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Biochemistry > Final Exam Review > Flashcards

Final Exam Review Flashcards

1
Q

Which organelle in the eukaryotic cell is responsible for generating ATP (energy)?

A

mitochondria

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2
Q

Which two organelles in the eukaryotic cell are responsible for handling waste products?

A

peroxisomes and vacuole

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3
Q

Water molecules form a dipole. Explain what this means (1-2 sentences)

A

Water (H2O) is a polar molecule with H having a positive charge and O having a negative charge. These charges pulling on each other create a dipole, while also being able to form covalent bonds within the molecule and hydrogen bonds with other water molecules.

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4
Q

Hydrophobic

A

does not dissolve in water (water-fearing); non polar molecule

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5
Q

Amphipathic

A

some regions dissolve in water, while others do not; polar and non polar regions

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6
Q

What are hydrogen bonds?

A

hydrogen atom bonds to a strong electronegative atom
weaker than covalent bonds
water forms hydrogen bonds

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7
Q

Acetic acid has a pKa of 4.75, hydrocyanic acid has a pKa of 9.21. Which one of these is a weaker acid? How do you know?

A

Hydrocyanic acid is a weaker acid, while acetic acid is the stronger acid. pKa tells you how acidic a molecule is; higher pKa’s indicate weaker acids while lower pKa’s indicate stronger acids.

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8
Q

In an solution with an excess of hydroxide (-OH), how would acetic acid act as a buffer?

A

H+ will be released from acetic acid to form water

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9
Q

In the structure of an amino acid, the alpha carbon is bound to 4 substituents. What are these substituents?

A

carboxyl group, R group, amino group, and a hydrogen

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10
Q

Peptide bonds are:

A

covalent bonds

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11
Q

Peptide bonds are formed with the release of

A

water

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12
Q

Explain why each polypeptide starts with the N-terminus and ends with the C-terminus.

A

N-terminus is the beginning of the polypeptide chain with a free amino group
C-terminus is the end of the polypeptide chain with a free carboxy

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13
Q

Provide one example of secondary structure.

A

alpha helix - rotates around longitudinal axis, R groups stick out of backbone

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14
Q

What type of bond holds antiparallel beta sheets together?

A

hydrogen

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15
Q

Which two amino acids are NOT found in an alpha helix?

A

glycine and proline

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16
Q

What is the tertiary structure of collagen?

A

-collagen triple helix
-high tensile strength, without stretch
-left-handed helix with about three amino acid residues per turn

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17
Q

When a protein loses its three dimensional structure, what is it called?

A

denaturation; causes loss of function

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18
Q

List one way a protein can lose its tertiary structure.

A

Denaturation can cause a protein to lose its tertiary structure. This can be cause by either pH changes heat, etc. leading to protein precipitation.

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19
Q

Iron (Fe) is required for oxygen binding of hemoglobin. Fe forms a total of 6 bonds in this complex. What are the components that Fe is bound to?

A

Fe is bound via four bonds to nitrogen atoms. There are two perpendicular bonds formed, one to a distal His residue and the other to an oxygen binding site.

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20
Q

Hemoglobin occurs in two, three-dimensional “states”, T and R. What triggers hemoglobin to change from one state to the other? How does this alter the affinity of hemoglobin for its ligand?

A

There are two conformations of hemoglobin, the R state and T state. In the R state, O2 has a higher affinity for hemoglobin. In the T state, hemoglobin is more stable when O2 is absent (predominant conformation of deoxyhemoglobin). When a molecule of oxygen binds to one of the heme groups, then hemoglobin is triggered to change from one state to another.
The hydrogen bond between the distal histidine residue pocket (opens and closes) altering the affinity of hemoglobin for its ligand. Oxygen binding in the Fe2+- O complex electrostatically stabilizes the polar complex decreasing the affinity of hemoglobin for its ligand (from 20,000-fold to 40-fold with oxygen binding).

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21
Q

You discover a genetic mutation in the myosin gene, which results in reduced affinity for ATP. How might this affect a person’s ability to use their muscles? (be specific about the role of mysosin and ATP in muscle contraction)

A

Muscle contraction is brought about by the sliding of actin (thin filaments) and myosin (thick filaments). To bring about muscle contraction, ATP binds to the myosin head, causing myosin and actin filaments to disassociate. ATP is then hydrolyzed causing a conformational change in the myosin head. This then allows actin to re-attach to the myosin head, releasing phosphorus. Lastly, the release of phosphorus results in a power stroke causing the actin and myosin filaments to slide past each other creating a muscle contraction (releases ADP). Moreover, with a reduced affinity for ATP would mean that it doesn’t attach to the myosin head in the first step of muscle contraction. With a reduced affinity for ATP in the myosin gene would mean that muscle contraction would not occur in an organism.

