Cell Biology Exam 1 Problem Sets
Free Energy defined
The energy of a system available to do work.
Types of Chemical bonds:
- Covalent (sharing of electrons) - Noncovalent Ionic (donation of electrons)
Functions of fatty acids
-main component of cell membranes (phospholipids). -food reserve -glycolipids for cell recognition
(Bioenergetics: Metabolism.) Process of biodegradation
1. Breakdown of food. *Catabolic Pathways* 2. Generates useful forms of energy. 3. Heat is lost. 4. Gather building blocks
Entropy- Energy Transfer in sunlight example
Electromagnetic light energy →chlorophyll molecule in excited state/high energy electrons →Photosynthesis. CO₂ + H₂O + NH₃ →small molecules, sugars, etc.
noncovalent interactions:
Electrostatic attractions H-bonds Van der Waals attractions Hydrophobic forces.
What are the four weak (noncovalent) interactions that determine the conformation of a protein?
Electrostatic attractions, H-bonds, Van der Waals attractions, Hydrophobic forces.
Entropy- Energy Transfer in a brick example
Raised brick has potential energy.→ Falling brick has kinetic energy→ Heat is released when brick hits the floor.
Nucleotide properties
Ribose sugar + phosphate group
Energy Transfer in Photosynthesis
Stage 1: Sunlight-captured light energy. *Energy carriers* Stage 2: Manufacture of sugars and H₂O and CO₂
The uniform arrangement of the backbone carbonyl oxygens and imino nitrogens in an α-helix gives the helix a net dipole, so that it carries a partial positive charge at the amino end and a partial negative charge at the carboxyl end. Where would you expect the ends of α-helices to be located in a protein? Why?
Surface of the protein - The ends of α-helices, like polar amino acids, are almost always found at the surface of a protein where they can interact with polar water molecules.
In the 1860s, Louis Pasteur noticed that when he added O2 to a culture of yeast growing anaerobically on glucose, the rate of glucose consumption declined dramatically. Explain the basis for this result, which is also known as the Pasteur Effect.
The Pasteur effect describes the fact that glycolysis is less efficient in making ATP than respiration.
Electronegativity of elements
The ability of an atom in a molecule to attract electrons to itself. Electronegativity increases from left to right and from bottom to top of table.
Glycolysis
The anaerobic breakdown of glucose into pyruvic acid, which makes a small amount of energy available to cells in the form of ATP. Happens in the cytosol.
If noncovalent interactions are so weak in a water environment, how can they possibly be important for holding molecules together in cells?
The combined effect of all the weak bonds is rather strong. This forms a network of interlocking hydrogen bonds. The weak bonds form between different regions that cause the macromolecule to fold into a unique 3D shape with a special chemistry.
Entropy- Energy Transfer in cells
(Energy = Food or photons.*?*) As heat is generated, work can be done. Total Entropy (cell + environment) has increased. Cell satisfies second law of thermodynamics because total energy has increased.
Each phosphoanhydride bond between the phosphate groups in ATP is a high-energy linkage with a ΔGo value of -7.3 kcal/mole. Hydrolysis of this bond in cells normally liberates usable energy in the range of 11 to 13 kcal/mole. Why do you think a range of values for released energy is given for ΔG, rather than a precise number, as for ΔGo?
The free energy of 11 to 13 kcal/mol (ΔG) liberated from this reaction depends on both ΔG° and the concentrations of the substrate and products. ΔG=ΔG°+RTln([product]/[substrate]). If the second term is negative (i.e. more substrate than product) then ΔG will be even more negative than ΔG° (i.e. releasing more energy). The reason a range is given is because the concentrations of ATP, ADP, and phosphate differ among cells, thus changing the value of the logarithm.
Noncovalent Ionic
donation of electrons
∆G=0
equilibrium
Enzymes cannot change the _________ of a reaction.
equilibrium point. Enzymes lower the activation energy required, making reactions happen faster.
Fatty acids are building blocks that give rise to
fats, lipids, membranes
disaccharide become monosaccharides through _____.
hydrolysis (adding a water molecule)
-∆G
is energetically favorable. ∆G <0, disorder increases.
+∆G
is energetically unfavorable. ∆G >0, disorder decreases. (+∆G) + (-∆G) = - ∆G. A coupled reaction may occur.
