BIOCHEM BLOCK 3 REVIEW PACKET 1

Block 3 Review Notes

What Enzymes Do

• HMG-CoA Reductase makes mevalonate from HMG-CoA
• Squalene monooxygenase adds oxygen to squalene, which is necessary for cyclical form
• Oxidosqualene lanosterol cyclase closes rings to generate cyclical form
• Acyl-CoA Cholesterol Acyltransferase (ACAT) esterifies cholesterol
• HMGR is the regulator of overall synthesis
• Squalene monooxygenase is regulated by levels of both substrate and product
• ACAT can alter the level of free cholesterol in a system directly because of its role in cholesterol esterification

Cholesterol Synthesis Matching

• HMG-CoA Reductase is the first product, the production of which commits to cholesterol synthesis
• HMG-CoA Reductase is the enzyme regulated to determine whether synthesis will take place
• "March 6 active" is a normal cholesterol level
• "March 6 inactive" is low squalene/high cholesterol
• Mevalonate is high squalene/high cholesterol
• Squalene monooxygenase inactive is high squalene/low cholesterol
• Squalene monooxygenase active is low squalene/low cholesterol
• Cholestasis/Gallstone Production is cholesterol:phospholipid > 1:1
• Cholesterol:phospholipid = 1:1 occurs when there is a normal cholesterol level

Cholesterol Synthesis (Substrate/Metabolic Product) Matching

• Lanosterol is a substrate of synthesis
• Squalene is a substrate of synthesis
• Mevalonate is a substrate of synthesis
• Bile salt is a metabolic product
• Specific steroid hormones are a metabolic product
• Cholesterol Ester is a metabolic product

Glycosylation

• Glycosyltransferases add sugars to the core, determining the final structure of N-glycan chains
• Variation in glycosylation is achieved by enzyme activity during glycosylation such as glycosyltransferases in N-linked glycosylation
• A protein’s amino acid sequence does NOT determine the sugars added, only if they could be glycosylated
• Glucosidase activity utilizes N-linked glycosylation where glucose should be removed if functional
• Hydroxyl functional groups are most likely essential for O-linked glycosylation, using amino acid residues like hydroxylysine, serine, threonine and tyrosine

Amino Acids

• A 36-year-old pregnant woman at 20 weeks should supplement her diet with arginine, cystine, glutamine, glycine, proline, and tyrosine, which are not dietarily required under normal metabolic conditions
• Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine are always required in the diet
• Isoleucine, leucine, lysine, phenylalanine, threonine, tryptophan, and tyrosine are ketogenic
• Isoleucine, phenylalanine, threonine, tryptophan, and tyrosine are both glucogenic and ketogenic
• Embryogenic determination of muscle mass is responsible for cell turnover and protein turnover
• The need for energy and maintenance of blood glucose contributes to the breakdown of muscle protein during starvation to regulate protein degradation in adults

HMGR Activity (Active/Inactive) Matching

• HMG-CoA Reductase is active when dephosphorylated, when there is more ATP and less AMP, when HMG-CoAR phosphatase is active and when insulin levels are high
• HMG-CoA Reductase is inactive when phosphorylated, when there is a high AMP/ATP ratio, when AMPK is active and when glucagon levels are high

Urea Cycle Pathways

• Urea cycle pathways are the same no matter how they are presented

Purine vs. Pyrimidine Biosynthesis

• Purine synthesis has a high energy cost, adds sugar, then base and has an IMP precursor
• Ribose 5-phosphate, PRPP, GAR, AIR, SACAIR, and AICAR are key intermediates in purine synthesis, which generates AMP and GMP
• Pyrimidine synthesis has a high energy cost, adds base, then sugar and has an UMP precursor
• Carbamoyl phosphate, dihydroorotate and orotate are key intermediates in pyrimidine synthesis, which generates CTP and TMP to TTP
• IMP does not bioaccumulate
• AMP = adenylosuccinate synthetase, CTP = CTP synthetase, GMP = IMP dehydrogenase, TTP = TK1, TYMS, and DTYMK are the most important enzymes in the synthesis of each nucleotide

Glycosylation Key Topics

• Proteoglycans have sugar and some protein

N-Linked Glycosylation

• Main location: ER
• Role of GlcNAc
• Utilizes glycosyltransferases and glycosidases
• Involves asparagine
• Important for mannose and dolichyl phosphate (a membrane bound lipid intermediate)
• Processing in the Golgi is similar to O-linked glycosylation, but overall N-linked glycosylation will not be affected by a lack of sialic acid

