FINAL EXAM Flashcards
Hydrogen bonds
Much weaker than covalent bonds
Unequal electron sharing when covalently
bound hydrogen is bound to a more
electronegative atom leads to partially
charged atoms
Van der Waals forces
Repulsion and attraction
Hydrophobic effect
Non-polar or hydrophobic molecules coalesce spontaneously (oil and water)
increases the disorder of the
surrounding water
Why are weak interactions important for life?
Reversibility allows for the flexibility of function
Define pH
measure of hydrogen ion concentration in a solution
Primary
Each amino acid is linked to the next amino acid by a peptide bond
Secondary
Primary amino acid sequences can fold into recurring structures (alpha-helices)
Stabilized by H-bonds between amino
acids 4 peptides apart
Tertiary
Quarternary
Describe the biochemical information that determines the final three-dimensional structure, and
explain what powers the formation of this structure.
○ 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
Structure of a fatty acid
Chains of
hydrogen-bearing carbon atoms (hydrocarbons) that terminate with
carboxylic acid groups
difference between a saturated and unsaturated fatty acid
Saturated: only single bonds
Unsaturated: one or more double
or triple bonds, lower melting points
This simplest type of lipid is most commonly used as a
Fuel
Lipids
Chains of hydrogen-bearing carbon atoms (hydrocarbons) that terminate with carboxylic acid groups
Protein digestion
Proteins - Pepsinogen, and also enteropeptidase → Trypsin → All other
enzymes
Lipid digestion
Emulsification, CCK/Bile Salt secretion, lipase access/cleavage
Carbohydrate digestion
alpha-amylase (mouth), ⍺-Dextinase, glucosidase,
sucrase, and lactase (intestine)
What are the important functions of different enzymatic and non-enzymatic events in digestion
○ 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)
What is a zymogen?
(catalytically inactive precursor of an enzyme) which are
activated by proteolytic cleavage
Identify the factors that make ATP an energy-rich molecule
○ Electrostatic repulsion of the four negative charges carried by the triphosphate
○ Relatively intermediate phosphoryl-transfer potential
Explain how ATP can power reactions that would otherwise not take place.
Large free energy release can be coupled with
thermodynamically UNfavorable reactions in order
to make them thermodynamically favorable
Describe the relation between the oxidation state of a carbon molecule and its usefulness as
a fuel.
○ 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
Describe how ATP is generated in glycolysis.
○ 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)
Explain why the regeneration of is crucial to fermentations.
○ 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
Describe the coordinated regulation of glycolysis and gluconeogenesis.
○ 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
Explain why the reaction catalyzed by the PDH complex is a
crucial juncture in metabolism.
Commits the carbon atoms of carbohydrates to oxidation by
the citric acid cycle or to the synthesis of fatty acids
Identify the means by which the PDH complex is regulated.
Products of the PDH complex inhibit its activity (acetyl-CoA
and NADH), either directly, or through activation of pyruvate
dehydrogenase kinase
Identify the primary catabolic purpose of the citric acid cycle.
Harvesting of high-energy electrons from carbon fuels.
Explain the advantage of the oxidation of acetyl CoA in the citric acid cycle.
Harvesting of high-energy electrons from carbon fuels.
Describe how the citric acid cycle is regulated.
There are three TCA enzymes that are highly regulated
Explain the benefits of having the electron-transport chain located in a
membrane.
Allows for build up of proton gradient, so that proton-motive force can be
used to generate ATP
Identify the ultimate determinant of the rate of cellular respiration.
Need for ATP
Explain the regulation of glycogen breakdown.
Hormonal regulation by glucagon (pancreas) and epinephrine
(adrenal gland)
Describe the steps of glycogen synthesis and identify the enzymes
required.
Glycogen synthase, Branching enzyme
Identify the repeated steps of fatty acid degradation.
2 carbons at a time
oxidation, hydration, oxidation, thiolysis
Explain how fatty acids are synthesized.
■ 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
Describe the relation between triacylglycerol synthesis and phospholipid synthesis.
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
Phosphatidic Acid Phosphatase (PAP, lipin 1) Is a Key Regulatory Enzyme in Lipid Metabolism
Controls the extent to which triacylglycerols are synthesized relative to phospholipids
List the regulatory steps in the control of cholesterol synthesis.
○ 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.
carbon atoms of cholesterol are
derived from acetyl CoA in a three-stage synthetic process:
- Stage 1 is the synthesis of isopentenyl pyrophosphate, an
activated isoprene unit that is the key building block of
cholesterol. (cytoplasm) - Stage 2 is the condensation of six molecules of isopentenyl
pyrophosphate to form squalene. (ER) - In stage 3, squalene cyclizes and the tetracyclic product is
subsequently converted into cholesterol. (ER)
Cholesterol and triacylglycerols are packaged into _____ _____ for transport through bodily fluids.
lipoprotein particles
The lipoprotein protein
components (called apoproteins) have two roles:
solubilize hydrophobic lipids and contain cell-targeting signals
Describe the fate of nitrogen that is removed when amino acids are used as fuels.
○ 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
Explain how the carbon skeletons of the amino acids are metabolized after
nitrogen removal.
○ They are converted into glucose or acetyl-CoA
Glucogenic amino acids
converted into pyruvate and will feed
into gluconeogenesis to produce
glucose.
Ketogenic amino acids
converted into acetyl-CoA, the
precursor to ketone bodies.
Identify the sources of carbon atoms for amino acid synthesis
intermediates of glycolysis, the
citric acid cycle, or the pentose phosphate pathway
Identify the two stages of the pentose phosphate pathway
○ The oxidative generation of NADPH.
○ The nonoxidative interconversion of sugars
Identify the enzyme that controls the pentose phosphate pathway.
Glucose 6-phosphate dehydrogenase
Pentose Phosphate Pathway
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)
