More Biochem Review

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




What is the cofactor of transaminase reactions?
PLP, pyridoxal phosphate (a form of vitamin B6)
What are the markers for tissue damage?

Syrum Glutamate Oxaloacetate Transanimase (SGOT(AST))

Syrum Glutamate Pyruvate Transanimase (SGPT(ALT)

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

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

Which AA’s produce oxaloacetate and what enzymes are used?

Asparagine to aspartate by L-asparaginase

Aspartate to oxaloacetate by transaminase (SGOT) PLP cofactor

What AA’s can be turned into a-ketoglutarate and by what enzymes?

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

Hydrophobic AA’s are metabolized by what enzymes into what products?
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)
Propionyl CoA is…
Acetyl CoA and acetoacetyl CoA are…
ketogenic and a ketone body (respectively)
explain the catabolism of methionine?
met is converted to S-adenosylmethionine (SAM), then to homocysteine, then to cystathionine, then to cystieine (glucogenic) and a-ketobutyrate to propionyl CoA (glucogenic)
Explain Lys Catabolism
Lys’s side chain is transaminated, and produces acetoacetyl CoA
Lys and Leu are both strictly
explain Trp Catabolism
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)
Explain catabolism of Phe and Tyr

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)

What is phenylketonuria (PKU)?
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.
What are the biological roles of nucleotides?

They are energy sources (like ATP

Cofactors like NAD FAD and ATP

Signaling like cAMP and cGMP

Creation of DNA and RNA

What are the 3 components of nucleotides?

Phosphate group

Pentose sugar

Aromatic base

What are the 2 bases that can be attached to nucleotides?
Purine (in adenine and guanine) and pyrimidine bases (cytosine, thymine (DNA) and uracil (RNA))
nucleosides are…
nucleotides without the phosphate
are there any essential nucleotides?
Name the types and purposes of biosynthesis pathways for nucleotides.

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

Explain the salvage pathways of nucleotide biosynthesis

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

Explain the De novo synthesis of purine bases

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

What are the products and reactants in synthesis of ATP and GTP, and what enzymes drive the reactions?

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.

Explain purine nucleotide degredation
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.
What problems are associated with heightened levels of uric acid?
Kidney stones, and uric acid crystal precipitation in joints (known as gout).  Gout leads to deformities.
What can cause Gout?

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).

How is gout treated?
Allopurinol inhibits xanthine oxidase
Explain de novo synthesis of pyrimidine bases

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

What enzymes are used to make orotate?

carbamoyl phosphate synthetase 2 (activated by ATP and PRPP, inhibited by UTP) , and aspartate transcarbamoylase (ATCase)

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



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

Tymidylate synthase (inhibited by uracil analogs)

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

;Serine transyhdroxymethylase

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