O-Linked Glycosylation

• Main location: Golgi
• Role of GalNAc
• Galactosyltransferases are involved
• Uses serine, threonine, hydroxylysine, and tyrosine
• CMP-sialic acid and sialyltransferases are used

Molecular Genetics and Testing Techniques

• DNA polymerase, repair mechanisms, RNA processing, and Aminoacyl tRNA synthetases have the ability to edit

Testing Techniques

• Genome: used for finding genetic mutations and known pathogenic variants by utilizing comparative analysis
• Transcriptome/Exome: used to find genetic expression profiles and tumor molecular profiling for more functional analysis of activity
• Proteome: is used to determine the functional consequences of genetic mutations, can find the functional consequences on protein shape and activity
• Metabolome: used in biochemical analysis of systemic activity for biomarker generation

Neurochemistry

• The inability to express norepinephrine in a cell correlates with the absence or reduced function of dopamine beta-hydroxylase
• Any step in the process could be asked about
• GABA appears to be amino acid-like and derives from amino acids, but it is not incorporated into proteins

Neurotransmitter Matching

• Acetylcholine - Expected only in the fetal neurons and important in pain perception
• Tyrosine - Processed into L-Dopa by tyrosine hydroxylase
• Tryptophan - Precursor of serotonin
• Dopamine - Can be processed into acetate
• Serotonin - Produced by 5-hydroxytryptophan decarboxylase
• Substance P - Produced from L-Dopa by dopamine decarboxylase

Digestion Enzymes

• Pepsinogen is activated by low pH to turn into pepsin, which hydrolyzes peptide bonds adjacent to aromatic amino acids
• Prolipase is activated by binding with colipase to turn into lipase
• Trypsinogen is activated by duodenal enteropeptidase hydrolyzing N-terminal peptide to turn into trypsin, which hydrolyzes peptide bonds adjacent to Arg and Lys
• Chymotrypsinogen is activated by hydrolysis by enteropeptidase or trypsin to turn into chymotrypsin which hydrolyzes peptide bonds adjacent to aromatic amino acids
• Proelastase is activated by hydrolysis by enteropeptidase or trypsin to turn into elastase, which hydrolyzes peptide bonds adjacent to aliphatic amino acids
• Procarboxypeptidase A is activated by hydrolysis by enteropeptidase or trypsin to turn into carboxypeptidase A which hydrolyzes peptide bonds at carboxy terminal amino acids with aromatic or branched aliphatic side chains
• Procarboxypeptidase B is activated by hydrolysis by enteropeptidase or trypsin to turn into carboxypeptidase B, which hydrolyzes peptide bonds at carboxy terminal amino acids with basic side chains

Digestion Enzymes and Functionality

• If an enzyme in digestion isn't functional, there will be reduced digestion and a corresponding inability to absorb that material
• Enzyme activity can be evaluated by what is excreted as well as what is absent from plasma

Metabolic Processes

• Resource availability and hormones determine the metabolic state and timelines for each

Specific Metabolic States

• Absorptive state: fed or during absorbtion of nutrients from ingestion
• Basal: postabsorptive state (short duration)
• Fasting: A few hours post absorptive to approximately 2-3 days
• Starvation: Shift observed at >5 days

Hormone Levels in Each State

• Glucagon levels are higher while fasting and starving
• Insulin levels are higher in absorptive states, but are reduced when post-absorptive states are entered

Processes for Each State

• The main fuel is glucose
• When glucose is scarce, glucose shifts to the brain and RBC
• During starvation, the brain utilizes ketone bodies which are produced by amino acid break down
• A short-term starvation shifts the body to use fats (TAGs and fatty acids from adipose tissue)
• Prolonged starvation then shifts to protein breakdown and ketone body production

Unique Considerations for Tissues Under Each State

• The liver regulates glucose
• Muscles experience protein breakdown in starvation
• The brain will begin using ketone bodies to ensure function

Linking Cause and Effect of Enzymes

• Increased cholesterol leads to gallstones
• Increased cholesterol intake leads to atherosclerosis
• Altered nitrogen metabolism leads to neurological symptoms and problems with the urea cycle

Linking Cause and Effect of Enzymes (Continued)

• Absorption deficiencies lead to short bowel syndrome which results in failure to thrive, vomiting, and chronic diarrhea, or electrolyte imbalance
• Digestion deficiencies / deficiencies in activity of digestive enzymes leads to lactase deficiency where a ptient experiences dietary associated diarrhea and an increase of material in the stool