Chemistry and Proteins
Why is Carbon (C) a part of so many different molecules?
Carbon has 4 valence electrons, resulting in its ability to form 4 bonds
What is the equation for cellular respiration?
What are the 3 steps of cellular respiration (include the location AND purpose of each step)
C6H12O6 + 6O2 ----> 6H2O + 6CO2 + ATP + heat
Glycolysis: occurs in cytoplasm, oxidize glucose into pyruvate
Krebs Cycle (Citric Acid Cycle): occurs in inner mitochondrial matrix, finish oxidizing acetyl-CoA
Electron Transport Chain: occurs in inner mitochondrial membrane, phosphorylate ADP (ADP + Pi --> ATP) using H+ gradient to create ATP
Define activation energy
How does activation energy relate effect the rate of a reaction?
Explain the mechanism behind substrate binding to the active site leading to lower activation energy
Activation Energy: kinetic energy required of two colliding molecules to react
Enzymes are able to lower activation energy resulting in the reaction rate to increase.
Substrate binds to active site --> enzyme changes shape, which will align substrates if it is a synthesis reaction, and strain the chemical bond if it is a degradation reaction.
What are the components of the plasma membrane, include functions?
What gives the plasma membrane its charecteristic of selective permeability?
Phospholipids: create a selective permeable membrane due to the arrangment of polar phosphate heads and non polar fatty acid tails.
Proteins: both structural (cytoskeleton) and functional (enzymes, receptors, carriers, etc.)
Carbohydrates: self identity
Cholesterol: membrane fluidity
What type of membrane transport would be most suitable in the following scenarios?
1. movement of glucose out of the epithelial cell going with its concentration gradient
2. movement of H+ into the stomach, driven by taking Na+ out of the stomach
3. Constant efflux of K+ going from a high to low concentration
4. Steroid hormone entering the cell from a high to low concentration
1. Carrier Mediated Facilitated Diffusion
2. 2o Active Transport (specifically countertransport)
3. Channel Mediated Facilitated Diffusion (via leaky non gated K+ channels)
4. Net diffusion (non-polar -> no carrier needed)
What are the types of bonds between atoms that directly involve electrons? Give an example for each
Polar Covalent bonds: 2 or more unequally shared electrons (H2O)
Non Polar Covalent bonds: 2 or more equally shared electrons (O2)
Ionic bonds: complete transfer (stealing) of electrons (NaCl)
(Hydrogen bonds NOT included because they are weak electrostatic attractions between the partially negative and positive ends of molecules)
Differentiate the following terms...
Catalyst vs Enzyme
Substrate vs Reactant
Kinase vs Phosphatase
Endergonic vs Exergonic
Catalyst is a chemical substance used to speed up chemical reactions whereas enzymes are chemical substances used to speed up biological reactions.
Substrates are molecules that bind to the active site of enzymes during biological reactions, whereas reactants are "starting material" of chemical reactions enacted on by catalysts.
Kinase is an enzyme responsible for phosphorylation of proteins (turning on) whereas Phosphatase is an enzyme responsible for dephosphorylation of proteins (turning off)
Endergonic reactions require an input of energy in order for the reaction to proceed, whereas exergonic reactions release energy as the reaction completes.
What is an isoenzyme? How are we able to distnguish between isoenzymes?
enzymes with the same active site (bind to the same substrate) that are found in different organs
eg. LDH in heart, kidney, and liver
the origin of the isoenzyme is distinguishable by a few amino acid differences
TRUE or FALSE:
1. 2o Active transport requires direct usage of ATP.
2. Small polar molecules like ions are able to diffuse through the plasma membrane
3. Water is not able to diffuse past the plasma membrane due to its polarity
4. Movement of glucose and amino acids past the plasma membrane with their concentration gradient is an example of channel-mediated facilitated diffusion
1. False, requires indirect usage of ATP (energy is stored in Na+ concentration gradient created by 1o Active transport.
2. False, ions are charged particles and are repelled by polar phosphate heads
3. False, water is an exception to other polar molecules in that it is able to diffuse past the plasma membrane in certain amounts.
4. False, it would be carrier-mediated facilitated diffusion
What is Bulk Transport? Give examples
Movement of large particles into (endocytosis) and out of (exocytosis) the cell
out of the cell: neurotransmitters and hormones
into the cell: LDL, cholesterol, vitamins, WBC's
How would a buffer act if added to the following solutions...
1. solution with 2 pH
2. solution with 12 pH
3. solution 7 pH
1. buffer would bind to free H+ in solution resulting in the pH of the solution to become more neutral (closer to 7)
2. buffer would release free H+ in solution resulting in the pH of the solution to become more neutral (closer to 7)
3. Solution is already neutral, so buffer would have no effect
What is the function of ATP?
Where is the energy harvested to create ATP?
Where is the energy stored in an ATP molecule?
ATP is a food energy conversion molecule that fuels our metabolism by storing + transfering a high energy phosphate
The energy to phosphorylate ADP (ADP + Pi --> ATP) is harvested from covalent bonds in carbohydrates (glucose) and lipids (free fatty acids, etc.)
