More Biochem Review

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What do kinases do and what are their cofactors?
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they add phosphate groups and require an ATP cofactor
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What are carboxylases and what is their cofactor?
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They ad carboxyl groups and require biotin cofactors
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what are synthases and what is their cofactor?
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they link 2 molecules together and don’t have a cofactor
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What are Methylases and what is their cofactor?
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methylases adds a methyl group and it’s cofactor is ""
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What breaks down proteins in the stomach, and into what?
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HCl and pepsin break down proteins into polypeptides
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What are the pancreatic enzymes?
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Trypsin and Chymotrypsin
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What is the transport mechanism to absorb amino acids?
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Facilitated Diffusion by carrier proteins
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What happens to proteins in the cells, and why?
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They are turned over as a way of storing nitregonous compounds, as a way of eliminating abnormal or dysfunctional proteins, and as a way of regulating enzyme function.
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What does protein degradation occur?
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In lysosomes and proteasomes
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What do lysosomes do in starved cells?
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They selectively degrade proteins containing the sequence KFERQ (lysine, fenyl alanine, glutamic acid, argenine, glutemine), only if nutrients are limited
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How are proteasomes different from lysosomes?
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They are large multiple protein complexes
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What is the function of 19S?
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it determines what proteins are to be degraded and allows them to the 20S complex.
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How is a protein marked for degredation?
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Attaching Ubiquitin, when the protein contains segments rich in PEST (proline, Glutamic Acid, Syrine, Threomine), or when proteins have destabilizing N-Terminal residues
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What N terminal residues destabilize proteins and what does this do?
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asp, arg, leu, lys, and phe all make the proteosome degrade the protein faster
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What residues stabilize proteins?
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Ala, Gly, Met, Ser, Thr, and Val
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What 2 reactions remove amino groups, and what is removed as? What removes this product?
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Transamination and Oxidative deamination and is removed as ammonia which is removed by the Liver and kidneys
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What uses do the carbon skeletons of deaminated amino acids serve?
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they are oxidized completely to create CO2 and H2O, they create glucose, Acetyl-CoA, and Ketone Bodies.
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Explain 1-Transamination reaction
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Amino group is transfered from an amino acid to another molecule by transaminase (cofactor PLP)
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What are the 3 pairs of transaminase reactions?
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Glutamate/a-ketoglutarate

Aspartate/oxaloacetate

Alanine/pyruvate

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What is the cofactor of transaminase reactions?
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PLP, pyridoxal phosphate (a form of vitamin B6)
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What are the markers for tissue damage?
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Syrum Glutamate Oxaloacetate Transanimase (SGOT(AST))

Syrum Glutamate Pyruvate Transanimase (SGPT(ALT)

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Where are SGOT and SGPT produced? How do they indicate tissue damage?
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The liver, kidneys and heart.  When the cells die they release their components into the blood, including these enzymes.
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Glucogenic amino acids produce
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any precursos to oxaloacetate, which leaves to the cytoplasm to be turned into glucose
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The only non-glucogenic amino acids produce…
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acetyl-CoA or acetoacetate which are used to make ketone bodies (Ketogenic)
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What AA’s produce pyruvate? What enzyme converts them to pyruvate, and what is it’s cofactor?
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Ala, Ser, Gly, Thr, and Cys

Alanine Transaminase converts to Pyruvate

Serine dehydratase

cofactor is PLP for both of the above

Glycine turns into serine by Serine-hydroxymethyltransferase (cofactor THF) or in mitochondria is turned into CH2=THF by Mitochondrial glycine cleavage complex (GCC)

Threonine aldolase makes acetaldehyde (ketogenic) and glycine (glucogenic)

Cys needs to have a sulfur removed

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Which AA’s produce oxaloacetate and what enzymes are used?
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Asparagine to aspartate by L-asparaginase

Aspartate to oxaloacetate by transaminase (SGOT) PLP cofactor

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What AA’s can be turned into a-ketoglutarate and by what enzymes?
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Arg Pro and His are converted to Glu, Gln is converted to glu by glutaminase.

Glu is converted to a-ketoglutarate by transaminase or gly dehydrogenase

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Hydrophobic AA’s are metabolized by what enzymes into what products?
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Val, Ile, Leu are converted into a-keto acids by transamination, then into propionyl CoA, Propionyl CoA and Acetyl CoA, and Acetyl CoA and acetoacetyl CoA by branched0chain a-Keto Acid dehydrogenase complex (respectively)
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Propionyl CoA is…
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glucogenic
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Acetyl CoA and acetoacetyl CoA are…
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ketogenic and a ketone body (respectively)
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explain the catabolism of methionine?
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met is converted to S-adenosylmethionine (SAM), then to homocysteine, then to cystathionine, then to cystieine (glucogenic) and a-ketobutyrate to propionyl CoA (glucogenic)
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Explain Lys Catabolism
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Lys’s side chain is transaminated, and produces acetoacetyl CoA
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Lys and Leu are both strictly
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ketogenic
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explain Trp Catabolism
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Trp is converted to 3-hydroxyathranilic acid and alanine (glucogenic), 3-hydroxyanthranilic acid is used to create either acetoacetyl CoA or NAD (converted to NADP)
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Explain catabolism of Phe and Tyr
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Phe is converted to Tyr by phenylalanine hydroxylase.

