BIOL 231 Exam 1

How is order kept by cells?

They (their boundaries) expend a lot of energy to overcome entropy.

What are the two main boundaries of cells?

The plasma membrane and the organelle membrane.

What makes up the lipid bilayer?

Two distinct layers of hydrophilic/phobic molecules 5 nm thick. The layers are distinct, with differing carbs, lipid, and proteins in them.

What are the seven Membrane Boundary Properties?

Continuous

Selectively Permeable

Asymmetric

Disequilibrium

Locus for Biochemical Activity

Respond to External Signals

Mediate Cell-Cell Ineractions

Why do membranes need to be continuous?

It is necessary for cells to function.

Why must membranes be selectively permeable?

They must undergo managed exchange, bringing fuel in and waste out. They also need to maintain their disqeuilibriums.

Why is it important for cells to constantly by in disequilibrium?

Equilibrium is only in dead cells. Diseq. is both chemical and electrical; for example, [Ca2+] is much higher outside the cell than inside, and the membrane exhibits 100 KV/cm.

Why is being a locus of biochemical activity important for a cell?

It helps to impose and maintain order.

In general, how do shape and size affect the surface area:volume (SA/V) ratio?

Shapes with greater surface area coverage support higher activity, and being smaller also supports higher activity.

What are the three compartments created by membranes?

The cytosol (cytoplasm - organelles), organelle lumens, and the outside cell.

Which compartments are connected to one another?

The organelle lumens and the outside cell.

If two organelles fused together, how would the lumens and a protein facing outward change?

The lumens would be in the fused organelle, and the protein would face outward.

If an organelle fused into the plasma membrane, how would organelle lumens and a protein facing outward change?

The lumens would be released into the ECF, and the protein would flip to face inward.

What are the two layers present in organelles and plasma membranes?

There is a cytosol layer (inward for cells, outward for organelles) and a noncytosol layer (outward for cells, inward for organelles).

What are some chemical properties of H2O?

It interacts well with itself and is a cohesive liquid (0-100C liquid). It is also electronegative thanks to the oxygen atom.

Additionally, cells are aqueous, so molecules are either hydrophilic or hydrophobic.

What is an example of an electronegative compound?

Glucose. With its 6 oxygens, it boasts a lot of pulling and EN charge. It’s highly soluble with 133 g/L, making it very hydrophilic.

What’s an example of a hydrophobic compound?

Hexane. It is nonpolar and not H2O soluble (<10 mg/L).

What is Kw?

The result of multiplying the concentration of hydrogen ions and hydroxide ions together. This is equal to 10^-14 and is the basis of the pH system.

What is pH?

-log[H+]. For example, pH5 = 10^-5 moles/L of H+.

How do carbon single and double bonds differ?

Single bonds can rotate and the carbon’s bonds are equivalently spaced.

Double bonds cannot rotate and the other elements bound to the carbons are in the same plane.

How are double carbon bonds useful for packing?

Double bonds make molecules harder to pack, which is good for preventing solidification.

What are the seven functional groups?

Methyl, carbonyl, hydroxyl, sulfide, phosphate, carboxyl, and amine.

Describe the methyl group.

It is CH3. It is non-ionized.

Describe the carbonyl group.

It’s a carbon double bonded to an oxygen. These are present in nucleic acid bases. They are non-ionized.

Describe the hydroxyl group.

It is an OH. As pH increases, the group ionizes into H+ and loses the O-.

Describe the sulfide group.

It is an SH. As pH increases, the group ionizes into H+ and loses the S-.

Describe the phosphate group.

It is a phosphorus bound to four oxygens; one oxygen is bonded to an H, another is double bonded, the third oxygen binds to the backbone, and the final oxygen has a negative charge.

As pH goes up, the H+ is lost, and two oxygens are negative now. Phosphates can lose 2Hs if pH is high enough.

Describe the carboxyl group.

