BIOCHEM UW: METABOLISM/ Nucleotides, CARBS & LIPIDS Flashcards
Draw the Citric Acid cycle
Fermentation
- is the reduction of pyruvate to generate NAD+ for continued glycolysis under anaerobic conditions
- in mammals, fermentation is carried out by the conversion of pyruvate ——->lactate
Glycolysis
- is the conversion of glucose—->pyruvate
Glycogenolysis
- is the degradation of glycogen for use in other metabolic pathways
Convert Glycogen to lactate
- glycogen is a form of energy storage
- when energy is needed, individual glucose units may be removed from glycogen through glycogenolysis
- The glucose-6-phosphate generated by glycogenolysis may then enter other metabolic pathways, including glycolysis & fermentation
Glial Cells
What is glycogen composed of?
Whata re the linkages?
what is phosphorylysis
-
Glycogen is primarily composed of several glucose subunits bound together by α-1,4 glycosidic linkages.
- Glycogen is cleaved into glucose-1-phosphate subunits by glycogen phosphorylase in a reaction called phosphorolysis.
- Phosphorolysis breaks bonds by adding an inorganic phosphate group across them.
- Glycogen is cleaved into glucose-1-phosphate subunits by glycogen phosphorylase in a reaction called phosphorolysis.
Hydrolysis
How can we provide evidence that a metabolic pathway worksby a proposed mechanism?
- a critical component of that mechanism should be inhibited & the effects observed
- the blocked component must be unique to the proposed mechanism to ensure that the observed effect is not due to a seperate pathway
in the mitochondria, pyruvate undergoes_________________ as it is converted to _______________ & enters the citric acid cycle
What happens to the carbon atoms in pyruvate precursors?
- 3 decarboxylation reactions
- acetyl-CoA
- will be released as CO2
what is the reaction that releases carbon atoms as CO2?
Peptide (amide) bond condensation
GLycosidic bond condensation
_______________ reactions produce chiral molecules in a specific arrangment
The citric acid cycle produces only 2 intermedicates with chiral centers, which are?
- Stereospecif reactions
- isocitrate (converted from citrate by aconitase) & malate (transformation of fumarate by fumarase)
Nucleotide structure
Which has the OH on the 2’ sugar? Ribose or deoxyribose?
- A nucleoside is a pentose (five-carbon) sugar linked to a nitrogenous base on the 1′ carbon by a covalent glycosidic bond.
- Nucleotides consist of a nucleoside attached to one or more phosphate groups by a phosphoester bond.
- If the pentose has a hydroxyl group at the 2′ carbon, it is ribose; if a hydrogen is present at the same position, it is deoxyribose.
Watson-Crick base pairing
How mancy donors & acceptors does each pair have?
- Hydrogen bond acceptors are electronegative atoms (nitrogen or oxygen) that have at least one lone pair of electrons, and hydrogen bond donors are hydrogen atoms bound to electronegative atoms.
DNA proofreading
exonuclease & endonucleases
- DNA polymerase I proofreads DNA and normally has exonuclease activity in the 5′-3′ as well as the 3′-5′ direction that allows it to remove primers and damaged or incorrect bases at the ends of the strand.
- It cannot fix mistakes in the middle of a strand; instead, base excision repair and nucleotide excision enzymes have endonuclease (mismatch repair enzyme, base excision repair) activity to remove damaged bases and mismatched nucleotides from the middle of a DNA strand, respectively.
- if an enzyme does not have a 5’-3’ exonuclease activity, thus can only proofread DNA in the 3’-5’ direction on the template strand, so only erros at the 3’ end of the growing strand can be repaired
Effect of hydrogen bonding on DNA melting temperature (Tm)
- The melting temperature Tm of DNA is the temoerature at which 50% of the double helices in solution have been seperted into snigle strands
- it is determined by the strength of intermolecular forces holding the strands together
- an inc in IMF=inc Tm bc more nergy is rquired to disrupt them
- DNA molecules with high GC content have higher melting temperatures than those with low GC content.
Polysaccharide Chain
Know the carbs orientation (D or L)
Fischer projections
- Fischer projections help distinguish anomers, epimers, and enantiomers.