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22
Q

Is starch a homopolysaccharide or a heteropolysaccharide? How do you know?

A

Homopolysaccharide: single monomeric sugar species that compose a polymer.
Starch is made up of chains of D-glucose single monomer units linked by glycosidic bonds, making it a homopolysaccharide.
Apparently, amylose and amylopectin are not two different monomers as they are both chains of D-glucose, which is why I thought starch would be considered a heteropolysaccharide.

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23
Q

Cellulose is made up of which monosaccharide

A

Cellulose is made up of a linear D-glucose (monosaccharide) chain with glycosidic bonds. Also, OH bonds with neighboring chains od the monosaccharides.

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24
Q

What is it about the structure of cellulose that makes it not digestible for humans? (be specific about the chemical bond).

A

Cellulose is found in the cell wall of plants, and is a linear polysaccharide of D-glucose in the B conformation. Unlike starch, cellulose is in the beta conformation (B1-4 linkage). This difference in acetal linkage results in major difference in digestability by humans. Ultimately, lacking the enzymes to breakdown the acetal beta linkages makes humans unable to digest cellulose.

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25
Q

Which component of the bacterial cell is impacted by the antibiotic penicillin?

A

cell wall

26
Q

When DNA forms the double helix, which bases are complementary to one another?

A

C (cytosine) and G (guanine) are complementary to each other in DNA
A (adenine) and T (thymine) are complementary to each other in DNA

27
Q

In the DNA molecule, what type of bond connects the complementary bases?

A

Hydrogen bonds connect the complementary bases in DNA. Three hydrogen bonds form between guanine and cytosine, whereas two hydrogen bonds form between adenine and thymine.

28
Q

What is the function of messenger RNA?

A

to convey the sequence of the gene from the DNA to the translation complex.

29
Q

The temperature at which ½ of a DNA molecule has denatured is called the

A

melting temperature

30
Q

Explain the difference between a saturated and an unsaturated fatty acid.

A

Saturated fats are solid at room temperature, whereas unsaturated fats are liquid at room temperature. Saturated fatty acids have a carboxyl group with hydrocarbon chains connected by single bonds only. Unsaturated fatty acids have a carboxyl group with hydrocarbon chains that have one or more double bonds. These double bonds can be in cis (H atoms on same side of double bond) or trans (H atoms on opposite sides of double bond) configuration.

31
Q

Oleic acid has the following chemical formula:

CH3(CH2)7CH=CH(CH2)7COOH
Describe the carbon skeleton using the delta nomenclature.

A

Delta nomenclature describes the carbon skeleton as, the chain length (number begins at carboxyl carbon) and number of bonds separated by a colon. The positions of double bonds are indicated by a delta and a superscript number.
Oleic acid under delta nomenclature would read as 18:1 (Δ9 )

32
Q

What is the basic structure of a triacylglycerol? (list the components)

A

Three fatty acids in ester linkage with a single glycerol. Triacylglycerols provide insulation and energy storage (non-polar and hydrophobic).

33
Q

Human blood groups are determined by the presence of what component on a sphingolipid?

A

oligosaccharide

34
Q

Describe the basic structure of a sterol.

A

The basic structure of a sterol is four, fused hydrocarbon rings. Steroids are an oxidized derivative of sterols.

35
Q

Name one function of cholesterol.

A

One function of cholesterol is seen in the polar derivative of cholesterol: bile acids. Bile acids emulsify fats in the intestines, so digestive lipases can break them down more efficiently.

36
Q

A complete catalytically active enzyme, together with its bound coenzyme and/or metal ions, is called a:

A

holoenzyme

37
Q

You are studying an enzyme inhibitor which can only bind to the ES complex at a location away from the active site. When you perform rate experiments on this enzyme, you observe that the addition of the inhibitor results in alteration of Km and Vmax. This inhibitor is a(n):

A

uncompetitive inhibitor

38
Q

A reaction has a Keq of 0.001, the ΔG would be:

A

> than 0

39
Q

The energy derived from the noncovalent enzyme-substrate interaction is called the:

A

the binding energy

40
Q

Is glycolysis an anabolic or catabolic reaction? Explain your answer.

A

Catabolic reaction: the degradative phase of metabolism (requires energy)
Glycolysis is a catabolic reaction because a molecule of glucose is degraded (broken down) in order to yield two molecules of pyruvate.

41
Q

The equation for free energy is ΔG = ΔH - TΔS. In this equation, what does ΔS stand for?

A

the change in entropy (disorder)

42
Q

In the reaction below, which molecule is oxidized, and which one is reduced?

pyruvate + NADH –> lactate + NAD+

A

Pyruvate is reduced to form lactate. Pyruvate gains electrons from NADH to form lactate and NAD+. NADH is losing electrons, therefore it is being oxidized.

43
Q

Define the standard reduction potential (E°).