Proteins are
long polymers of amino acids linked by peptide bonds
Nucleotides are building blocks that give rise to
nucleic acids
Sugars are building blocks that give rise to
polysaccharides
Amino acids are building blocks that give rise to
proteins
Monosaccharides
simple sugars, i.e. fructose, glucose
The ____ and ____ present determine the outcomes/products.
substrates and enzymes
Disaccharides are
sugar made up of 2 linked monosaccharides, i.e. sucrose, maltose, lactose
Carbon Cycle
the movement of carbon from the atmosphere to living organisms and back to the environment in a continuous cycle
The common amino acids are grouped according to
whether their side chains are acidic, basic, uncharged polar, non polar.
G= Gibbs Free Energy
∆G determines whether a reaction is likely to take place. A chemical reaction can occur spontaneously only if it results in *a net increase in disorder.* ∆G reflects the degree to which a reaction creates a more (or less) stable environment.
Peptide bonds form from ______ reactions
condensation
Monosaccharides become a disaccharide through _____.
condensation (expelling a water molecule)
Sugar functions and roles:
-Energy source. -structure. -Cell recognition (like ABO Blood groups)
Common compositions of cells:
70%- water, 1% to .5% of each precursors.
Oxidation=
Dehydrogenation (Removed)
∆G=
∆G= RTln[x]/[Y]
(Bioenergetics: Metabolism.) Process of biosynthesis
*Anabolic Pathways* 1. build macromolecules. 2. Use energy that was generated by catabolic reactions.
Association rate. A + B → AB
Association rate = association rate constant x concentration of A x concentration of B. Association rate = Kon [A][B]
Biology requires the modification of many molecules. Example: s
-Polysaccharides from simple sugars. -Chemical reactions require reactants to collide. -Cells contain enzymes to catalyse reactions.
Nucleotide functions:
-Subunits of DNA/RNA. (uracil, cytosine, thymine, adenine, and guanine.) -Energy carriers. -Nucleotide polymers -Cofactors/coenzymes that allow other interactions to occur; required for protein activity.
Rapid movement is required for enzyme-substrate encounter.
1. Translational motion from one place to another. 2. Vibrational motion. 3. Rotational motion (10⁶/sec). Diffusion rate= 50 μm/sec. 1/5 sec to diffuse across a cell.
Gas constant (R)=
1.987 cal/mol∙k
Disaccharides can form:
11 different glycosidic bonds. 1. complex branching. 2. Specific cleavage (breaking)
Entropy, Heads- Tales example
2 H/T x 2 H/T x 2 H/T x 2 H/T = 16 Combinations. HHHH- 1/16, takes work. Non-random. HHHT- 4/16. HHTT- 6/6, most probable. TTTT- 1/16, takes work. Non-random.
Macromolecules make up ____ of cell content
25%
Absolute Temperature (T)=
273⁰K
There are many different chemically diverse ways in which small molecules can be linked to form polymers. For example, ethene (CH2=CH2) is used commercially to make the plastic polymer polyethylene (...CH2-CH2-CH2-CH2-...). The individual subunits of the three major classes of macromolecules, however, are all linked by similar reaction mechanisms, namely, by condensation reactions that eliminate water. Can you think of any benefits that this chemistry offers and why it might have been selected in evolution?
A major advantage of condensation reactions is that they are readily reversible by hydrolysis (and water is readily available in the cell). This allows cells to break down their macromolecules (or macromolecules of other organisms that were ingested as food) and to recover the subunits intact so that they can be "recycled," i.e., used to build new macromolecules. Won't run out of building blocks.
K-Equilibrium constant.
A measure of the binding strength b/w two reactants. As K becomes larger, reflects greater difference between associated and dissociated states. K= dissociation rate/dissociation rate. (Smaller K on top, larger K on bottom)
What does the term "amphiphilic" mean? The figure below shows a fatty acid, a triacylglycerol, and a phospholipid. Indicate which of these molecules are amphiphilic and illustrate why. How do their amphiphilic characteristics account for the typical structures that these molecules form in cells?
Amphiphilic: a molecule having a polar, water-soluble group attached to a nonpolar, water-insoluble hydrocarbon chain.
favorable/unfavorable reactions
An energetically favorable reaction can occur spontaneously. An energetically unfavorable reaction can occur only if it is coupled to an energetically favorable reaction.
Polysaccharides make up
Animal glycogen and plant starches
Energy transfer Carbon cycle Picture
CO₂ from respiration goes back to photosynthesis side, while O₂ goes from photosynthesis side to respiration side
Major molecules: Fatty acids
Can be saturated or unsaturated. The key property is that its ampiphyllic /amphipathic (allows membranes to form.)