- Enantiomers are compounds with the same chemical formula that differ at every stereocenter
- Epimers and anomers (are diastereomers) differ at only one stereocenter.
- Anomers can exist only in cyclized sugars (furanose or pyranose) and differ at the anomeric carbon.
Descrube how OAA is synthesized by 3 reactions? in a single step!
- via (citric acid cycle) malate, (gluconeogenesis,) pyruvate, and (aa degradation) aspartate to glutamate to OAA
how is pyruvate converted to OAA?
- Alanine can be deaminated to yield pyruvate, which can then be converted to oxaloacetate by pyruvate carboxylase.
- This process requires two enzymatic steps instead of one.
When different molecules enter the citric acid cycle at different points, the cycle will oxidize these molecules to produce the ______________
- the reduced electron carriers NADH & FADH2
- the number of electron carries produced depends on the number of oxidative steps remaining int he cycle at the point of entry
- example: methionine
Fermentation
higher eukaryotes: fermentation occurs_______________
Bacteria & lower eukaryotes (yeast) fermentation occurs by: ____________
- reduction of pyruvate to lactate
-
decarboxylation of pyruvate to form acetladehyde, followed by reducation of acetaldehyde to form ethanol
- inc in partial pressure, yeast cells would exhibit INC function of the ETC & the need for fermentation to regenerate NAD+ would decrease
- Becuase fermentation in yeast generates ethanol, increased partial pressure of oxygen (& decreased fermentation) would most likely result in reduced ethanol production
Structural Lipids
Steps of cholecsterol synthesis?
- Steroid hormones are derived from cholesterol.
- Cholesterol has a characteristic four-ring backbone, which is synthesized from five-carbon subunits called isoprenes.
- Two isoprenes joined together form a monoterpene, and six isoprenes can join to form a triterpene called squalene, which then cyclizes and, after several steps, forms cholesterol.
Fat-Soluble Vitamins
- Certain biomolecules such as vitamins and the essential amino and fatty acids cannot be synthesized in the human body and must be obtained through the diet.
- Water-soluble vitamins (B series, C) are excreted in the urine whereas fat-soluble vitamins (A, D, E, and K) are stored in adipose and other fatty tissues.
Steroid hormones & Peptide Hormones
-
Steroid hormones are produced primarily in the adrenal cortex and the gonads from cholesterol and other precursors.
- They are not required in the diet and do not generally accumulate in adipose tissue.
-
Peptide hormones are readily synthesized by the body, and are not required in the diet.
- They are generally soluble in water, and are not stored in adipose tissue.
Example of Semiconservative DNA replication:
Escherichia coli bacteria containing only 15N-labeled DNA were grown in media containing only 14N nucleotides. What percentage of double helices would be composed of one 15N strand and one 14N strand after three generations?
- DNA replication is a semiconservative process that results in each double helix containing one parental strand and one newly synthesized daughter strand.
- DNA polymerase synthesizes each new daughter strand by using a parental strand as a template.
- Answer to question & explained: 25%
- In the experiment described, Escherichia coli bacteria initially have the heavy isotope 15N in their DNA. Once the bacteria are transferred to 14N media and allowed to replicate, newly synthesized strands will contain 14N.
- In Generation 1, all new strands will be paired with parental strands that contain 15N. Therefore, 100% of double helices produced in Generation 1 will have one 15N strand and one 14N strand
- In generation 2, both the 15N and 14N strands from Generation 1 are used as templates for the synthesis of new 14N strands. In the DNA that used a 14N strand as a template, both parental and daughter strands will contain 14N nucleotides. In DNA that used a 15N strand as a template, the parental strand will contain 15N and the daughter strand will contain 14N. Because half of the parental strands are 15N and half are 14N, 50% of the Generation 2 double helices will contain one 15N strand and one 14N strand. The other 50% will contain two 14N strands.
- In generation 3, the percentage of double helices containing one 15N strand and one 14N strand will be half the percentage of the previous generation. Therefore, in Generation 3, 25% of double helices will contain a 15N strand and a 14N strand.
describes the ribose component of a nucleotide triphosphate?