It’s the biological acid (extremely important for proteins!!!) made up of a carbon double bonded to an oxygen and bonded to a hydroxyl. As pH increases, the H+ is lost.

Describe the amine group.

It’s the biological base made up of a nitrogen and two hydrogens. As pH decreases, it gains a H+.

How do the charges of carboxylic acids (CA) and amine change depending on the pH?

At high pH, CA is -1 and amine is 0. At low pH, CA is 0 and amine is -1.

What is pK?

The transition between charged or no charge for ionizing functional groups.

What are the four covalent linkages?

Ester, phosphoester, and phosphoanhydide.

Describe the ester bond.

It is a bond between CA and an alcohol. Through a condensation reaction, the oxygen and carbon connect and H2O is lost. This is present in phospholipids.

Describe the phosphoester bond.

It is a bond between a phosphate and alcohol. Through a condensation reaction, the oxygen and carbon connect, and an H2O is lost. This is present in DNA, RNA, and phospholipids.

Describe the phosphoanhydide bond.

This is a bond between two phosphates. Through a condensation reaction, the oxygen and phosphate combine, and an H2O is lost. This is present in XTP and XDP; the negative oxygens possess a lot of energy.

Describe the amine linkage, also known as the PEPTIDE BOND.

This is a bond between an amine and CA. This bond cannot rotate and is the foundational bond of all proteins. The O in the CA and the H in the amine are OPPOSITE of each other.

What are some characteristics of non-covalent bonds?

They are easier to break than covalent bonds and possess 1-10% of the energy of covalent bonds. Large numbers of these bonds can have large effects.

Describe ionic bonds.

This is charge attraction between charged parts of molecules; for example, the O- of a CA and the H+ of an amine attract one another.

These are most common where water and ions can be excluded.

What are some disruptors of ionic bonds?

Ions, water, and pH.

Describe hydrogen bonds.

Two molecules “share” a hydrogen; N and O do this frequently. H-bonds are strongest when the the three atoms involved are in a straight line. A disruptor of this is H2O.

Describe hydrophobic forces.

Attributable to entropy, these are when hydrophobic molecules cluster together in H2O environments. When they cluster together, disruptions on the H2O network are minimized.

Describe Van der Waals forces.

These are nonspecific, small but significant attractions at the right distance (3-4 angstroms) that have low energy (.4 kJ/mol).

What are the six main atoms that make up our macromolecules?

C, N, O, H, P, and S.

Describe steroid lipids such as cholesterol.

Cholesterol is a hydrophobic, planar rigid ring with a C8 flexible tail. It has a small polar (OH) head group.

Describe Acyl Glycerols.

These are molecules made up of a glycerol backbone (CH2-OH) and a fatty acid chain. The O- of the fatty acid chain bonds with an O from the backbone as an ester bond, losing an H20 in the process.

Examples of these are the glyceride molecules.

Describe phospholipids.

These have a hydrophilic head and a hydrophobic tail. They made via a phosphate connecting to a acyl glycerol (glycerol + FA chains) through a phosphoester bond. Water is lost.

What are the two types of glucose, and how do they differ?

Alpha glucose: hydroxyl group at carbon 1 is down.

Beta glucose: hydroxyl group at C1 is up.

Draw and number a glucose ring.

Start after the O for numbering! Make sure you note both types of glucose.

What are the two linkages between glucose molecules?

C1-C4 and C1-C6, the latter of which is branched.

Draw the connection between C1-C4 on beta and alpha glucose. What are these larger molecules of each called?

A = starch, is usable by us.

B = cellulose, not usable by us.

Draw an alpha glucose forming both a C1-C4 and a C1-C6 bond. What macromolecule exhibits this?

Glycogen.

What are the three parts of nucleic acids?

The base, the sugar, and the phosphate.

Describe the bases of nucleic acids.

They consist of two groups: the 6-member pyrimidines (C, T, and U) and the 9-member purines (A and G).