Major molecules: Sugars
Can be straight chains or rings. General formula is (CH2O)n, where n can be 3-8.
Entropy- Energy Transfer in gas molecules example
Chemical bond energy in H₂ and O₂→rapid vibrations of molecules→Heat dispersed to surroundings.
In the reaction 2 Na + Cl2 → 2 Na+ + Cl-, what is being oxidized and what is being reduced? How can you tell?
Chloride is being reduces because it is gaining an electron . Sodium is being oxidized because it loses an electron
Dissociation rate. AB→A + B
Dissociation rate = dissociation rate constant x Concentration of AB. Dissociation rate = Koff[AB]
Like α−helices, β-sheets often have one side facing the surface of the protein and one side facing the interior, giving rise to an amphiphilic sheet with one hydrophobic surface and one hydrophilic surface. From the sequences listed below pick the one that could form a strand in an amphiphilic β-sheet. A. ALSCDVETYWLI B. DKLVTSIAREFM C. DSETKNAVFLIL D. TLNISFQMELDV E. VLEFMDIASVLD
D. TLNISFQMELDV
_____ lower the activation energy for reactions.
Enzymes. Many reactions require a catalyst. Enzymes open a particular path among many.
Thermodynamically, it is perfectly valid to consider the cellular phosphorylation of glucose as the sum of two reactions. *See Picture* But biologically it makes no sense at all. Hydrolysis of ATP (reaction 2) in one part of the cell can have no effect on phosphorylation of glucose (reaction 1) elsewhere in the cell, given that [ATP], [ADP] and [Pi] are maintained within narrow limits. How does the cell manage to link these two reactions to achieve the phosphorylation of glucose?
Hexokinase: a single enzyme with multiple binding sites. Two reactions are coupled.
Reduction=
Hydrogenation (Add)
Small proteins may have only one or two amino acid side chains that are totally inaccessible to solvent. Even in large proteins, only about 15% of the amino acids are fully buried. A list of buried side chains from a study of 12 proteins is shown in the table. The list is ordered by the proportion of each amino acid that is fully buried. What types of amino acids are most commonly buried? Least commonly buried? Are there any amino acids that are buried either more or less frequently than might be expected from your knowledge of side chain properties?
Hydrophobic groups hiding from water, bury themselves. A2.41 As expected, hydrophobic amino acid side chains are most frequently buried and hydrophilic side chains are least commonly buried. Perhaps the biggest surprise in this list is the high proportion of cysteine (C) side chains that are buried. Cysteine is generally grouped with polar amino acids because of its -SH group, but its hydrophobic/hydrophilic properties indicate that it is, at best, weakly polar. Tyrosine (Y) also deserves comment. Tyrosine is usually grouped with polar amino acids because of its hydroxyl moiety; however, its measured hydrophobic/hydrophilic properties are ambiguous, indicating that it is only weakly polar. By the criterion of 'buriedness,' it clearly behaves like other polar amino acids.
For sequential reactions, ∆G is additive:
If ∆G is negative for the entire reaction = favorable. If one reaction was unfavorable, the entire sequence can be made favorable.
H-bonds
Occur when a δ+ H is shared by two -δ atoms.
Electrostatic attractions
Ionic Bonding, attractive forces between oppositely charged atoms.
Sugars and precursors, Amino acids and precursors, nucleotides and precursors, and fatty acids and precursors all give rise to ______.
Macromolecules.
Comparison of a homeodomain protein from yeast and Drosophila shows that only 17 of its 60 amino acids are identical. How is it possible for a protein to change over 70% of its amino acids and still fold in the same way?
Many different strings of amino acids can give rise to identical protein folds. The many amino acid differences between the homeodomain proteins from yeast and Drosophila are among the many possible ones that do not alter folding and function. This question could have been framed in another way; namely, how many amino acid changes are required to convert, say, an á helix into a â sheet? The A2.is: surprisingly few! This question underscores the difficulty in predicting protein structures from amino acid sequences.
Van der Waals attractions
Momentary dipoles may cause weak attractions.
Hydrophobic forces
Occur when a hydrogen bonded network forces out non-polar surfaces.
How do enzymes work? Active Site
The molecules that an enzyme works with are called substrates. The substrates bind to a region on the enzyme called the active site. There are two theories explaining the enzyme-substrate interaction. In the lock-and-key model, the active site of an enzyme is precisely shaped to hold specific substrates. In the induced-fit model, the active site and substrate don't fit perfectly together; instead, they both alter their shape to connect.
