Molecular Bio: Cellular Respiration Flashcards
B-pleated sheet
A beta pleated sheet is a secondary structure of a protein in which the single polypeptide chain of the primary structure “lies alongside itself.” Connecting segments of the two strands of the sheet can lie parallel or anti-parallel. Like alpha helices, beta sheets are reinforced by hydrogen bonds between the carbonyl oxygen and the hydrogen on the amino group.
Alpha helix
An a-helix is a secondary structure of a protein. It twists the single chain of polypeptides of the primary structure into a helix. Alpha helices are reinforced by hydrogen bonds between the carbonyl oxygen and hydrogen on the amino group.
Water
Water is the solvent in which the chemical reactions of living cells take place. It makes up 70 to 80% of a cell’s mass. Water is a small, polar molecule that can hydrogen bond.
Water maintains its liquid state in a cell because it can hydrogen bond. Hydrogen bonding also provides strong cohesive forces between water molecules. These forces squeeze hydrophobic molecules away.
Hydrophobic molecules
These “water-hating” molecules are squeezed away from water, which causes them to aggregate elsewhere.
Hydrophilic molecules
These “water-loving” molecules dissolve easily in water. Their negatively charged ends attract the positively charged hydrogens of water, while their positively charged ends attract the negatively charged oxygen on water. Water molecules surround a hydrophilic molecule, separating it from the group.
Lipids
A lipid is any biological molecule with low solubility in water, and high solubility in nonpolar organic solvents.
Lipids are hydrophobic and make excellent barriers separating aqueous environments.
The six major groups of lipids are: fatty acids, triacylglycerols, phospholipids, glycolipids, steroids, and terpenes.
Fatty acids
Fatty acids are lipids. Fatty acids are also the building blocks for most, but not all, complex lipids.
Structure is a long chain of carbons, truncating in a carboxylic acid.
Fatty acids can be saturated or unsaturated.
Oxidation of fatty acids liberates large amounts of chemical energy, which can be used by the cell. Most fats reach the cell as fatty acids, not as triacylglycerols.
Saturated vs. unsaturated fatty acids
Fatty acids can be saturated or unsaturated. Saturated fatty acids possess only single carbon-carbon bonds. Unsaturated fatty acids contain 1+ carbon-carbon double bonds.
Triacylglycerols
Triacylglycerols are a type of lipid that, along with phospholipids and glycolipids, are sometimes called fatty acids.
Triacylglycerols a.k.a. triglycerides, fats, or oils.
Structure: 3-carbon backbone called glycerol attached to three fatty acids.
Function: They store energy in cells, provide thermal insulation, and padding.
Glycerol
Glycerol is the three carbon backbone that makes up triacylglycerol
Adipocytes
Adipocytes are also called fat cells. They are specialized cells who cytoplasm contains almost nothing but triglycerides.
Phospholipids
Phospholipids also have a glycerol backbone, but a polar phosphate group replaces one of the fatty acids.
This phosphate group lies opposite the fatty acids on the glycerol. This makes phospholipids amphipathic.
The amphipathic nature of phospholipids makes them good components of membranes.
Steroids
Steroids are four-ring structures. They include: hormones, vitamin D, and cholesterol.
Proteins
Proteins are built from chains of amino acids linked together by peptide bonds. Proteins are a.k.a. polypeptides.
Digested proteins reach the cells of the human body as single amino acids.
Proteins have four levels of structure.
Proteins can be divided into two types-globular and structural.
Globular proteins can be enzymes, hormones, membrane pumps and channels, membrane receptors, intercellular and intracellular transport, storage, regulators, immune response, etc.
Structural proteins are made from long polymers, and adds strength to cellular and matrix structure. An example is collagen, the most abundant protein in the body.
“Essential”
Something being essential means that the body cannot manufacture it and it must be ingested directly. Examples of essential nutrients are 10 of the 20 amino acids.
Amino acids
There are 20 amino acids. Amino acids have the general structure: amine group directly across from a carbonyl group, both attached to a central carbon with an R group (“side chain”) on top.
Each amino acid in a polypeptide chain is called a residue. Very small polypeptides are sometimes called peptides.
Tertiary structure
Tertiary structure refers to the three-dimensional shapes formed when the peptide chain curls and folds.