Draw and number a pyrimidine and a purine.

Know where to start for each! Start at the bottom N for pyrimidine, and start at the top right N for purines.

Describe AND draw the sugars present in nucleic acids.

These are the backbones of the nucleic acids. There are two types: ribose for RNA and deoxyribose for DNA.

Both are five-ring sugars, but the hydroxyl group on 2’C determines whether it is ribose or deoxyribose.

Describe the phosphate portion of nucleic acids.

This is attached to the 5’ CH2OH. It exhibits a phosphodiester linkage when linking 3’ and 5’ ends of ribose together.

Draw and describe the basic amino acid structure.

A single AA is both amphoteric (both acid and base) and zwitterionic (+ & - charge). It consists of an amine, CA, H, and an R group of varying complexity.

They are polar molecules with an N terminus and C terminus. Addition happens at the C terminus.

How are two amino acids linked, and what happens to them?

Via a PEPTIDE BOND. Once they are linked, they become AA residues.

Describe equilibrium and its presence in cells.

It is the lowest energy state, but cells are always at diseq.; this higher energy is used to create and do useful work.

What is the first law of thermodynamics?

Energy is converted among forms, never made or destroyed.

What is the second law law of thermodynamics?

Systems tend to disorder; this is called entropy.

How does Gibbs Free Energy (G) use both energy and entropy?

It combines total energy (enthalpy) with what’s lost due to disorder.

AG = AH - TAS

What can G tell us about the spontaneity of a reaction?

If G is negative, the reaction is spontaneous.

What is Keq?

[C]eq*[D]eq/[A]eq*[B]eq. It is the concentration of the products over reactants at equilibrium.

If Keq > 1, the reaction proceeds right and is spontaneous.

What is the difference between G and G^o?

G varies, whereas G^o is under standard conditions.

What is the main equation that uses both G^o and Keq?

G^o = -5.7kJ/mol*log(K_eq)

What is q?

The concentration of products over reactants at the current state. If it is less than K_eq, the reaction proceeds right.

What is an example of a coupled reaction?

Glucose phosphorylation in glycolysis. If ATP hydrolysis is added, then the total reaction is spontaneous.

How do enxymes affect reactions?

They ONLY change the Energy of Activation, known as E_A. They do this by stabilizing the transition state.

What are three important facts about enzymes?

They do get consumed in reactions, they have an active site where substrates are manipulated, and there are very specific interactions between enzymes and substrates.

What are the three ways enzymes lower E_A?

They bind to substrates and orient them to encourage a reaction.

They change the substrate’s chemistry by rearranging electrons.

The enzyme physically strains the molecule’s covalent bonds to force it into a transition state that favors a reaction.

Which enzyme has the highest rate enhancement of any enzyme?

OMP decarboxylase.

Draw a Michaelis Menton Plot (V v.s. [S]). Explain the parts of it.

V_max is when [S] approaches infinity. K_m is the x value of ½ V_max, which is halfway between 0 and V_max.

Draw a Lineweaver-Burk Plot (1/V v.s. 1/[S]). Explain the parts and how the function works.

Y-intercept is V_max, drawn x-int is -1/K_m.

Equation: 1/V = K_m/V_max*(1/[S]) + 1/V_max. This is like y=mx+b!

How does temperature affect enzyme activity?

Enzymes work best at an optimal temperature, which varies across the human body.

What are some reversible forms of enzyme inhibition?

A competitive inhibitor blocks the active site, whereas a noncompetitive inhibitor binds at a different place to disrupt the structure.

How can enzyme activity be permanently inhibited?

Irreversible inhibitors covalently bond to the enzyme and render it dysfunctional.

For example, the Sarin nerve agent inhibits acetylcholinesterase.

What is an example of beneficial enzyme inhibition?

Enzyme protease inhibitors prevent viral maturation; they block HIV protease, which is critical for the life of HIV.