- pentofuranose
- Ribonucleotide triphosphates contain a nitrogenous base, ribose, and a triphosphate group linked to the 5′ carbon of ribose.
- Ribose is a five-carbon sugar (pentose) that must adopt the furanose form to be incorporated into the nucleotide triphosphates. In this form, it can be classified as a pentofuranose.
Difference in Furnose & pyranose forms of ribose
Apoptosis is induced by ____________
- oxidative stress
ATP yeild calculation
- 1 NADH= 2.5 ATP
- 1 FADH2=1.5 ATP
- 1 glucose=32 ATP
Complex V of ETC
- Complex V activity depends on proton availability.
- Proton concentration in the intermembrane space can be increased by increasing the number of NADH molecules that enter the electron transport chain.
- NADH from glycolysis can indirectly enter the mitochondrial matrix by first passing its electrons to oxaloacetate, forming malate (via malate-aspartate shuttle)
Glycerol 3-Phosphate
- converts cytocolic NADH to mitochondrial FADH2 by OXIDIZING glycerol 3-phosphate to DHAP
how to calculate rate of chemical output
- by dividing the total output by the time it takes to achieve that output
When one chemical process provides the energy for another, the processes are said to be ____________.
- Coupled
- When two processes that are normally coupled become decoupled, the process that provides the energy continues but the process driven by that energy slows or stops, as the two have become disconnected.
Regulation of glycolysis & gluconeogenesis by insulin in the fed state
Question: Which of the following regulatory mechanisms helps increase net glucose catabolism in the liver after a meal?
- Insulin stimulates glycolysis by activating the enzyme PFK-2, which synthesizes fructose-2,6-bisphosphate.
- Fructose-2,6-bisphosphate allosterically activates PFK-1 and inhibits fructose-1,6-bisphosphatase, which stimulates glycolysis and reduces gluconeogenesis.
- Answer: allosteric inhibition of fructose-1,6-bisphosphatase catalysis
Insulin & glucagon signaling
a deficiency in the pyruvate dehydrogenase complex (PDHC) activity causes lactic acid build up, what can be indicated by this?
- impaired ability to synthesize lipoic acid
- The pyruvate dehydrogenase complex (PDHC) is an enzyme composed of three subunits (E1, E2, and E3).
- It catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, along with the reduction of NAD+ to form NADH.
- During this process, electrons are passed from one subunit in the complex to the next until they can be transferred to NAD+. This transfer is facilitated in part by the cofactor lipoic acid.
Fatty Acid Oxidation/Saturated/Unsaturated FA
- Fatty acids can be oxidized to form_________, and those with an even number of carbons produce half as many ____________ molecules as they have carbons.
- Fatty acids with an odd number of carbons produce _______________
- ____________require isomerization reactions to convert cis-bonds to trans-bonds whereas ___________ do not.
- acetyl-CoA, acetyl-CoA
- propionyl-CoA in addition to acetyl-CoA. (# of Acetyl-CoA produced=total carbons-3/2)
- Unsaturated fatty acids (they have at least 1 double bond)
- Saturated fatty acids (no isomerization)
if we have a final product of 9 acetyl coA, know that the state point is 18 carbons
Fatty Acid Oxidation
Entry into the mitochondrial matrix is tightly regulated by transport proteins in the______________ membrane. Fatty acids must be activated with ___________ followed by _________________ to enter the mitochondrial matrix. Activation requires ______________.
- inner mitochondrial membrane
- coenzyme A
- carnitine
- ATP hydrolysis
note that FA are not recognized by any transport proteins; they must be modified or “activated” to enter the matrix (like what is said on top and shown in the attached pic)
Oxaloacetate
is an intermediate in the __________&____________&______________:
- citric acid cycle, gluconeogenesis, & transport of acetyl-CoA FROM the mitochondria INTO the cytosol for fatty acid synthesis
- NOTE: IT IS NOT INVOLED IN THE TRANSPORT OF FATTY ACIDS FROM CYTOSOL INTO THE MITOCHONDIRA
CORI CYCLE
- During anaerobic exercise, pyruvate is reduced to lactate to regenerate NAD+.
