BIO 110 Final Exam Flashcards
Complied questions and answers of past exams
Explain why hydrogen bonds can form between two water molecules. What forces make up this bond?
Electronegativity differences between O and H create regions of partial positive and negative charges. The attraction between these partial charges make up hydrogen bonds
During the formation of a peptide linkage, a(n) ____ is formed.
molecule of water
What is the general chemical formula for carbohydrates?
(CH2O)n
What does Keq indicate? What is the relationship between delta G and Keq?
- Keq indicates the tendency of a chemical reaction to go to completion, it is the ratio of products to reactants at equilibrium. Delta G is a log version of Keq
- Delta G = [energy]products - [energy]reactants
- Delta G is negative if the reaction is spontaneous
Starch and glycogen, which are both polysaccharides, differ in their functions in that starch is ____, whereas glycogen _____.
the main energy storage of animals; is a temporary compound used to stare glucose
A “typical” adult human has about 1 day supply of energy stored in the form of carbohydrates but 3 months energy stored as lipids. Explain the logic behind this observation. Why store more energy as lipids and not sugars?
Lipids (specifically tricylglycerides) are more efficient way to store energy because the carbons are less oxidized than sugars, so more ATP per carbon is derived from lipids than carbohydrates. Lipids also take up less space since they are hydrophobic (water doesn’t take up extra space)
What are purines?
one of two classes of bases found in nucleic acids, contains two rings; adenine and guanine
Double-stranded DNA looks like a ladder that has been twisted into a helix, or spiral. Describe the two outer rungs of this ladder.
The backbone is composed of alternating phosphate groups and deoxyribose
Telomerase is a ___ dependent ___ polymerase.
RNA, DNA
Primase is a ___ dependent ___ polymerase.
RNA, DNA
Transcription uses a ___ dependent ___ polymerase.
DNA, RNA
During formation of the mitotic spindle, there is/are ___ centriole(s) while each chromosome consists of ___ chromatid(s), ___ centromere(s), and ___ kinetochore(s).
4;2;1;2
When you slowly and carefully increase the temperature of a chromosome, you notice that some regions become single stranded at lower temperatures than other regions. What is the likely cause of these differences?
Those regions that become single stranded dat lower temperatures likely have a lower GC content. These are likely regions that ‘unzip’ frequently - such as the origin or replication of promotor regions.
Why is RNA incorporated into the DNA molecule during DNA replication?
DNA polymerase cannot begin a new strand, but can only add on to the 3’ end of the preexisting nucleic acid strand. RNA polymerase can begin a new strand, so the replication is begun as a short RNA primer onto which DNA polymerase can add.
Describe the changes that occur for a molecule of hemoglobin as it travels through the blood, beginning as it enters the lungs and then transported to exercising muscles and then back to the lungs. Include in your description the changing structure of hemoglobin, its association(s) with oxygen and any factors that may be influencing the structure and function of hemoglobin.
Entering lungs, without O2 hemoglobin is the T-state, which has a low affinity for oxygen. In the lungs, oxygen concentration is high. Binding of O2 to one subunit will cause it to convert to the R-state by moving the Fe in the heme, causing the attached histidine residue to move - causing the alpha helix which that histidine is located to bend slightly - causing a change in subunit confirmation. That change in confirmation is translated to the other subunits which increase the binding of O2. pH can also influence T versus R state via changes in ionic interactions between subunits. Lower pH (in active tissues) will cause hemoglobin to be in the T state and release oxygen easier. Higher pH will ten to stabilize the R state.
What is negative cooperativity of binding? Give an example when this is an appropriate strategy for ligand binding.
Negative cooperativity occurs when a ligand binds to a protein and decreases the affinity of the same protein for a second ligand binding. The insulin receptor uses this strategy.
What is a cofactor? List a specific enzyme that uses a cofactor - what is the role of that cofactor?
Cofactors are parts of proteins but are not composed of amino acids and are required for protein function. They include metal ions, NAD+, FAD, heme, cytochromes. When a coenzyme is covalently bound to an enzyme, it is called a prosthetic group.
Describe the different steps involved in translation elongation.
bind - binding of new charged tRNA to A site of ribosome
bond - peptide bond formation between AA in A site to AA/peptide in the P site
move - move mRNA 3 bases (one codon) downstream
A mutation occurs such that a spliceosome cannot remove one of the introns in a gene. What effect will this have on that gene?
Translation will continue, but a nonfunctional protein will be made
Translation of messenger RNA into protein occurs in a ____ direction, and from the ___ terminus to the ___ terminus.
5’ to 3’, N, C
Which of the following statements about transfer RNA is true?
Activating enzymes (aminoacyl-tRNA synthases) link together a specific amino acid with a specific tRNA
The expression of the gene that encodes cyclin A varies considerably across the cell cycle, reaching a peak at the G2 phase. Based on this information, one can conclude that cyclin A is:
encoded by an inducible gene
Describe all the major environmental conditions under which the Lac Operon is normally expressed. If glucose is then added to the bacterial culture, what protein(s) will change structure and function?