Five forces create the tertiary structure: 1. Covalent disulfide bonds between two cysteine amino acids on different part of the chain
- Electroststatic (ionic) interactions between acidic and basic side chains
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic side chains pushed away from water toward the center of the protein
The amino acid proline induces turns in the polypeptide that will disrupt both Alpha helix and beta-pleated sheet formation
Secondary structure
The alpha helix and the beta pleated proteins are the secondary structure and contribute to the conformation of the protein. All proteins have a primary structure and most have a secondary structure. Larger proteins (globular, fibrous/structural, etc.) can have a tertiary and quaternary structure.
Quaternary structure
When two or more polypeptide chains bind together, they formed the quaternary structure of the protein.
Larger proteins- like globular, fibrous, structural etc., have tertiary and coronary structure.
Five forces create the quaternary structure: 1. Covalent disulfide bonds between two cysteine amino acids on different part of the chain
- Electroststatic (ionic) interactions between acidic and basic side chains
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic side chains pushed away from water toward the center of the protein
Denaturing proteins
When confirmation is disrupted, the protein is said to be denatured. A denatured protein has lost most of it’s secondary, tertiary, and quaternary structure. Very often, once the denaturing agent is removed, the protein will spontaneously refold to its original confirmation.
Urea denatures hydrogen bonds.
Salt or change in pH denatures electrostatic bonds.
Mercapthoethanol denatures disulfide bonds.
Organic solvents denature hydrophobic forces.
Heat denatures all forces.
Carbohydrates
Carbohydrates are also called sugars or saccharides, and are made from carbon and water. Five and six carbon carbohydrates are the most common in nature. The six carbon carbohydrate glucose is the most commonly occurring six carbon carbohydrate.
Glucose
Glucose accounts for about 80% of the carbohydrates absorbed by humans. Glucose exists in aqueous solution in an unequal equilibrium that favors its ring form over its chain form.
If the cell has sufficient ATP, glucose is polymerized to the polysaccharide glycogen, or converted to fat.
Only certain cells in the digestive tract and kidney can absorb glucose against a concentration gradient. This uses a second transport mechanism. All other cells use facilitated diffusion to absorb glucose.
Insulin increases the rate of facilitated diffusion for glucose and other monosaccharides. In the absence of insulin, only neural and hepatic cells are capable of absorbing enough glucose using facilitated transport.
Plants form starch and cellulose from glucose.
Anomers
The ring form of glucose has two anomers. In the first anomer, alpha glucose, the hydroxyl group and the methoxy group are on opposite sides of the carbon. In beta glucose, the hydroxyl group and the methoxy group on the same side of the carbon. The cell can oxidize glucose - transferring its chemical energy to a more usable form, ATP.
Glycogen
When a cell has sufficient ATP, glucose is polymerized to the polysaccharide glycogen.
Glycogen is a branched glucose polymer with alpha linkages. Glycogen is found in all animal cells, with especially large amounts in muscle and liver cells.
Starch
Plants form starch from glucose. Starch comes in two forms. Most animals have the enzymes to digest the alpha linkages of starch and glycogen but not the beta linkages of cellulose.
Cellulose
Plants form cellulose from glucose.
Cellulose has beta linkages. Most animals have the enzymes to digest the alpha linkages of starch and glycogen but not the beta linkages of cellulose. Some animals like cows have bacteria in their digestive systems that release an enzyme to digest the beta linkages in cellulose. Some insects may also have this enzyme.
Note that water is a reactant in the breaking of beta linkages of chitin and cellulose.
Chitin
Chitin is a polysaccharide like cellulose which cannot be digested by animals due to it’s beta linkages.
Note that water is a reactant in the breaking of beta linkages of chitin and cellulose.
Nucleotides
Nucleotides have three components: a five carbon sugar, a nitrogenous base, and a phosphate group.
Nucleotide polymers create the nucleic acids RNA and DNA. Other important nucleotides are ATP, cAMP, NADH, and FADH2.
Phosphodiester bonds
Nucleotides form polymers to create the nucleic acids DNA and RNA. In nucleic acids, nucleotides are joined together by phosphodiester bonds between the phosphate group of one nucleotide, and the third carbon of the pentose of the other nucleotide - forming a long strand.
