Answer:
(Horton 1.2 p 5-6) C, H, N, O, S, and P. The fact that there are so few elements involved greatly simplifies the chemistry that YOU have to remember. For example, the fact that the oxygen of an -O-H group can act as a nucleophile is something you are going to see over and over again.
Answer:
We get these elements from the food we eat; the basic molecules we need are often found ready-made there, although we can make many of them ourselves, provided we eat the right starting materials. Plants are more independent; they can take carbon (as CO2) out of the air itself using the energy from light. Some bacteria are able to "fix" both carbon and nitrogen from air. The rest of us are in fact parasites.
Answer:
C usually prefers 4
H usually prefers 1
N usually prefers 3
O usually prefers 2
S usually prefers 2
P usually prefers 5
Answer:
N and O are the most electronegative, that is, that they like to attract electrons to themselves. Their location at the top right corner of the periodic table means that their outer shell of electrons is nearly complete; they can "fill" this outer shell by borrowing someone else's electrons, and so approach the stability of the nearby "noble" gases. They like that. We often refer to these atoms as being "polar", that is, they'd rather spend their time with the like-minded atoms of water, and not the non-polar ones found (e.g.) inside a membrane.
Answer:
(Horton 2.6 p 33-34) We will see the electronegative O, N, (and sometimes S) atoms acting as nucleophiles in various chemical reactions. In the example you were given, the product would look like:
Answer:
(Horton 2.5 p 31-33) A covalent bond is a chemical bond where outer shell electrons are shared between the two bonded atoms. The primary non-covalent forces involved in holding biological molecules together are charge-charge interactions, hydrogen bonds, and van der Waals interactions. Horton has a very good description of how each one works, and you should by now have carefully read and understood that part. These different interactions rank approximately in strength:
covalent > charge-charge > hydrogen bond > van der Waals
but they are each quite variable depending on their exact composition, and where they are found. All, however, are much weaker than a covalent bond.
Answer:
(Horton 2.5C p 32-33) A van der Waals radius is essentially the space that an atom takes up, which is usually viewed as spherical for a single atom; the radius varies with the type of atom (usually 1.0 to 1.8 Å). When two atoms are placed so that these spheres touch, they make a van der Waals contact; the distance between their centers is the van der Waals contact distance. Atoms that are bonded to each other come closer than the sum of the van der Waals radii of the two atoms (that is, the spheres get squashed together). If the two atoms come closer than the sum of the van der Waals distances, but don't form a chemical bond, there is a huge repulsive force trying to push them apart. But if they happen to be at the sum of the van der Waals distances, there is a weak attactive force holding them together; the attraction gets weaker if the atoms move further apart. (See the picture on p. 32 of Horton.)
What type of molecule is this, and what special properties might it have?
Answer:
The non-polar portion is at left, and the polar group at right. This is an amphiphilic molecule (a fatty acid, which is a kind of lipid), and will have some of the properties of a detergent. That is, it will be able to associate with itself (making micelles), with non-polar molecules, and with water.
F = q1 q2/r2 D
where
q1 and q2 are charges on the two groups
r is their separation
D is the dielectric constant
what would you expect for the relative strength of an electrostatic interaction in water, compared to that inside a membrane?
Answer:
The high dielectric constant of water is going to mean that electrostatic interactions (such as hydrogen bonds) will be much weaker there, than in a non-polar medium such as the inside of a membrane. So, if you wanted to have the biggest impact from charged groups, you would place them in a low-dielectric medium. This has important consequences that you will learn about later!
Answer:
(Horton 2.7-2.9 p 35-42) An acid is any compound that can lose a proton (H+) to a base; a base is one that can take on a proton from an acid. An acid that has lost its proton becomes a base; of course, the charge of the molecule changes when it does this. If we define the equilibrium:
acid <=> H+ + base
where
Ka = [H+] [base] / [acid]
then the pKa is:
pKa = -log K
In practice, the pKa is the pH at which the concentrations of the acidic and basic components of the solution are equal.
More generally, a dissociation constant (Kd) for an equilibrium where AB is dissociating to A and B is:
Kd = [A] [B] / [AB]
In the example you were given, the [OH-] would be 10-4, and the pH would be 10. This is a basic solution.
Answer:
(Horton 2.9 p 37) Physiological pH is 7.4-7.6. The pH matters, of course, because you have to work there for the chemistry you need. The physiological buffer is generally phosphate, and sodium chloride is the most prevalent salt; it's kind of like sea water. In fact, a solution of 10 mM sodium phosphate, 150 mM sodium chloride, pH 7.5 is often referred to as "physiologically-buffered saline", and you'll find something similar used in every hospital, or in contact lens solution. Almost every reaction you have takes place in that general environment, but the cell soup also contains a lot of proteins, lipids, sugars and other molecules, and so it is really pretty different from what you find in a test tube. And a membrane is going to be completely different: it is basically 2-dimensional (and has two sides) and hydrophobic inside!
Answer:
(Horton chapter 2) Water is the solvent in which nearly all of our chemistry takes place. It can form hydrogen bonds to itself and to other molecules, participate directly in the chemistry, force hydrophobic compounds "out of solution", and basically affects everything in one way or another.
Answer:
(Chapter 1.3 p 8-14) A polymer is a long chain made up of smaller, similar units linked to each other covalently. Proteins (polypeptides), complex carbohydrates (oligo- and polysaccharides), and polynucleotides are polymers of amino acids, sugars and nucleotides, respectively. You can see the structures of the individual units in Horton. Polymers are important because they make proteins long enough to fold up into specialized shapes (which can have many different jobs), and because they can store and carry information in a code form (like DNA). Lipids have a polar head part and a non-polar tail part. All of these compounds may be used as energy and a source of raw materials. Proteins have a variety of structural roles and are the most important catalysts in the cell. Simple sugars are the basis of energy-producing reactions. Complex polysaccharides mark different kinds of proteins and cells, and store energy. Lipids form membranes. Polynucleotides such as DNA and RNA store and carry genetic information.
DNA, RNA, proteins, membranes, nucleus, endoplasmic recticulum, organelles, cytoplasm, chloroplasts, mitochondria, Golgi apparatus, cytosol, chromosomes
Answer:
| Procaryotic | Eucaryotic | Role | ||
| DNA | DNA | store and carry genetic information | ||
| RNA | RNA | carry genetic information, helps make proteins | ||
| proteins | proteins | structure and catalysis | ||
| membranes | membranes | form boundaries of cell, divide cell into compartments | ||
| nucleus | seperate DNA from rest of cell | |||
| endoplasmic recticulum | synthesis and transport of lipids and proteins | |||
| organelles | smaller compartments with specific function | |||
| cytoplasm | cytoplasm | the inside of the cell | ||
| chloroplasts | (plants only) photosynthesis | |||
| mitochondria | combining food and O2 to make energy | |||
| Golgi apparatus | modifying, sorting and packaging macromolecules for export or delivery | |||
| cytosol | cytosol | everything inside the cell, except organelles | ||
| chromosomes | divide DNA into manageable pieces | |||
| (cell wall) | (cell wall) | protect the cell in some procaryotes and plants | ||
| cytoskeleton | determine cell shape and help them move |
a) nM > mM > M
b) m > Å > nm
c) nM < mM < M
d) mg < g < mg
Answer:
(Horton 1.10 p 23-24) Only c) is correct.
Answer:
We have about 100,000 genes (the simplest bacteria have about 400), and any cell doesn't use all genes at any given time. Cellular specialization depends almost solely on control of the expression of different genes. So the different things in our cells are made at different times, or never, as is needed by the situation, and job, of that particular cell.