Tyr is converted to p-hydroxyphenylpyruvate by transaminase, which is then converted to fumarate (glucogenic) and acetoacetate (ketogenic)

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What is phenylketonuria (PKU)?
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a genetic disorder results in a deficiency in phenylalanine hydroxylase, which causes high levels of Phe in blood, which is converted to phenylpyruvate, and can cause mental retardation if not treated in a few months.  (treated by limiting phenylalanine in diet, and increasing tyrosine) disappears after 10 years of age.
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What are the biological roles of nucleotides?
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They are energy sources (like ATP

Cofactors like NAD FAD and ATP

Signaling like cAMP and cGMP

Creation of DNA and RNA

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What are the 3 components of nucleotides?
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Phosphate group

Pentose sugar

Aromatic base

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What are the 2 bases that can be attached to nucleotides?
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Purine (in adenine and guanine) and pyrimidine bases (cytosine, thymine (DNA) and uracil (RNA))
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nucleosides are…
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nucleotides without the phosphate
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are there any essential nucleotides?
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no
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Name the types and purposes of biosynthesis pathways for nucleotides.
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Salvage pathways: invlocve use of dietary nucleotides or re-use of nucleic acids degredation products

De novo: biosynthesis with new materials: amino acids and pentoses

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Explain the salvage pathways of nucleotide biosynthesis
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Nucleic acids from diet: NA’s are broken down into nucleotides in GI, pancreatic nucleotidases convert into nucleosides, then nucleosides are absorbed from intestines.

Tissue nucleic acids: NA’s from dead cells are broken down into nucleosides by lysosomal nucleotidases

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Explain the De novo synthesis of purine bases
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Synthesised on PRPP in 3 steps:

1. Synthesis of PRPP

2. Formation of inosine monophosphate (IMP)

 3. Conversion of IMP to AMP and GMP

*ATP, dATP, GTP, and dGTP can be synthesized from AMP or GMP

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What are the products and reactants in synthesis of ATP and GTP, and what enzymes drive the reactions?
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GMP+ATP –> GDP +ADP by guanylate kinase

GDP+ATP–> GTP +ADP by NDP kinase

AMP+ATP–> 2 ADP by adenylate kinase

 ADP goes to oxidative phosphorylation pathway to become ATP.

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Explain purine nucleotide degredation
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AMP is turned into hypoxanthine, and GMP into xanthine.  Xanthine oxidase turns hypoxanthine into xanthine, and xanthines are turned into uric acid by xanthine oxidase.
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What problems are associated with heightened levels of uric acid?
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Kidney stones, and uric acid crystal precipitation in joints (known as gout).  Gout leads to deformities.
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What can cause Gout?
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Excessive synthesis of purine nucleotides due to elevated levels of PRPP synthetase or mutations leading to loss of feedback inhibition of PRPP synthetase.  Impared excretion of uric acid (kidney malfunctioning).

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How is gout treated?
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Allopurinol inhibits xanthine oxidase
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Explain de novo synthesis of pyrimidine bases
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Bases are made and then linked to PRPP

4 steps:

1. synthesis of orotate

2. linking of orotate to PRPP and synthesis of UMP

3. Synthesis of CTP

4. Synthesis of deoxythymidine

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What enzymes are used to make orotate?
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carbamoyl phosphate synthetase 2 (activated by ATP and PRPP, inhibited by UTP) , and aspartate transcarbamoylase (ATCase)

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what enzymes are used in linking of PRPP and synthesis of UMP
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orotate phorphoribosyl transferase and OMP carboxylase
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What is the path of synthesis of CTP (note enzymes)?
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UMP–>UDP–>UTP- (CTP synthetase, inhibited by CTP and activated by GTP)->CTP
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dTMP is synthesized….
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from dUMP by thymidylate synthase
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Detail the path of pyrimidine nucleotide degredation
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CMP–>cytidine–>uridine–>uracil–>dihydrouracil–>

B-alanine

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What enzyme synthesizes deoxyriobnucleotides?
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Ribonucleotide diphosphate (rNDP) reductase, by removal of 2′ OH
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Tymidylate synthase….
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turns dUMP to TMP
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talk about the enzymes used in dTMP biosynthesis
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Tymidylate synthase (inhibited by uracil analogs)

Dihydrofolate reductase (inhibited by methotrexate, aminopterin, and trimethoprim)

;Serine transyhdroxymethylase

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