Structure of DNA and RNA
In DNA, two strands are joined by hydrogen bonds to make a double helix. Adenine and thymine form two hydrogen bonds, while cytosine and guanine forms three.
In RNA, there is only one strand and no helix. Uracil replaces thymine.
cAMP
And important component in many second messenger systems. A nucleotide.
NADH, FADH2
Nucleotides. Also, the co-enzymes involved in the Krebs cycle.
Minerals
Dissolved inorganic ions inside and outside the cell. Create electrochemical gradients across membranes, and thus assist in the transport of substances entering and exiting the cell. Can combine and solidify to give strength to a matrix. Also act as cofactors, assisting enzymes and protein function.
Enzymes
Enzymes are protein catalysts for reaction.
Enzymes lower the energy of activation for reactions and increase the rate of that reaction.
Extreme control of reaction rates gives enzymes the ability to pick and choose which reactions will will not occur inside a cell.
Enzymes are not consumed nor permanently altered by the reactions which they catalyze.
Enzymes do not alter the equilibrium of a reaction.
Substrates
The reactant or reactants upon which an enzyme works.
The position on the enzyme where the substrate binds, usually with noncovalent bonds, is called the active site.
When the enzyme is bound to the substrate, this is called the enzyme-substrate complex.
Lock and key theory
Lock and key theory is an example of enzyme specificity. The enzyme is a lock, the specific substrate is the key.
Induced fit model
The induced fit model is a second theory about enzyme specificity.
The shape of both the enzyme and substrate are altered upon binding.
This increases specificity and helps the reaction to move forward.
When there is more than one substrate, the enzyme may also orient the substrates relative to each other, creating optimal conditions for a reaction.
Saturation kinetics
As the relative concentration of substrate increases, the rate of the reaction also increases, but to a lesser and lesser degree until a maximum rate has been achieved (vmax).
As more substrate is added, individual substrates must wait in line for and unoccupied enzyme.
Vmax is proportional to enzyme concentration, and varies when enzyme concentration is changed.
The Michaelis constant (Km) is the substrate concentration where the reaction rate equals one half vmax. It does not very one enzyme concentration is changed. It is a good indicator of an enzyme’s affinity for its substrate.
Factors affecting enzymatic reactions
Temperature and pH affect enzymatic reactions. For temperature, reaction rate goes up as temperature increases. At some point the enzyme denatures and the rate of reaction drops off dramatically. For enzymes in the human body optimal temperature is most often around 37°C.
For pH, the optimal pH varies depending on the enzyme. For instance, pepsin, which is active in the stomach, prefers a pH below two. Trypsin which is active in the small intestine, prefers a pH between six and seven
Cofactor
A cofactor is a nonprotein component which enzymes pair with to reach their optimal activity.
Cofactors can be coenzymes or metal ions.
Coenzymes are divided into two types: Cosubstrates and prosthetic groups. ATP is an example of a co-substrate.
Many coenzymes are vitamins or vitamin derivatives. Vitamins are essential.
Irreversible inhibitors
Irreversible inhibitors are agents which bind to enzymes and disrupt their function. Irreversible inhibitors are highly toxic. Penicillin is an example.
Competitive inhibitors
Competitive inhibitors compete with substrates by binding reversibly with noncovalent bonds to the active site.
They block the substrate from binding for a very short period of time. The reverse is also true: if the substrate binds first, it blocks the inhibitor from binding.
Competitive inhibitors raise Km but do not change vmax.
Noncompetitive inhibitors
Noncompetitive inhibitors bind noncovalenty to an enzyme at a spot other than the active site, and change the conformation of the enzyme.
They do not prevent the substrate from binding. They do not resemble the substrate, so they can act on more than one enzyme. Unlike competitive inhibitors, they cannot be overcome by excess substrate, and they lower vmax. They do not lower enzyme affinity for the substrate, so km remains the same.
Zymogen
A zymogen is one of the ways enzymes are regulated. These are enzyme precursors, and often have the suffix -ogen.
Proenzyme
A proenzyme is one of the ways enzymes are regulated. They are in the same group with zymogens.