- Lactate that builds up in muscles is sent to the liver, where it is converted back to glucose (gluconeogenesis) and returned to muscles.
- The process of carrying lactate from the muscle to the liver and moving regenerated glucose from the liver back to muscles is called the _Cori cycle, which connects gluconeogenesis and glycolysis._
Pentose Phosphate pathway
The pentose phosphate pathway generates _________&___________. The NADPH is generated by reduction of ____________, which is catalyzed by the oxidoreductases __________________&__________________
- ribose 5-phosphate and NADPH
- NADP+
- glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase.
Catabolic vs. Anabolic
- Citric Acid Cycle:*
- is allosterically regulated at the irreversible steps catalyzed by ___________&______________&______________. The enzymes are inhibited by___________&_______________&______________, and are activated by ________&____________. The Krebs cycle enzymes are not under_____________control.*
- Citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase.
- NADH, ATP, citrate, and succinyl-CoA
- ADP and calcium
- hormonal control
Electron Transport Chain
In the electron transport chain, four electrons are required to fully reduce one O2 molecule to two H2O molecules. Given this information, how many NADH molecules are required?
- Answer: 2
- Electron donors and acceptors in the ETC have different carrying capacities. Full reduction of oxygen to water requires four electrons, so two copies of a two-electron carrier such as NADH would be required to fully reduce oxygen. Four copies of a one-electron carrier, such as reduced cytochrome C, are required.
Anobolic processes
- Anabolic processes require __________, which is typically provided by _________________________________________
- These cleavage events either release the γ-phosphate as inorganic phosphate (Pi) or they release the γ- and β-phosphates as pyrophosphate. The α-phosphate remains attached to the NTP.
- energy input
- cleaving phosphodiester bonds in nucleotide triphosphates (NTPs) such as ATP, GTP, or UTP.
During prolonged fasting, which of the following liver enzymes has upregulated activity?
During periods of fasting, the liver helps maintain _____________. The liver initially synthesizes glucose by degrading ____________. However, after glycogen stores are depleted in prolonged fasting, _____________ is upregulated, increasing the synthesis of glucose from precursors such as ____________. _In the fasting state, the liver downregulates key enzymes of ______________ and upregulates enzymes of ________________._
- Pyruvate carboxylase
- blood glucose levels
- glycogen
- gluconeogenesis
- pyruvate
- glycolysis
- gluconeogenesis
Nucleaotide Bases
Sugar Cyclization
Pyranose
Furanose
Hemiacetal & hemiketal
- In their linear form, monosaccharides contain multiple alcohol groups and one carbonyl group.
- For aldoses, the carbonyl is an aldehyde, whereas for ketoses the carbonyl is a ketone.
- All** monosaccharides contain at least **one primary alcohol,** and **most** contain **at least one secondary alcohol.
Hydrolyzable lipids
- Those with sphingosine backbones are sphingolipids; those with glycerol backbones are glycerolipids; phosphate modifications yield phospholipids; and carbohydrate modifications yield glycolipids.
- Complex lipids may involve a combination of these characteristics and are named accordingly (ie, glycosphingolipid, glycerophospholipid).
- hydrolyzable linakges contain esters or amides
Nonhydrlyzable lipids
Example of Glycosphingolipid
Mutarotation
Anomeric Carbon & glycosidic bonds
- A glycosidic bond is a bond between the anomeric carbon of a carbohydrate and any other biomolecule.
- A single carbohydrate may participate in many glycosidic bonds by linking to the anomeric carbons of other carbohydrates, allowing a high level of diversity among carbohydrate chains.