The drug thalidomide was once prescribed as a sedative to help with nausea during the early stages of pregnancy. One of its optical isomers (R)-thalidomide (see the figure below), is the active agent responsible for its sedative effects. It was synthesized, however, as a mixture of both optical isomers -a not uncommon practice that usually causes no problems. Unfortunately, the other optical isomer is a teratogen that led to a horrific series of birth defects characterized by malformed or absent limbs. On the structural formula below identify the carbon that is responsible for its optical activity (its chiral center). Sketch the structure of the teratogenic form of thalidomide.
The only chiral center...
Entropy defined
The quantitative measure of the degree of disorder in a system. Spontaneous
Covalent Bonds
The sharing of electrons. Very Strong: 10X to 100X stronger than non covalent bonds. Requires a chemical reaction to break. These bonds are regulated by enzymes. May be polar or non-polar.
At first glance, fermentation of pyruvate to lactate appears to be an optional add-on reaction to glycolysis. After all, couldn't cells growing in the absence of oxygen simply discard pyruvate as a waste product? In the absence of fermentation, which products derived from glycolysis would accumulate in cells under anaerobic conditions? Could the metabolism of glucose via the glycolytic pathway continue in the absence of oxygen in cells that cannot carry out fermentation? Why, or why not?
To keep glycolysis going, cells need to regenerate NAD+ from NADH. There is no efficient way to do this without fermentation. In the absence of regenerated NAD+, step 6 of glycolysis (the oxidation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate) could not occur and the product glyceraldehyde 3-phosphate would accumulate. The same thing would happen in cells unable to make either pyruvate or ethanol: neither would be able to regenerate NAD+, and so glycolysis would be blocked at the same step.
Reactions can be coupled to accomplish ________ reactions.
Unfavorable. This is done by coupled reactions, in which an energetically favorable reaction (such as oxidation of glucose) is coupled to an energetically unfavorable one that produces an activated carrier molecule. The activated carrier molecules store energy in an easily exchangeable form, either as a readily transferable chemical group (such as the g-phosphate on ATP) or as high-energy electrons (as on NADH).
Major molecules: Nucleotides (nucleic acid subunits)
Uracil, cytosine, thymine, adenine, and guanine
Oxidation and reduction reactions
When a molecule picks up an electron, it also picks up a proton. The net effect is the addition of a hydrogen atom. A + e⁻ + H →AH
Sugar isomerases interconvert ___ and ___.
chains and rings.
The citric acid cycle generates NADH and FADH2, which are then used in the process of oxidative phosphorylation to make ATP. If the citric acid cycle, which does not use oxygen, and oxidative phosphorylation are separate processes, as they are, then why is it that the citric acid cycle stops almost immediately upon removal of O2?
Without oxygen the chain wont be able to pass electrons. The cell runs out of NAD+ so NADH cannot be made in the citric acid cycle of the chain. NAD+ and FAD are termed "coenzymes". They are simply carriers for the protons which are released during the citric acid cycle. If oxidative phosphorylation stops, then you rapidly run out of NAD+ and FAD, because it's all turned into NADH and FADH2. While oxidative phosphorylation and the citric acid cycle are nominally separate, the citric acid cycle absolutely depends on oxidative phosphorylation in order to proceed. In fact, the only reason why glycolysis can proceed without oxygen is not because it "has nothing to do with oxidative phosphorylation" - because it kind of does, it produces NADH as well - it's because it also happens to produce pyruvate in a 1:1 ratio with NADH. This means that pyruvate becomes the terminal electron acceptor, not oxygen (it's converted to lactate in the process). You could imagine that you might be able to produce the odd metabolic product from the citric acid cycle that you could use as a terminal electron acceptor, but the problem is that the cycle makes LOTS of NADH and FADH2, and you really need that 1:1 ratio, otherwise you will rapidly run out of NAD+ and FAD. The only way to recycle those coenzymes once you're past glycolysis is oxidative phosphorylation.
At equilibrium, association rate = dissociation rate.
[AB]/[A][B] =Kon/Koff=K=equilibrium constant.
Amino acids usually form when a peptide bond forms between:
a carboxyl group and an amino group.
Macromolecules form by
addition of monomers, covalent bonds. Via condensation. Through enzymatic process through input of energy