Allosteric interactions
Allosteric regulation of an enzyme is when the enzyme is modified by a configurational change resulting from the binding of an activator inhibitor had a specific binding site on the enzyme
Negative feedback
Also called feedback inhibition, this happens if one of the downstream products in a reaction comes back and inhibits the enzymatic activity of an earlier reaction. This can provide a shutdown mechanism when a series of enzymatic reactions has produced enough product, for instance, with amino acids.
Positive feedback
Positive feedback is less frequent the negative feedback. This happens when a product returns to activate an enzyme.
Allosteric regulation
when inhibitors or activators bind to an enzyme and cause a confirmational change. These are not necessarily noncompetitive inhibitors, because many alter km without affecting vmax.
Metabolism
All cellular chemical reactions. Consists of anabolism and catabolism.
Three stages of catabolic metabolism:
1. macromolecules broken down into constituent parts, releasing little or no energy.
- Constituent parts oxidized to acetyl CoA, pyruvate and other metabolites, forming some ATP and reduced coenzymes.
- If oxygen is available, these metabolites go into the citric acid cycle to capture large amounts of energy. Otherwise, coenzymes and other byproducts are either recycled or expelled as waste.
Positive cooperativity
At low substrate concentrations, small increases in substrate concentration increase enzyme efficiency as well as reaction rate. The first substrate changes the shape of the enzyme, allowing other substrates to bind more easily. There is also an inverse called negative cooperativity.
Anaerobic respiration
Respiration in which oxygen is not required.
Glycolysis
The first stage of anaerobic and aerobic respiration.
The series of reactions that breaks a six-carbon glucose molecule into 2 3-carbon molecules of pyruvate. Other important products from glycolysis are two molecules of ATP each from ADP, inorganic phosphate, and water. Also, two molecules of NADH each from the reduction of NAD+.
Glycolysis occurs in the cytosol.
Substrate level phosphorylation
The formation of ATP from ADP and inorganic phosphate, using the energy released from the decay of high-energy phosphorylated compounds
Oxidative phosphorylation
Using the energy from diffusion of ions down their concentration gradient to form ATP
Fermentation
Fermentation is anaerobic respiration. It includes glycolysis, the reduction of pyruvate to ethanol or lactic acid, and oxidation of NADH back to NAD+.
fermentation causes yeast to produce ethanol and human muscle cells to produce lactic acid. Fermentation happens when a cell or organism cannot assimilate the energy from NADH and pyruvate or has no oxygen to do so.
In fermentation, NAD+ is restored for use in glycolysis as a coenzyme, and lactic acid or ethanol with carbon dioxide is expelled as waste.
The net ATP production from fermentation is two molecules.
Aerobic respiration
Requires oxygen. The products of glycolysis- pyruvate and NADH- move into the matrix of the mitochondria. Once inside the matrix, pyruvate is converted to acetyl CoA in a reaction that produces NADH and carbon dioxide.
Aerobic respiration produces about 36 net ATPs including glycolysis.
Krebs cycle
Also called the citric acid cycle, each turn produces 1 ATP, 3 NADH, and 1 NADH2. Begins when acetyl CoA transfers two carbons from pyruvate to the four-carbon oxaloacetate acid. (The major input for the Krebs cycle is acetyl CoA.)
ATP production in the Krebs cycle is called substrate level phosphorylation.
During the Krebs cycle, two carbons are lost as carbon dioxide and oxaloacetate acid is reproduced to begin the cycle over again. Note that the Krebs cycle turns twice, once for each pyruvate generated by glycolysis.
Electron transport chain
A series of proteins, including cytochromes with heme, in the inner membrane of the mitochondria. The first protein complex in the series oxidizes NADH by accepting its high-energy electrons. Electrons are then passed down the protein series and accepted by oxygen to form water. As electrons are passed along, protons are pumped into the intermembrane space for each NADH.
As electrons move within the electron transport chain, each intermediate carrier molecule is reduced by the preceding molecule and oxidized by the following molecule.
Proton-motive force
As protons are pumped into the intermembrane space at the end of the electron transport chain, this establishes a proton gradient called the proton motive force. This propels protons through the ATP synthase motor to manufacture ATP. Production of ATP in this fashion is called oxidative phosphorylation.
2-3 ATP’s are manufactured for each NADH. FADH2 works similarly, but only produces about two ATPs.