Example of glycosidic bond
Sphingolipids are strucural lipids
Sphingolipids are structural lipids that help influence the ___________&____________of biological membranes. The long hydrocarbon chain of the sphingosine head group cannot be readily _______________, and sphingolipids are not a primary means of _____________
- fluidity and curvature
- CANNOT hydrolyze
- energy storage
- sphingolipids produce _one fatty acid upon hydrolysis_
Membrane Fluidity
fluidity of a cell membrane is largely dependent on the ___________________ in the bilayer and on the ____________ in each tail. ________________ yield the highest fluidity because they participate in the___________________
- lengths of the fatty acyl tails
- number of double bonds
- Short chains with double bonds
- fewest hydrophobic interactions with neighboring lipids
Nucleotide bases:
Thymine and adenine have _________ donor and ________ acceptor each, whereas guanine has _________ acceptor and ________ donors and cytosine has ________ acceptors and ________________
- 1 donor & 1 acceptor
- 1 acceptor & 2 donors
- two acceptors & 1 donor
Metabolic pathways and their allosteric activators & inhibitors
Cori Cycle:
- one glucose molecule is converted to __________ pyruvate molecules in the muscle, which are then sent to the liver (as ____________), where they are converted back to glucose.
- Because gluconeogenesis consumes _________equivalents and glycolysis produces __________ equivalents, a net total of __________equivalents are consumed in one round of the cycle.
- two
- lactate
- 6 net ATP
- 2 net ATP
- 4 ATP
Active transport processes
- Uniport*
- Antiport*
- Symport*
How do fatty acids enter the mitochondria?
-
via L-Carnitine
- B-oxidation occurs in the mitochondria and produces acetyl-CoA
- palmitate is an example of fatty acids
- Inhibiting FA synthesis, might result in an increase in what?
- What are the reactants needed to generate FA chains during lipid synthesis?
-
NADPH (conversion of NADPH to NADP+ will occur less frequently) thus, cystolic NADPH will build up
- pentose phosphate pathwat generated the NADPH needed to reduce the carbonly groups from each molecule of acetyl-CoA
- acetyl coA will most likely increase
- Acetyl-CoA, NADPH, ATP
- Insulin stimulates lipid synthesis by activating the majoy enzymes involved in fatty acid production: __________&__________&____________
- pyruvate dehydrogenase complex, acetyl-CoA carboxylase & fatty acid synthase
- PDH converts pyruvate produced from glucose into acetyl-CoA, which is transported to the cytoplasm for fatty acid synthesis
- Protein catabolism refers to the breakdown of polypeptide chains and proteins into_____________ to produce______&__________&___________
Transamination & deamination of amino acids?
- individual amino acids
- ATP, glucose, or new proteins
- Transamination reactions generate α-keto acids from amino acids by transferring the NH3 group to α-ketoglutarate, which is converted to glutamate.
Protein metabolism
- Glucogenic amino acids are converted to pyruvate, which can be used to make glucose or citric acid cycle intermediates.
- Ketogenic amino acids are converted directly to acetyl-CoA, which can enter the citric acid cycle or be used to form ketone bodies.
- In the absence of oxygen, pyruvate is reduced to lactate to regenerate NAD+ during fermentation.
Reducing & Non-reducing sugars
-
Reducing sugars contain free anomeric carbons that provide reducing power when they are oxidized.
- In linear form the anomeric carbon is an aldehyde or a ketone, and in cyclic form reducing sugars have hemiacetal or hemiketal configurations.
- Nonreducing sugars contain acetal or ketal structures in their cyclic forms.
Sphingolipids are structural lipds
Glycerophospholipds
Triglycerides Structure
Example of constituitonal isomers
same molecular formula but distanct arrangements
Examples of Enantiomers
differ at all centers
Gycosidic bonds and reducing sugars
Glycosidic bond formation requires a sugar with a free anomeric carbon, called a reducing sugar.
- All free monosaccharides are reducing sugars whereas disaccharides are reducing only if one anomeric carbon does not participate in a glycosidic bond.
- Sucrose is the most common nonreducing sugar.
glucose 6-phosphatase & the Cori cycle:
- Several biological processes, including gluconeogenesis, glycogenolysis, and the Cori cycle, help buffer blood glucose levels. All of these processes require glucose 6-phosphatase (G6Pase) to catalyze the final step to release free glucose.
- The pentose phosphate pathway uses glucose 6-phosphate as a substrate, but does not produce free glucose or require dephosphorylation and is unaffected by changes in G6Pase activity.
Inactivation of PEPCK:
catalyzes the second step in gluconeogenesis, the conversion of oxaloacetate to phosphoenolpyruvate, and its inactivation can indeed lead to both lactate buildup and glucose depletion in the blood
Hormones regulating glucose metabolism chart
Genetic mutations that inhibit gluconeogenesis and glycogenolysis can prevent effective hormonal control of blood glucose levels, how can this be counteracted? like how can hypoglycemia be counteracted?
