADH’s
Where does glycolysis occur? Cytosol. If there’s adequate oxygen, the resultant pyruvates will then be shuttled into the mitochondria to enter the citric acid cycle.
Once in the mitochondria, what happens to the pyruvate molecules? They’re oxidized by NAD and combined with CoA to acetyl CoA, a molecule with two parts: a 2-carbon acyl unit, derived from pyruvate, and a coenzyme. Each molecule loses a CO2 as well.
What role does CoA play? Coenzyme A is made from the vitamin pantothenic acid. The CoA portion of acetyl CoA is immediately displaced by oxaloacetate upon entering the citric acid cycle and thus it’s not consumed and is continuously reused
The citric acid cycle is also known as… …The Krebs Cycle
MEMORIZE ENTIRE CITRIC ACID CYCLE. KNOW AT WHICH POINT ATP, NADH, FADH2, AND GTP IS CREATED MEMORIZE ENTIRE CITRIC ACID CYCLE. KNOW AT WHICH POINT ATP, NADH, FADH2, AND GTP IS CREATED
Net yield during citric acid cycle Each full turn yields two CO2, one ATP, three NADH, and one FADH2 (remember to multiply by two to account for entire glucose molecule if required)
Electron transport system A group of mitochondrial proteins made up of enzymes and iron-containing proteins known as cytochromes located in the inner mitochondrial membrane
Chemiosmotic theory The model that describes the movement of electrons in the electron transport system. In this model, as pairs of electrons pass through the proteins, some of the released energy is used to pump H+ across the membrane
What is the significance of loading the intermembrane space with H+? It builds up a concentration gradient. The protons then move back across the membrane, down their concentration gradient, and the potential energy is converted to ATP via ATP synthase
Oxidative phosphorylation The name of the process of generating ATP from the electron transport system, derived from the fact that the electron transport system requires oxygen to act as the final acceptor of electrons and H+
After the electrons travel through the cytochromes what happens to them? They combine with the leftover H+ and also meets up with the all-important oxygen to yield H2O. 4 e- will yield 2H2O
Maximum potential energy yield for the catabolism of one glucose molecule 30 – 32 ATP
Why do we say potential yield? (1) Some of the H+ leak out from the intermembrane space back into the mitochondrial matrix
Why do we say potential yield? (2) The cytosolic NADH electrons can’t enter the mitochondria and must be shuttled in via electron carriers, afterwards meeting up with either NADH or FADH2. FADH2 has a lower yield (1.5 rather than 2.5).
So, how much NET ATP/NADH/FADH2 comes from each step using one glucose molecule? Glycolysis: 2 ATP (and 2 NADH); oxidation of pyruvate: 2 NADH; citric acid cycle: 2 ATP (and 6 NADH, 2 FADH2); electron transport system: 26-28 ATP
When glucose supplies from outside the body are less than what the body needs to synthesize ATP, what do cells first rely on? Cells FIRST rely on the energy stored in the chemical bonds of glycogen
Glycogenolysis The breakdown of glycogen
How does the process of glycogenolysis work? Glycogen is either broken down into glucose (only 10%) and then turned into glucose 6-phosphate or broken down directly into glucose 6-phosphate (90%) which saves an ATP for a total yield in aerobic respiration of 31-33
How are proteins broken down and used by the body? Proteins are catabolized into smaller polypeptides by proteases and then hydrolyzed to their constituent amino acids by peptidases. Deamination of the acid creates an organic acid which can be used in glycolysis or citric acid cycle
During deamination of the amino acid, an organic acid is created by the removal of the amino group. What happens to the ammonia after it’s removed? Ammonia picks up H+ to become NH4+ (ammonium). NH3 and NH4+ are toxic so liver cells quickly convert them into urea (CH4N2O) which is the main nitrogenous waste of the body and excreted by the kidneys
Lipolysis A series of reactions by lipases that break down lipids into glycerol and fatty acids. Glycerol is fed into glycolysis about half way through. Fatty acids are transported into the mitochondria to undergo beta-oxidation
Beta-oxidation The disassembling of fatty acids into 2-carbon chains (acyl units) which can combine with CoA to form acetyl CoA, which can be used to kick off the citric acid cycle.
The energy contained in lipids compared to carbs and proteins Lipids = 9kcal per gram; proteins and carbs = 4kcal per gram.
What happens if the body’s acetyl CoA production exceeds the capacity of the citric acid cycle to metabolize the acyl units? This occurs in the liver and excess CoA is converted to ketone bodies, strong metabolic acids that can seriously disrupt the body’s pH balance.
