FINAL EXAM

Question 1

Hydrogen bonds

Answer 1

Much weaker than covalent bonds
Unequal electron sharing when covalently
bound hydrogen is bound to a more
electronegative atom leads to partially
charged atoms

Question 2

Van der Waals forces

Answer 2

Repulsion and attraction

Question 3

Hydrophobic effect

Answer 3

Non-polar or hydrophobic molecules coalesce spontaneously (oil and water)
increases the disorder of the
surrounding water

Question 4

Why are weak interactions important for life?

Answer 4

Reversibility allows for the flexibility of function

Question 5

Define pH

Answer 5

measure of hydrogen ion concentration in a solution

Question 6

Primary

Answer 6

Each amino acid is linked to the next amino acid by a peptide bond

Question 7

Secondary

Answer 7

Primary amino acid sequences can fold into recurring structures (alpha-helices)
Stabilized by H-bonds between amino
acids 4 peptides apart

Question 8

Tertiary

Question 9

Quarternary

Question 10

Describe the biochemical information that determines the final three-dimensional structure, and
explain what powers the formation of this structure.

Answer 10

○ primary sequence drives secondary structure - alpha helices, beta sheets, coiled-coil
○ R-group properties of amino acid sequences drive tertiary structure
○ Secondary structure and tertiary structure are stabilized by weak force interactions (H-bonds,
electrostatic interactions, Van der Waals forces) - and these forces also drive quaternary
structure

Question 11

Structure of a fatty acid

Answer 11

Chains of
hydrogen-bearing carbon atoms (hydrocarbons) that terminate with
carboxylic acid groups

Question 12

difference between a saturated and unsaturated fatty acid

Answer 12

Saturated: only single bonds
Unsaturated: one or more double
or triple bonds, lower melting points

Question 13

This simplest type of lipid is most commonly used as a

Answer 13

Fuel

Question 14

Lipids

Answer 14

Chains of hydrogen-bearing carbon atoms (hydrocarbons) that terminate with carboxylic acid groups

Question 15

Protein digestion

Answer 15

Proteins - Pepsinogen, and also enteropeptidase → Trypsin → All other
enzymes

Question 16

Lipid digestion

Answer 16

Emulsification, CCK/Bile Salt secretion, lipase access/cleavage

Question 17

Carbohydrate digestion

Answer 17

alpha-amylase (mouth), ⍺-Dextinase, glucosidase,
sucrase, and lactase (intestine)

Question 18

What are the important functions of different enzymatic and non-enzymatic events in digestion

Answer 18

○ Proteins - Low pH, pepsinogen, enteropeptidase → Trypsin → All other enzymes
○ Lipids - Emulsification, CCK/Bile Salt secretion, lipase access/cleavage
○ Carbohydrates - alpha-amylase (mouth), ⍺-Dextinase, glucosidase, sucrase, and lactase
(intestine)

Question 19

What is a zymogen?

Answer 19

(catalytically inactive precursor of an enzyme) which are
activated by proteolytic cleavage

Question 20

Identify the factors that make ATP an energy-rich molecule

Answer 20

○ Electrostatic repulsion of the four negative charges carried by the triphosphate
○ Relatively intermediate phosphoryl-transfer potential

Question 21

Explain how ATP can power reactions that would otherwise not take place.

Answer 21

Large free energy release can be coupled with
thermodynamically UNfavorable reactions in order
to make them thermodynamically favorable

Question 22

Describe the relation between the oxidation state of a carbon molecule and its usefulness as
a fuel.

Answer 22

○ Energy of oxidation is initially trapped as a high phosphoryl-transfer potential compound
and then used to form ATP
○ Fats are a more efficient fuel source than carbohydrates such as glucose because the
carbon in fats is more reduced

Question 23

Describe how ATP is generated in glycolysis.

Answer 23

○ Stage 1 requires 2 ATP input, Stage 2 generates 4 ATP, netting 2 ATP total per
glucose molecule
○ Series of enzyme catalyzed reactions which generate ATP (usable energy) and
NADH (electron transporter to electron transport chain)

Question 24

Explain why the regeneration of is crucial to fermentations.

Answer 24

○ NAD+ is a finite resource needed for the oxidation of glyceraldehyde 3-phosphate
into pyruvate
■ This is regenerated through conversion of pyruvate to either ethanol
(alcoholic fermentation) or lactic acid (lactic acid fermentation)
■ This allows for regeneration of NAD+ to continue the glycolytic cycle

Question 25

Describe the coordinated regulation of glycolysis and gluconeogenesis.

Answer 25

○ Reciprocal regulation ■ within a cell, one pathway is relatively inactive while the other one is highly active ■ when glucose is abundant, glycolysis will predominate. When glucose is scarce, gluconeogenesis will take over

Question 26

Explain why the reaction catalyzed by the PDH complex is a crucial juncture in metabolism.

Answer 26

Commits the carbon atoms of carbohydrates to oxidation by the citric acid cycle or to the synthesis of fatty acids

Question 27

Identify the means by which the PDH complex is regulated.

