Chemistry of Cells
What are the most common elements?
Nitrogen, Oxygen, Hydrogen, and Carbon
Explain spontaneous vs nonspontaneous
Spontaneous reactions have a negative change in Gibbs free energy meaning it does not need energy to occur while nonspontaneous reactions have a positive change in gibbs free energy meaning it needs energy to occur making it unfavorable
Name and describe the four levels of protein structure
primary: the amino acid sequence that creates a protein
secondary: alpha helices (twisted coil of AA, occurs based on AA compilation) and beta sheets (laterally connected beta strands by H bonds)
tertiary: the configuration of the protein in 3D based on AA and backbone interactions
quaternary: the fully functional group of proteins together that perform one function, not all proteins have a quaternary structure
Describe the function of the Golgi Apparatus
post office of the cell, reads the AA zip code to know where to send the products by vesicle
Compare enzymes and catalysts
enzymes are biological catalysts, a type of catalyst
both speed up the reaction and enhance the rate of the reaction
enzymes do this by lowering the activation energy, energy required to start the reaction
What is the difference between polar and nonpolar covalent bonds?
Polar covalent is unequal sharing of electrons because of different electronegativities of the two elements involved in bond
nonpolar covalent is equal sharing of electrons because the electronegativities are close or are the same
Describe the difference between NADH and NADPH
both carry electrons and have a very similar structure aside from the additional phosphate group in NADPH, both play a primary role in cellular metabolism
NADH: mostly in catabolic reactions
NADPH: mostly in anabolic reactions
What is a scaffold protein?
A scaffold protein is a protein that binds to different proteins to help bring them all together to perform their function. Its like a guide getting everyone to the same location so they can work together
What are the big 6 atomic profiles?
O: 8
H: 1
C: 6
P: 15
S: 16
N: 7
Explain Redox reactions
a pair of redox reactions occur when oxidation is the loss of an electron and reduction is the gain of an electron so to have a loss someone has to gain these reactions are paired together
What are 3 examples of small molecules and name a structure they are in?
fatty acids: found in phospholipid membranes, length, and saturation determine characteristics
nucleotides: found in nucleic acids, essential in DNA and transfer of energy in ATP/GTP , are split into two groups pyrimidines: Cytosine, thymine, uracil and purines: adenine and guanine
How are nonspontaneous reactions possible?
Nonspontaneous reactions are made possible by reaction coupling. Reaction coupling occurs when a spontaneous favorable response with a negative delta G is paired with an unfavorable positive delta G reaction. The two reactions must have a net negative delta G to overcome the energetic hill of the unfavorable reaction.
What is a high-energy intermediate? use glutamic acid to glutamine to describe
A high-energy intermediate is a state in between the starting molecule and the product which is the least favorable state. Energy in the form of ATP is used to turn glutamic acid into an intermediate containing the Pi from the dissociated ATP molecule. The intermediate is then made into glutamine by favorably removing the Pi and attaching the NH2 without the use of more energy because the high-energy state favors the creation fo the lower energy state product
What is Km?
Km is equal to one-half of Vmax. Vmax is the point of full saturation where the reaction can no longer get any faster
What is a noncompetitive inhibitor?
a noncompetitive inhibitor binds to a second binding site and prevents binding of the enzyme. it is noncompetitive because since it is a second binding site it can't be overcome
Who discovered how to view macromolecules and what is the machine called?
Theodor Svedberg, ultracentrifugation: identify a pattern within the material to see the macromolecules which can then be viewed in x-ray diffraction to see the smaller monomers within the macromolecule
explain the difference between kinetic and potential energy
potential energy: energy of a position, energy that is stored in chemical bonds, concentration gradients, and electrical potential - meaning the ability to break a bond for energy or move across a gradient to create energy
kinetic energy: energy of action, energy that does work in the form of heat, light, electric, or mechanical - the small movement of all things with energy
A researcher wants to know if there is a mutation within a protein that has a critical function in cellular replication. What type of antibody should be used?
monoclonal antibody because it binds specifically to the antigen present on the mutation. Monoclonal antibodies are more specific, so would be best used in this situation because of the specificity of a single mutation in a specific protein
What are hydrophobic forces?
hydrophobic forces are a name for nonpolar molecules moving together to minimize the effects of a repellent. The nonpolar molecules move together to make having nonpolar molecules in polar water more favorable by decreasing the surface area of nonpolar exposed
Give an example of a polar (positive, negative, and uncharged) and nonpolar AA
polar
uncharged: Tyrosine
negative: glutamic acid
positive: Lysine
nonpolar: alanine
What is the most common interaction?
noncovalent
Describe the effects of equilibrium across a membrane
equilibrium across a membrane is detrimental to cells. Without a gradient to use for getting things inside and outside the cell based on the cell needs. The gradient across a membrane facilitates the production of ATP through the ATP synthase that spans the membrane. Without the gradient of H+ the pump would not be able to spin and create ATP. Without ATP to power cellular processes, the cell will not prosper.
How are proteins controlled?
phosphorylation is one-way proteins can be controlled. When a protein has a Pi added it can change the conformation (structure) which leads to functional changes of the protein. Since Pi is highly negatively charged it can change the folding of the protein based on the charges of the AA around it causing changes in function. The reversible process can be seen as an on-off switch because without a correct formation a protein can't perform the function
Name two factors that affect protein formation.
chaperones: bind to partially folded proteins to make sure that the protein folds correctly
enzymes: enzymes speed up the process of binding the AA together with peptide bonds to create the protein
What is a regulatory GTP binding protein?
A protein that works as a molecular switch. The protein is active when a GTP binding site has a Pi present and is inactive without. This is a reversible process. a malfunction in this process may lead to cancer