Energy harvested from covalent bonds of macromolecules is transferred to the covalent bond between the 2nd and 3rd phosphate in ATP
Define the following terms related to control of enzyme activity
1. Allosteric Modulation
2. Covalent Modulation
3. Genetic Regulation
4. Proteolytic Cleavage
1. Binding of a regulatory molecule on an enzyme in the "allosteric site" (site other than the active site) that can either activate or inhibit that enzyme
2. Covalent bonding of a high energy phosphate (phosphorylation) turning an enzyme on, and removal of a high energy phosphate (dephosphorylation) turning enzyme off.
3. Cells turn on genes that code for proteins when needed; especially important during development and pregnancy
4. Inactive enzyme is released as a zymogen, and must be activated (pepsionogen + HCl ---> pepsin)
What are the two components that are required in all membrane transport?
Driving force: can be ATP (travelling against the gradient; active) or concentration gradient (travelling with the gradient; passive)
Pathway: based on molecule polarity and size
What are the different types of intercellular signaling?
Autocrine
Paracrine
Endocrine
Neuroendocrine
Synaptic Signaling
Name the biological macromolecule, the monomer (if applicable), and the function that each of the following substances pertains to...
1. glycogen
2. cholesterol
3. ATP
4. triglyceride
5. peptides
1. carbohydrate; glucose; form of energy storage in skeletal muscle and in the liver
2. lipid; cholesterol is a monomer!!; allows for membrane fluidity and is a precursor to various steroids
3. nucleic acid; adenine (nucleotide) + ribose (sugar) + 3 phosphates; food energy conversion molecule
4. lipid; glycerol + 3 fatty acids; forms cell membranes
5. proteins; amino acids; can be various structural or functional proteins
1. What are the two types of metabolism (give examples)?
2. What are the components of intermediary metabolism
Body Wide Metbolism: blood glucose regulation (insulin and glucagon), metabolic rate control (thyroid hormone), stress response (cortisol)
Cell (Intermediary) Metabolism: anabolism, catabolism, transformation of molecules
2. transfer of energy, transformation of matter, membranes, and enzymes
What were the two inborn (genetic) enzyme disorders talked about in lecture?
*if Colette said this information was only FYI, then dont worry. Still know it though, better safe than sorry*
Phenylketonuria (PKU):
musty smelling urine
lack enzyme responsible for converting phenylalanine ----> tyrosine which leads to an accumulation of phenylpyruvic acid (can cause brain damage).
Tay-Sachs Disease:
lack of lysosomal enzyme caused by genetic mutation leading to accumulation of gangliosides in neural tissue ----> nervous system degeneration.
What is transported using channel mediated facilitated diffusion? List the different categories of channels
Ions and Water
Voltage gated channels, mechanically gated channels, ligand gated channels, aquaporins, non gated (leaky) channels
What determines the location of a receptor for a messenger molecule?
If the messenger molecule is polar, it will not be able to diffuse past the plasma membrane. Therefore its receptor will be embedded in the plasma membrane.
If the messenger molecule in non polar, it is able to diffuse past the plasma membrane, and its receptor will be in the cytosol.
What are the essential life functions of water? Give an example for each
Why is water able to be such a great solvent for POLAR molecules and ions?
cushion: CSF
lubrication: synovial fluid
chemistry: dehydration synthesis and hydrolysis
solvent: for all the body's electrolyte solutions
cooling: sweat
Water is an excellent solvent for polar molecules and ions because water itself is polar. Due to waters polarity, it is able to form electrostatic attractions with other polar molecules and ions to "pull them apart" or dissolve them.
List the steps of protein synthesis
Relate this concept to a form of enzyme activity regulation
1. DNA unraveled and transcribed into mRNA..
2. Messenger RNA (mRNA) leaves nucleus and binds to ribosome.
3. Translation: Codon (3 base pair sequence) located on the mRNA strand are paired with an anticodon carried by the transfer RNA (tRNA) coding for various amino acids
Genetic Regulation: cells turn on genes that code for certain proteins ---> create enzymes when/if needed
List the ways that we are able to control enzyme activity
Temperature optima, pH optima, saturation, specificity, allosteric modulation, covalent modulation, genetic regulation, proteolytic cleavage, cofactors, coenzymes
What are the essential functions of the Na/K ATPase pump?
1. Maintains resting membrane potential (RMP)
2. Creates the Na+ gradient that runs 2o Active Transport
3. Prevents osmotic damage to cells (water follows Na+)
1. What is resting membrane potential?
2. What creates/maintains the resting membrane potential?
3. What did the results of the RMP experiment tell us about the importance of K+?
1. RMP is -70mV; some cells like neurons and muscle cells use the RMP for intracellular signaling (neurotransmitter release and muscle contraction)
2. Na+/K+ ATPase Pump, large (-) charged proteins in cell, leaky K+ channels
3. RMP is closer to K+ equilibrium potential compared to Na+, and also that the plasma membrane must be more permeable to K+ compared to Na+