Answer 27

Products of the PDH complex inhibit its activity (acetyl-CoA and NADH), either directly, or through activation of pyruvate dehydrogenase kinase

Question 28

Identify the primary catabolic purpose of the citric acid cycle.

Answer 28

Harvesting of high-energy electrons from carbon fuels.

Question 29

Explain the advantage of the oxidation of acetyl CoA in the citric acid cycle.

Answer 29

Harvesting of high-energy electrons from carbon fuels.

Question 30

Describe how the citric acid cycle is regulated.

Answer 30

There are three TCA enzymes that are highly regulated

Question 31

Explain the benefits of having the electron-transport chain located in a membrane.

Answer 31

Allows for build up of proton gradient, so that proton-motive force can be used to generate ATP

Question 32

Identify the ultimate determinant of the rate of cellular respiration.

Answer 32

Need for ATP

Question 33

Explain the regulation of glycogen breakdown.

Answer 33

Hormonal regulation by glucagon (pancreas) and epinephrine (adrenal gland)

Question 34

Describe the steps of glycogen synthesis and identify the enzymes required.

Answer 34

Glycogen synthase, Branching enzyme

Question 35

Identify the repeated steps of fatty acid degradation.

Answer 35

2 carbons at a time oxidation, hydration, oxidation, thiolysis

Question 36

Explain how fatty acids are synthesized.

Answer 36

■ Citrate shuttle (oxacloacetate shuttle) in and out of mitochondria ■ Conversion of acetyl-CoA to malonyl-CoA in cytoplasm (commit step) ■ Fatty acid is synthesized in a 5 step elongation cycle

Question 37

Describe the relation between triacylglycerol synthesis and phospholipid synthesis.

Answer 37

Both begin with the precursor phosphatidate (diacylglycerol 3-phosphate) in the endoplasmic reticulum ■ Triacylglycerol primarily synthesized in the liver ■ Phospholipid synthesis requires the combination of a diacylglycerol with an alcohol

Question 38

Phosphatidic Acid Phosphatase (PAP, lipin 1) Is a Key Regulatory Enzyme in Lipid Metabolism

Answer 38

Controls the extent to which triacylglycerols are synthesized relative to phospholipids

Question 39

List the regulatory steps in the control of cholesterol synthesis.

Answer 39

○ Controlled by the transcription factor sterol regulatory element-binding protein (SREBP) ○ Translation is inhibited by nonsterol metabolites derived from mevalonate as well as by dietary cholesterol ○ Degradation is stringently controlled via increasing concentrations of sterols such as cholesterol ○ Phosphorylation by the AMP-activated protein kinase decreases the activity of HMG-CoA reductase.

Question 40

carbon atoms of cholesterol are derived from acetyl CoA in a three-stage synthetic process:

Answer 40

1. Stage 1 is the synthesis of isopentenyl pyrophosphate, an activated isoprene unit that is the key building block of cholesterol. (cytoplasm) 2. Stage 2 is the condensation of six molecules of isopentenyl pyrophosphate to form squalene. (ER) 3. In stage 3, squalene cyclizes and the tetracyclic product is subsequently converted into cholesterol. (ER)

Question 41

Cholesterol and triacylglycerols are packaged into _____ _____ for transport through bodily fluids.

Answer 41

lipoprotein particles

Question 42

The lipoprotein protein components (called apoproteins) have two roles:

Answer 42

solubilize hydrophobic lipids and contain cell-targeting signals

Question 43

Describe the fate of nitrogen that is removed when amino acids are used as fuels.

Answer 43

○ Nitrogen is removed in the form of ammonium ions ■ Some ammonium is used in biosynthesis of nitrogen compounds ■ Excess is converted into urea via the urea cycle and excreted in the urine

Question 44

Explain how the carbon skeletons of the amino acids are metabolized after nitrogen removal.

Answer 44

○ They are converted into glucose or acetyl-CoA

Question 45

Glucogenic amino acids

Answer 45

converted into pyruvate and will feed into gluconeogenesis to produce glucose.

Question 46

Ketogenic amino acids

Answer 46

converted into acetyl-CoA, the precursor to ketone bodies.

Question 47

Identify the sources of carbon atoms for amino acid synthesis

Answer 47

intermediates of glycolysis, the citric acid cycle, or the pentose phosphate pathway

Question 48

Identify the two stages of the pentose phosphate pathway

Answer 48

○ The oxidative generation of NADPH. ○ The nonoxidative interconversion of sugars

Question 49

Identify the enzyme that controls the pentose phosphate pathway.

Answer 49

Glucose 6-phosphate dehydrogenase

Question 50

Pentose Phosphate Pathway

Answer 50

Ribulose 5-phosphate is converted into ribose 5-phosphate In the nonoxidative phase, the pathway catalyzes the interconversion of three-, four-, five-, six-, and seven-carbon sugars in a series of nonoxidative reactions Excess ribose 5-phosphate formed by the pentose phosphate pathway can be completely converted into glycolytic intermediates (fructose 6-phosphate and glyceraldehyde 3-phosphate)