- Dietary supplementation with a glucose source such as starch can help maintain glucose levels in these cases
Acetylation of lysine residues in histones increases gene expression because:
- the salt bridges between charged amino acids and phsophate groups are disrupted
- Histones associate with DNA by forming salt bridges between their positively charged residues and negatively charged phosphate groups on DNA. Acetylation of histones involves the transfer of an acetyl group to positively charged amino groups on lysine or arginine residues, increasing gene expression by disrupting salt bridges between histones and DNA.
Complex II (succinate-ubiquinone reductase or succinate dehydrogenase)
- Oxidizes succinate to fumarate and transfers electrons to Complex III.
- Electrons are transferred from flavin adenine dinucleotide (FAD) to iron-sulfur centers in Complex II, then to ubiquinone (coenzyme Q), which carries them to Complex III through the inner membrane.
Complexes I, III, and IV
- pump protons into the intermembrane space against their concentration gradient, but Complex II does not pump protons against their gradient, and therefore does not contribute to the decrease in pH in the intermembrane space.
redox potentials
In the electron transport chain, electrons are transferred to carriers with higher redox potentials at each step
Cell communication
- Cells communicate through chemical signals called hormones.
- Hydrophilic hormones such as peptide hormones cannot cross the cell membrane and require second messengers.
- Hydrophobic hormones such as steroid hormones can cross the cell membrane and do not need second messengers.
starvation response: lipid metabolism
- Triacylglycerols, also known as triglycerides, are storage lipids that consist of three fatty acid chains attached to a glycerol molecule.
- During prolonged starvation, acetyl-CoA produced from fatty acid oxidation in the mitochondria is converted into alternative fuel molecules known as ketone bodies.
phospholipids in cell membrane could be seperated by:
- Phospholipids are composed of a hydrophilic head group that contains a phosphate and a hydrophobic tail with one or two fatty acid chains.
- Phospholipids have either a glycerol or a sphingosine backbone.
- The composition of the head groups and the length of the tails create lipids with distinct solubility (TLC), charge( HPLC), and mass (size-excluson chromatogrphy)
lipid processing & classification
Emulsification & micelles
- Lipid processing begins in the small intestine (dduodenum), while bile salts break down lipid globules into smaller droplets in a process called emulsuificaiton
- Emulsification increases the surface area of lipids by breaking down large globules into spherical structures called micelles.
- Micelles have a hydrophobic core, which contains the nonpolar hydrocarbon tails of lipids, and an outer shell of polar head groups, which make contact with water.
- Lipases can cleave the ester bonds in hydrolyzable lipids such as triglycerides, phospholipids, and waxes by adding a water molecule (hydrolysis).
Catalysts (including enzymes)
- increase reaction rate constants by stabilizing transition states and decreasing activation energy.
- They do not affect the energy states of products or reactants, and therefore they do not affect the equilibrium positions of the reactions they catalyze.
branched alkyl chains
Prostagladins
- Prostaglandins are nonhydrolyzable, 20-carbon (eicosanoid) lipids involved in autocrine and paracrine signaling.
- They are derived from arachidonic acid and often help mediate localized inflammatory responses.
- Nonsteroidal anti-inflammatory drugs (NSAIDs) such as aspirin and ibuprofen treat inflammation by inhibiting prostaglandin synthesis.
Terpenes
- are precursors in the synthesis of cholesterol and steroid hormones. They are derived from isoprenes
Ketone bodies
- are fuel sources that are produced under low glucose conditions. They are derived from acetyl-CoA
Catecholamines
- such as epinephrine and norepinephrine are hormones derived from the amino acid tyrosine.
- They can play a role in inflammatory responses but generally do so as endocrine signals (acting on cells that are distant from their origin).
Chargaff’s rules
- Chargaff’s rules state that there is a 1:1 nucleotide mole ratio of pyrimidines to purines and that for any double-stranded DNA sample:
A=T and G=C
G+A = C+T