Where is glycogen found in the body? It’s found in all cells, but of especially high concentration in the liver (source of glucose between meals) and skeletal muscles (for muscle contraction)
How much of an energy supply is stored as glycogen in the liver? About 4hrs worth of energy. Any energy used in excess of that will come from catabolized lipids and proteins
How is glycogen made? Individual glucose molecules can be linked together to form glycogen. Glucose 6-phosphate can also be turned into glycogen with the removal of the phosphates
Give one reason why glucose is so important. How is this evident? Glucose is the only substrate used for ATP synthesis in neural tissue. The brain will die without glucose. For this reason, the body has multiple metabolic pathways to synthesize glucose ensuring continuous supply to the brain
The simplest source of glucose in the body. What if this source is depleted? Glycogenolysis. If all the glycogen is used up, cells will turn lipids and proteins into intermediates for glucose (biosynthesis of glucose commences via the production of glucose from nonglucose precursors)
Gluconeogenesis The production of glucose from nonglucose precursors such as proteins and the glycerol portion of lipids
Note: why do athletes need carbs? Why do athletes get tired? When carb stores are depleted, lipids and proteins must be converted to ATP. They can’t be converted as quickly as carbs so the athlete must exercise at a slower pace to give the body time to generate ATP
Explain the process of gluconeogenesis Essentially the reverse of glycolysis but with different enzymes. Pyruvate is combined with glycerol (or lactate) and a series of amino acids to generate glucose 6-phosphate. In the liver glucose 6-phosphate is turned into glucose
Why does the transformation of glucose 6-phosphate to glucose occur in the liver? Only liver and kidney cells have significant amounts of glucose 6-phosphatase (the required enzyme), thus during periods of fasting the liver is the primary source of glucose synthesis, producing about 90% of the glucose
How are triacylglycerides synthesized? Glycerol is abstracted from glycolysis intermediates. The fatty acid chain is synthesized by fatty acid synthetase as it links acyl units taken from acetyl CoA. They’re then combined in the smooth ER to form triacylglycerides
Where are phospholipids generated? In the SER there are phosphorylation steps that turn triglycerides into phospholipids
How/where is cholesterol synthesized? It’s actually usually obtained from consumed animal products. If deficient in dietary sources, cholesterol is made from acetyl CoA and can be further modified into various steroids or other hormones if necessary.
Review: how many amino acids are there which may constitute proteins? 20
How is mRNA translated into proteins? By identifying and translating codons. Codons are triplets of mRNA bases with each triplet corresponding to an amino acid. There is some redundancy: two different triplets can code for the same amino acid
How many triplet combinations are there? How many are start/stop codons? There are 4 different bases arranged in triplets, so the total possible triplet combinations equals 4^3 = 64. DNA codon TAC is a start codon and there are three stop codons. The remaining 60 code for amino acids.
How does information in the DNA translate to physical proteins? DNA is transcribed to RNA (mRNA, tRNA, or rRNA). mRNA leaves the nucleus, enters the cytosol and works with rRNA and tRNA to translate its code to an assembly of amino acids
Gene A region of DNA that contains information needed to make a functional piece of RNA
Gene to protein: (1) Section of DNA containing the gene must be activated. Some genes are *constitutively* active (always being transcribed), others are *regulated* (they can be turned on, or *induced*, or turned off, or *repressed*)
Gene to protein: (2) Transcription converts its DNA base sequence to a piece of RNA. mRNA is then processed in the nucleus where it may undergo alternative splicing or may be “silenced” and destroyed by enzymes through RNA interference
Gene to protein: (3) In the cytoplasm mRNA works with tRNA and rRNA to be translated where mRNA’s message is turned into amino acid sequences
Gene to protein: (4) Newly synthesized proteins are then subject to *post-translational modification*, wherein they’re folded split, and or have various chemical groups attached to them.
RNA polymerase The synthesis of RNA requires this enzyme plus magnesium or manganese ions and energy. It binds to DNA and unwinds it by breaking H-bonds, and the mRNA strand is produced. It then detaches along with the polymerase
Promoter region Each gene is preceded by a promoter region that must be activated before transcription can begin. The promoter itself is not transcribed
How is the promoter activated Regulatory-protein transcription factors bind to DNA and activate the promoter, which tells RNA polymerase where to bind.