If the change in E° (ΔE°) is negative, what happens to ΔG?

A

Standard Reduction Potential: a measure (in volts) of the relative affinity of the electron acceptor of each pair of redox pair for electrons
If the change in delta E is negative, then delta G is positive (inverse relationship)

44
Q

Glycolysis occurs in 2 phases, the preparatory phase and the payoff phase. Explain, in general, why each phase is named in that way.

A

Preparatory Phase: ATP is consumed, delta G of the intermediates increase, and hexose carbon chains are converted to glyceraldehyde-3-phosphate
-Called preparatory phase because it is preparing for glycolysis to occur
Payoff Phase: yields (energy conserved as 2 ATP and 2 NADH) and 2 pyruvate
-Called payoff phase because this is when products are form/yielded

45
Q

During step 1 of glycolysis, what happens to glucose during the reaction (be specific)?

What enzyme catalyzes this reaction?

A

Glycolysis Step 1: phosphorylation of carbon 6 of glucose…hexokinase catalyzes this reaction
Reactants: glucose + ATP
Products: glucose-6-phosphate + ADP

46
Q

In glycolysis, the enzyme phosphohexose isomerase catalyzes which reaction?

A

glucose-6-phosphate to fructose-6-phosphate

47
Q

In glycolysis, at the start of the payoff phase, glyceraldehyde-3-phosphate is oxidized to what product?

What enzyme catalyzes this reaction?

What molecule is reduced during this reaction?

A

Glyceraldehyde-3-Phosphate is oxidized to 1,3, bisphosphoglycerate + NADH + H+
Enzyme that catalyzes this reaction: glyceraldehyde 3-phosphate dehydrogenase
NAD is the molecule that is reduced to form NADH

48
Q

Which of the following are products of glycolysis?

A

ATP, NADH, pyruvate

49
Q

After glycolysis, what happens to pyruvate under anaerobic conditions?

A

Under anaerobic condition, pyruvate is reduced to lactate or ethanol. Under anaerobic conditions, energy is extracted without consuming oxygen or changing the concentrations of NAD+ or NADH. NADH is important because its electrons are used to reduce pyruvate into lactate. Then, lactate can be recycled (converted to glucose for recovery)

50
Q

In yeast, fermentation results in pyruvate being converted to:

A

ethanol

51
Q

During the conversion of pyruvate to Acetyl-CoA, there are 5 coenzymes present. One of them is FAD. Explain the role of FAD in this reaction. Why is it important?

A

FAD (flavin adenine dinucleotide) is important because it is an essential coenzyme if the PDH complex. Electron transfer is necessary to regenerate the oxidized FAD cofactor, forming NADH creating the proton gradient.

52
Q

During the citric acid cycle, acetyl-CoA is broken down and energy is stored in which molecules?

A

GTP, NADH, FADH2

53
Q

The presence of NADH inhibits several steps of the citric acid cycle. Explain why this is the case.

A

NADH inhibits several steps of the citric acid cycle. NADH is essential because it is reduced and its electrons are used in further reactions of the citric acid cycle. Therefore, NADH will inhibit several steps of the citric acid cycle since its electrons are needed to continue the reactions.

54
Q

The pyruvate dehydrogenase complex is regulated by the activity of which enzyme?

A

pyruvate dehydrogenase kinase

55
Q

In the electron transport chain, the energy is derived from ___________________ and stored as _______________________.

A

the oxidation of NADH and FADH2 ; a proton gradient

56
Q

In oxidative phosphorylation, which complex does participate in proton transfer?

A

succinate ubiquinone oxidoreductase

57
Q

In complex III of oxidative phosphorylation (the cytochrome bc1 complex) what is the final electron acceptor?

A

cytochrome c

58
Q

In the electron transport chain, what molecule is the final electron acceptor?

If this molecule is absent, what happens to the electron transport chain and the other steps of cellular respiration?

A

The final electron acceptor is oxygen, it pulls H+ ions to form water at the end of the electron transport chain.
If the molecule is absent, the electron transport chain and other steps of cellular respiration will not finish and produce all of its products. It will be forced to undergo anaerobic conditions if oxygen is not present, yielding less ATP than if it were to undergo the process in aerobic conditions.

59
Q

In ATP synthesis, proton movement across the membrane catalyzes movement of which component?

A

the C-ring of the Fo

60
Q

Which component of ATP synthase catalyzes the reaction: ADP + P –> ATP

A

β subunit of F1

61
Q

In the binding-change model for ATP synthesis, the β catalytic subunit has 3 binding states, what are they?

A

B Catalytic Subunits: (B-ATP, B-ADP, and B-empty)

62
Q

During ATP synthesis, what provides the energy for release of ATP from the enzyme complex?

A

proton transfer through the membrane

Biochemistry (11 decks)

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