Lactose must be present and glucose absent. Adding glucose would change the confirmation of the CAP protein (due to reduce cAMP levels)
During carbohydrate catabolism, one molecule of glucose can be used to produce up to ___ mole of ATP. For each mole of glucose, substrate level phosphorylation is used to create __ moles of ATP during ____, while __ moles of GTP are produced during ____. Most of the ATP made from oxidizing glucose is produced by the enzyme called ____, which is located in the ____ membrane of the ____. Before most of the ATP is produced, high energy molecules called _____ are produced during several stages of carbohydrate catabolism including ____, _____, and the krebs cycle. These high energy molecules are used to create a ____ which is used to produce the majority of the ATP.
32; 2; glycolysis; 2; the krebs cycle; ATP synthase; inner; mitochonria; NADH (e-carriers); glycolysis; pyruvate dehydrogenase; proton gradient
Animals inhale air containing oxygen and exhale air with less oxygen and more carbon dioxide. After inhalation, the oxygen missing from the air will mostly be found in:
water
What are all the direct products of pyruvate oxidation?
CO2, NADH, Acetyl-CoA
Both mitochondria and chloroplasts employ an electron transport chain. Compare and contrast both of these electron transport chains.
both use the energy from high energy electrons to pump protons to create a proton gradient which is used to make ATP. The mito ETC begins with NADH ands with O2, while chloroplast ETC uses electrons from H2O and ends with NADPH
How does the reduction of pyruvate to lactic acid during fermentation allow glycolysis to continue in the absence of oxygen?
it regenerates NAD+. Glycolysis requires NAD+ and stops without it.
Explain how heavy ethanol consumption can result in low blood glucose levels the next day.
metabolism of ethanol yields NADH which alters the NADH/NAD+ ratio. This ratio is important in regulating many aspects of carbohydrate metabolism, including gluconeogenesis
If a cell has an abundant supply of ATP, what will be the likely fate of excess acetyl-CoA?
excess acetyl-CoA is made into fat
When a suspension of algae is incubated in a flask in the presence of light and CO2 and then transferred to the dark, the reduction of 3-phosphoglycerate to glyceraldehyde 3-phosphate is blocked. This reaction stops in the dark because:
the reaction requires ATP and NADPH
Explain how alcohol consumption alters kidney function.
Alcohol inhibits the release of ADH - which controls the permeability of the collecting tubule (via aquaporin regulation)
Resting potential
NaK pump active, leak K+ channel open
Increasing potential
Na channel opens (then close)
Decreasing potential
K+ channels open (then close)
What is a cell cycle checkpoint? What is the relationship of cyclins to cell cycle checkpoints?
Cell cycle checkpoints prevent progression through the cell cycle until specific conditions are met. The three main checkpoints occur during mitosis (spindle checkpoint), G1 (DNA replication checkpoint) and G2 (DNA damage and replication). Cyclins are proteins necessary to activation CDKs. Cyclins are necessary, but not sufficient to progress through the cell cycle, including past checkpoints
What is HAART treatment for HIV? Explain why HAART treatment has been so effective in controlling HIV while previous strategies had been limiting.
HAART treatment is the strategy of giving multiple anti-HIV drugs at the same time. This decreases the chance that the virus can evolve resistance
A reaction has a delta G of -20 kcal/mol. What can you say about the energy levels of the substrates and products in this reaction? How might an enzyme change this delta G?
There is more energy in the substrates than products; enzymes do not change delta G
What conditions must occur for a covalent bond to be polar?
Electronegativity differences between the 2 atoms
At high concentrations, the molecule pictured to the right can disrupt the structure of some complex biological molecules. How and why would it alter another molecule’s structure?
Since ethanol is less polar, the ability to participate in H bonds is less. Among other consequences, the fewer H bonds will alter the strength of the hydrophobic effect - which is essentially in the maintenance of the membrane structure and protein folding/structure
Which of the following statements concerning energy transformation is true?
increases in entropy reduce usable energy
Which of the following statements about carbohydrates is false?
monomers of carbohydrates have six carbon atoms
Triglycerides are synthesized from ____ and ____.
glycerol; fatty acids
How would you be different if we used carbohydrates exclusively for long term energy store?
It is more efficient to store energy as fats than carbohydrates. So, if you used carbohydrates instead of fats to store energy, you would have to be much larger
How do primers differ in PCR versus in chromosomal replication? Why the difference?
PCR primers are DNA, primers used in chromosomal replication are RNA. The inability of DNA polymerases to start synthesis of a new strand necessitates the use of RNA polymerase, which can start a new strand
Describe the changes in eukaryotic chromosome structure throughout the cell cycle.
During interphase, the chromosomes are more diffuse, composed of heterochromatin and euchromatic. During mitosis or meiosis, chromosomes become very compact.
How is Chargaff’s rule a manifest in DNA structure?