Sense strand vs. antisense strand Sense strand is the strand of DNA that’s being transcribed, the antisense strand is its complementary strand that’s sitting idly by
How fast is transcription 40 bases are linked per second
mRNA processing: RNA interference Newly synthesized mRNA is inactivated or destroyed before it can be translated into proteins.
mRNA processing: alternative splicing Enzymes clip pieces (introns: noncoding portions) out of the mRNA strand. Other enzymes then splice the remaining pieces (exons: coding portions) back together
What happens once mRNA leaves the nucleus? mRNA binds to ribosomes which are composed of two subunits (one large, one small) that come together at this point. The small RNA subunit binds to the mRNA then adds the large subunit.
After the RNA subunits attach to the mRNA, what happens? tRNAs floating around have one side with codons complementary to the mRNA strand called the *anticodon*, and the other side bound to an amino acid. They attach to the mRNA
What happens after tRNA attaches to the mRNA in the ribosome? The ribosome binds the amino acids together via a peptide bond by means of dehydration syntheses. The empty tRNAs then leave the ribosome to find more amino acids.
When the last amino acid has been joined to the chain the ribosome… …The termination stage has been reached whereby the mRNA, ribosome, and peptides separate. The ribosome can be reused while the mRNA is either catabolized by ribonucleases or translated again.
Protein sorting After leaving ribosomes proteins are sent where they’re needed (e.g. an organelle) according to their “identification tags” which are amino acid sequences known as signal sequences or targeting sequences.
What if a protein doesn’t have a targeting sequence? It stays in the cytosol
Peptides with targeting sequences on RER ribosomes They usually direct them through the membrane of the RER into the lumen of the RER
What is the initial structure of the protein after detaching from the ribosome? What happens next? Primary structure. It then undergoes post-translational modification. There are over 100 different types of modifications, including folding or assembly into polymers of quaternary structure
Post-translational modification: Protein folding Occurs when H-bonds, covalent bonds, and ionic bonds form in the protein. This occurs with the help of molecular chaperones
Post-translational modification: What happens to misfolded proteins? They’re tagged with a protein called ubiquitin and sent to proteasomes, cylindrical cytoplasmic enzyme complexes that catabolize proteins
Post-translational modification: Cross-linkage Strong bonds formed within a protein during post-translational modification, e.g. disulfide bonds between two amino acids with sulfur atoms
Post-translational modification: Cleavage Some proteins are initially inactive, including many enzymes, must have segments removed (“cleaved”) before becoming active.
Post-translational modification: Addition of other molecules or groups Proteins can be modified by the addition of sugars (glycosylation) to create glycoproteins, or by combination with lipids to form lipoproteins. They can also be phosphorylated or methylated, etc.
Post-translational modification: Assembly into polymeric proteins Creations of proteins with quaternary structures, having multiple subunits e.g. dimers, trimers, or tetramers. E.g. hemoglobin
What happens once a protein enters the ER lumen The targeting sequence is enzymatically removed. After modification, they’re packaged into transport vesicles that bud off the ER. The vesicles fuse with the Golgi and they enter the Golgi’s cisternae.
After entering the Golgi’s cisternae what happens to the proteins? They migrate from the cis-face to the trans face during which they may be modified. They bud off the trans-face and then transported wherever they’re needed. E.g. to be lysosomes, secretory vesicles, back to the ER, etc.
Where do proteins with targeting signals created from free ribosomes go? To peroxisomes or mitochondria
Two very important enzymes in metabolism (important note?) Hexokinase (glucose -> glucose 6-phosphate) and glucose 6-phosphatase (the reverse). Important note: only the liver can do the reverse reaction (i.e. produce glucose in times of fasting). Other tissues only have Hexokinase
Anaerobic pathway of ATP production Glycolysis
Acetyl CoA can come from… …either glycolysis or fatty acids
Why are dehydrogenases important in the citric acid cycle Because they make NADH or FADH2 (the high energy electron shuttles)
Where is glucocorticoid formed? In the cortex of the adrenal glands
Why is it called a “reverse reaction” when the protons pump across the ATP synthetase enzyme in oxidative phosphorylation? Because everywhere else in the body, that ATP pump works the opposite direction
How are fatty acids catabolized? Lipases chops several 2-carbons acyl units off the fatty acids in a process called “beta-oxidation”
What happens to the resultant acyl units? They become acetyl-CoA
Gluconeogenesis Glucose from non-glucose precursors: lactate/amino acids come together to form pyruvate. Glycerol/amino acids/etc. come together to form glucose-6 phosphate from pyruvate. Then to glucose in only liver/kidney
Lipid anabolism (synthesis) Cleaving acyl units from acetyl-CoA and anabolizing (via **fatty acid synthetase**) them into fatty acids. Also, shuttling glycerol from glycolysis to be combined to the fatty acids. Note: lipase does the opposite: breaks it down
Created by: Intellex_