Biochemistry
Which of these bonds is polar and which is nonpolar?
C-H
O-H
C-H -> nonpolar
O-H -> polar
In the condensation reaction, where is the peptide bond formed?
Between the N-H group (amine) of one amino acid and the C=O group (carboxyl) of a different amino acid
What is more favorable: △G<0 or △G>0
Which is nonspontaneous?
△G<0 is more favorable
△G>0 is nonspontaneous
True or false: membranes are symmetric
False
What eukaryotic organelles feature a double membrane?
chloroplasts and mitochondria
What functional group is the following?
O
O P O
O
Phosphate group
What are the two primary secondary structures of protein folding?
What distinguishes them other than shape?
Alpha Helix - h-bonds form between backbones of amino acids within same polypeptide
Beta Sheets - h-bonds form between backbones of amino acids on different sheets
Is this reaction Josh drew on the board spontaneous?
Yes
What is the main difference between phospholipids, glycolipids, and sphingolipids?
Their backbone structures.
Phospholipids have a glycerol
Sphingolipids have a sphingosine
Glycolipids could have either, but connected to a sugar
Prokaryotic and Eukaryotic DNA differ in what ways?
Prokaryotic -> circular, floats freely in cytosol
Eukaryotic -> linear, organized in nucleus
In polar covalent bonds, what does electron distribution look like
Electrons are shared, but closer to the more electronegative atom
What part of the amino acid determines the 3D folding of a polypeptide chain?
The side chains.
Polar side chains will interact with each other and water. Nonpolar side chains will interact with each other and stay away from water.
What is allosteric regulation and what are the two types?
A regulatory molecule that binds to a different site (not active site) on the enzyme.
a) make it more likely to bind to the substrate (activation)
b) make it less likely to bind to the substrate (inhibition)
What are the three main functions of all lipids?
Energy storage
Membrane Makeup
Chemical Signalling
Describe endosymbiotic theory in one sentence
Chloroplasts and mitochondria originally were self-functioning cells that were absorbed by eukaryotes and now function as two systems, one within the other.
Molecules that have one polar end and one non-polar end are amphipathic. What happens when you put a bunch of these in water?
They form a sphere "micelle" to minimize interactions with water. Nonpolar tails on the inside and polar heads on the outside.
Both high temperatures and high/low pH affect protein function negatively. Why?
These conditions will break weaker interactions holding the protein together. This will unfold and denature the protein. (Peptide bonds will still be holding backbone together - covalent bond)
How would a mutation in the active site of a protein affect enzymatic activity?
The side chains along the active site dictate what substrates can interact with the enzyme. Changing those through a mutation alters the enzyme-substrate interactions, affecting enzymatic activity.
What would happen to the physical characteristics if all of the hydrocarbon tails in a membrane were saturated? unsaturated?
saturated - much less fluid
unsaturated - much more fluid
A microscopic eukaryotic marine organism is heavily involved in the production of fatty acids and oils. What organelle would you expect to be at a higher-than-normal concentration in this organism.
Smooth Endoplasmic Reticulum (lipid production)
An experiment features the addition of perchloric acid (HClO4) to water. Label all ions (cation or anion) that would result and describe the expected change in hydronium ion concentration in each reaction (will it go up or down?)
HClO4 + H2O ⇋ H3O+ + ClO4-
acid gives up H+ cations and ClO4- anions.
H+ cations interact with water to increase hydronium ion concentration (more acidic)
Assume the following amino acids are present in a cross-membrane protein. Where would you expect them to be located?
Ser, Leu, Lys, His, Cys-S-S-Cys (two cysteines that are disulfide-bonded)
intermembrane: Leu, Cys-S-S-Cys
exterior/cytosol: Ser, Lys, His
(Note: the formation of a disulfide bond between two Cys eliminates their ability to H-bond, making them more hydrophobic)
An isolated enzyme grown at 20°C works in a test tube at 20°C but not at 37°C. Once the enzyme has been exposed to the higher temperature it no longer works at the lower one. Can you suggest what happens to the enzyme as the temperature increases?
The heat caused the enzyme to denature (unfold).
Since enzyme structure dictates function, changes in structure result in alterations in function.
Draw an example of an integral and peripheral membrane protein
Check boards
A protein needs to be produced and transported out of the cell, what organelles/cell components would need to be used
Nucleus (DNA needs to be read and turned into RNA)
Ribosome (RNA is read and turned into protein)
Golgi Apparatus (Protein is packaged)
Cytoskeleton (Pathway for package to travel)
Cell Membrane (Protein leaves the cell)