Complimentary base pairing via hydrogen binds across the double helix.
Which nitrogenous base will only temporarily be found in a double helix? Why?
Uracil, it will only be part of the DNA double helix when temporarily found in RNA primers
The following sequence is listed from 5’ to 3’: AATGCGA. What is the nucleotide sequence of the complementary strand of the DNA molecule?
3’- TTACGCT -5’
What is the complementary strand of an RNA molecule to the above DNA sequence?
3’- UUACGCU -5’
Explain why the following statement is either true or false: RNA does not participate in complimentary base pairings?
All RNA participates in complimentary during synthesis and also in many cases complimentary base pairing is crucial to RNA structure, including tRNAs, rRNAs
Which of the following statements about proteins is true?
an amino acid can act both as an acid and as a base
In epinephrine/adrenaline signaling, describe three separate roles of nucleotides or nucleosides outside of the nucleus
1) GTP/GDP - in the G protein serves as a molecular timer
2) ATP/cAMP - activates protein kinase A via inactivation of repressor
3) protein kinase A uses ATP as a source of phosphates to phosphorylate protein targets
You are tasked with producing a drug that disables the function of a specific cell receptor protein. In general terms, explain the approach that you would take to develop such a drug.
The simplest approach is to design a drug that binds to and changes the confirmation of the receptor protein, inactivating the receptor. A drug that mimics the normal ligand of the receptor is usually the easiest to design.
What regions of a gene are transcribed but not translated?
introns and the 3’ and 5’ untranslated regions on the ends of the mRNA
The ‘adapters’ that allow translation of the four-letter nucleic acid language into the 20-letter protein language are called ___.
tRNA
Which molecule transfers hereditary information from the nucleus to the cytoplasm?
mRNA
Describe the different steps involved in translation initiation.
1) the small subunit binds mRNA along with initiation factors (helper proteins)
2) fMET tRNA binds - along with initiation factors
3) the large subunit binds and locks in place - initiation factors leave
A transcription factor is a ___ that binds to ___.
Protein; DNA
Which of the following would lead to an increase in the expression of gene X.
a mutation that lowers the efficiency of a repressor of gene X
You have engineered a copy of the Lac Operon lacking a functional operator. How would the regulation of expression change compared to a wild-type under the following condition:
glucose present, lactose absent - no difference; not expressed in wt, not expressed in mutant
glucose absent, lactose present - no difference; expressed in wt, expressed in mutant
glucose present, lactose present - no difference; not expressed in wt, not expressed in mutant
If glucose labeled with 14C were fed to yeast in anaerobic conditions, where would the 14C label be in the products?
in ethanol and CO2
Which of the following statements is not true concerning glycolysis in anaerobic muscle?
its rate is slowed by a high [ATP]/[ADP] ratio
Based on your knowledge of metabolism and energy production, what diet recommendations would you give to someone with beriberi? why?
Avoid eating carbohydrates, instead eat more fats. Fatty acids are broken down to acetyl-CoA, just as pyruvate normally is when ATP production is needed
Compare and contrast this conversion to what occurs when glycogen is oxidized to make ATP. Include in your answer, substrates and ending products as well as the conversion of energy from one molecule to another.
Glycogen and cellulose are both composed of glucose. When completely oxidized, both will ultimately produce CO2 and H2O. The major difference is that energy from glucose when oxidized in metabolism will release energy slowly, mainly as electron carriers which are used to pump proton gradient. The energy of the proton gradient will be converted to mechanical energy and then into the covalent bonds of the ATP.
Glycogen is highly soluble in water, while cellulose is largely insoluble. How are these molecules similar and different in terms of structure? What accounts for the differences in solubility? What about strength and stability?
both are made from glucose. they differ in ability to make intramolecular hydrogen bonds. cellulose has many intramolecular bonds, making it stronger and insoluble.
The catabolism of what type of biomolecule necessitates the production of urea in mammals?
proteins/amino acids and nucleotides
Untreated diabetes can alter kidney function by causing physical damage to the glomerulus. How is the resulting urine of a diabetic individual different from a healthy individual?
the damaged to the glomerulus causes more molecules (such as glucose and amino acids) to end up in the urine
How might the events in the above question be changed following demyelination?
nerve signals terminate, reverse or jump from one axon to another.
Insulin signaling involves a receptor tyrosine kinase. This receptor belongs to a family of receptors involved mostly in regulating cell growth. A G protein involved in these signaling pathways has been implicated in a large number of cancers. How might you change the structure/function of this G protein to create cancer.
For a signal which controls cell growth, a requisite for cancer. The G protein is the molecular timer that determines when the signal is turned off. Modifying the G protein to take longer to hydrolyze GTP will prolong the signal and increase cell growth
From a public health perspective, why is treatment of HIV also prevention?
infectivity is correlated to viral titer, treatment results in very low or undetectable levels of virus, usually rendering an infected individual non-infectious or very unlikely to transmit the infection