How does competitive inhibition work?

The inhibitor (Inh.) competes with the substrate for the active site on an enzyme. The greater the affinity of the Inh. and the lower [S], the better the Inh. works.

It requires more substrate to reach K_m, but V_max itself is unchanged.

How does PURE noncompetitive inhibition work?

The Inh. binds elsewhere on the molecule, so it is independent of [S]. The more [Inh.], the greater the inhibition, so V_max will be lower than without the Inh. present.

Draw both the Michaelis-Menton and Lineweaver-Burk curves with a CI and NCI.

Did the intersections with the original lines happen at the right places? Did you mark the changes in V_max and K_m?

How does allosteric regulation work?

The molecule binds at the regulatory site, not the active site, and changes the conformation of the enzyme’s active site. It is not pure NCI because if affects the substrate’s ability to bind to the enzyme.

This type of regulation is seen in feedback inhibition, where the presence of one molecule or product can inhibit an earlier step in its creation.

Describe an example of allosteric regulation.

The third step of glycolysis uses the enzyme PFK. The presence of ATP, lactate, and citrate (last two are end products of glycolysis) inhibit the enzyme, but AMP activates the enzyme.

Draw two amino acids being bonded together. What is the bond called, and what are its properties?

PEPTIDE BOND. It does NOT rotate, and the H and O are OPPOSITE of each other.

Draw the three amino acids that will be on the exam. What are they?

Glycine, aspartic acid, and lysine.

What determines the identity of an AA?

The R group. There are 20 of them.

Describe nonpolar AAs.

There are seven of them; their R groups are exclusively C and H, and they tend to make up the interior of proteins.

Describe polar uncharged AAs.

There are five of them; they aren’t charged at a neutral pH but have a polar group in them.

The ones with a hydroxyl can be phosphorylated!

Describe polar charged AAs.

There are five of them; they have a charge and can participate in ionic interactions. These AAs have a profound effect on reactions and folding, particularly when the pH changes.

What are the three unique AAs, and what makes each of them unique?

Glycine has only an H as its R group and is great for packing.

Cysteine (-CH2-SH) can form unstable covalent bonds and be ionized (pK = 8.3).

Proline restricts backbone rotation by binding to the amine as well! It forms a ring with the N, C, and three CH2.

What characterizes the 1^o structure?

It is the chain of AAs; the linear sequence. It is encoded from DNA.

We have about 20000 different proteins.

What characterizes 2^o structure?

Local, 3-D folding that consists of 10-30 AAs.

Describe alpha helixes.

This folding involves only the backbone of the AAs. H-bonding between the CA’s O and the amine’s H (4 AAs away) causes a helical structure to form that proceeds along the C-terminus end. The R groups stick out of the helix.

Describe beta sheets.

These share the same backbone and bonding of alpha helixes, but the H-bonding happens between long strands. These can either be parallel (C-terminus in same direction) or antiparallel (opposite directions). The R groups are on different sides of the sheet, which can result in wildly different chemistry.

What characterizes 3^o structure?

The whole protein folds on itself via non-covalent interactions. This involves the R-groups that were previously left out, and certain sections of the protein form protein domains.

What are protein domains?

Parts of a protein that can fold independently from the rest and maintain their structure. Most proteins have more than one domain, and most domains are in more than one protein.

How can we reproduce protein domains in vitro?

Domains can be cleaved apart with proteases or DNA expression can transcribe only that part of the protein.

Describe 4^o structure.

Quaternary structure is multiple proteins coming together via interprotein interactions. These tend to be complex and exhibit noncovalent interactions, apart from cysteine residues disulfide bonding to each other.

How can we classify the subunits of proteins?

Subunits of proteins, since most proteins are more than one subunit (4^o structure), can be identical, similar, or different.

What are the names given to proteins with a certain number of subunits?

Dimer for 2, trimer for 3, tetramer for 4, and polymer for anything more.