Biochem. greek flashcards

Enzymes that use FAD

Acyl–Coa dehydrogenase

Succinate dehydrogenase (complex II)

Mitochondrial glycerol–3–P dehydrogenase

Enzymes that use PLP

Glycogen phosphorylase

Amino transferases (alanine, aspartate, tyrosine)

Serine dehydratase

Cystathionine beta–synthase

Glutamate decarboxylase

Histidine decarboxylase

Enzymes that consume GTP

PEP carboxykinase

Enzymes that produce GTP

Succinyl–Coa synthetase

Enzymes that consume TPP

Pyruvate decarboxylase

Transketolase

Enzymes that consume NADPH

Aldose reductase with galactose

Ketoacyl–ACP reductase (rev)

Enoyl–ACP reductase

Overall palmitate synthesis

HMG–CoA reductase

Squalene synthase

NO synthase

Glutathione reductase

Ribonucleotide reductase

Dihydrofolate reductase

Heme oxygenase

Enzymes that produce NADPH

Glucose–6–P dehydrogenase

6–phosphogluconate dehydrogenase

Malic enzyme

Hill reaction

Enzymes that use TPP, FAD and Lipoate

Pyruvate dehydrogenase complex

𝛂–ketoglutarate dehydrogenase complex

Branched chain 𝛂–ketoacid dehydrogenase complex

Enzymes that use BIOTIN

Pyruvate carboxylase

Propionyl–CoA carboxylase

Acetyl–CoA carboxylase

Name the enzymes that during the degradation of glucose lead to cleavage of covalent bonds between two C–atoms.

Aldolase (hexose –> two trioses)

Pyruvate dehydrogenase complex (release CO2)

Isocitrate dehydrogenase (release CO2)

alpha–ketoglutarate dehydrogenase (release CO2)

Which enzymes do we have in the glycolysis but not gluconeogenesis?

Hexokinase

PFK1

Pyruvate kinase

Which enzymes do we have in the gluconeogenesis but not glycolysis?

Pyruvate carboxylase

Fructose–1,6–bisphosphatase

Glucose–6–phosphatase

Which enzymes are needed for glycogen metabolism?

Hexokinase

Phosphoglucomutase

UDP–glucose pyrophosphorylase

Glycogen synthase (primer)

Glycogen branching enzyme

In which reactions is citrate an allosteric activator for lipid metabolism? (enzyme)

Acetyl–Coa carboxylase

HMG–CoA reductase

In which reactions does citrate inhibit? (enzyme)

Pyruvate kinase

PFK1

Branching points in metabolic pathway:Glucose–6–phosphate (pathways and enzymes)

Glycolysis: phosphohexose isomerase

Pentose phospate pathway: Glucose–6–phosphate dehydrogenase

Gluconeogenesis: glucose–6–phospatase

Glycogen pathway

Branching points in metabolic pathway:Fructose

Muscle:Hexokinase (can also phosphorylate fructose)

Liver:No hexokinase, but GLUCOkinase, which is specific for glucose)Instead:Fructokinase –\> fructose–1–PFructose–1–P aldolase –\> glyceraldehyde + dhapTriose kinase –\> glyceraldehyde –\> ga3P

Fructosemia

Fructose–1–P aldolase deficiency

No gluconeogenesis – hypoglycemia

Fructosuria

Fructokinase deficiency

Diarrhea

Branching points in metabolic pathway: DHAP

Glycolysis

Gluconeogenesis

Enzymes: Aldolase, Triose phosphate isomerase, Glycerol–3–P dehydrogenase (All reactions are reversible)

Mitochondrial enzymes that converts glucose to fatty acids

Citrate lyase

Pyruvate dehydrogenase complex

Branching points in metabolic pathway:Pyruvate (enzymes)

Lactate dehydrogenase → Lactate (Only in muscle)

Pyruvate decarboxylase → Acetaldehyde

Pyruvate carboxylase → Oxaloacetate

Pyruvate dehydrogenase complex → Acetyl–Coa

Malic enzyme → Malate (Uses NADPH)

Alanine amino-transferase (In both muscle and liver)

Branching points in metabolic pathway: Oxaloacetate

PEP carboxylase (rev)

Malate dehydrogenase (rev)

Aspartate aminotransferase (rev)

Consumes: PEP carboxykinase (gluconeogenesis)

Citrate synthase (TCA)

Reversible ammonia producing/consuming reactions

Glutamate dehydrogenase

Glycine cleavage enzyme

Irreversible ammonia consuming reactions:

Glutamate synthase

Carbamoyl synthase

Irreversible ammonia producing reactions:

Desaminase (adenosine)

Serine/Threonine dehydratase

Glutaminase

Why does adipose tissue have the enzyme PEP carboxykinase, even though gluconeogenesis only happens in kidney and liver?

Glyceroneogenesis!

Glycerol–3–phosphate production

Ketone calculation:Acetoacetate (How many ATP?)

20 ATP

Ketone calculation:Beta–hydroxybutyric (...)

22.5 ATP

In which tissues does gluconeogenesis happen?

Kidney and liver

Comparison of cori cycle and alanine cycle.Similarities:

Glucose goes back to muscle

Pyruvate is an acceptor molecule(Picks up NH4+ –\> produces alanine ORPicks up proteins and electrons –\> produces lactate)

(Pyruvate is produced in liver from alanine OR lactate. Enters gluconeogenesis and produces glucose –\> returns to muscle)

Comparison of cori cycle and alanine cycle.Differences:

Onset:

* Cori cycle: Hypoxia
* Alanine cycle: Starvation

Transporting molecule

* Cori cycle: Lactate (is transported to liver from muscle)
* Alanine cycle: Alanine (is transported to liver from muscle)

Describe glucose–6–phosphate dehydrogenase deficiency and benefits.

RBC disorder.

No pentose phosphate pathway, so no NADPH formation. Glutathione reductase doesn't work, so free radicals are not neutralized. Free radicals attack hemoglobin's globin chains → globin precipitates as HEINZ BODIES. This alters the membrane deformability of RBCs.

BUT: It can protect against malaria – because malaria lives in RBCs (which are destroyed). Therefore there is a bigger prevalence of G6PDH deficiency in countries with malaria.

Which molecules can transport toxic ammoniac?

Glutamine (from brain), alanine (from muscle) and glutamate (other tissues)

Components (?) needed purines

CO2, Glycine, Aspartic acid, Glutamate, THF

Components (?) needed for pyrimidines

Aspartic acid, Carbamoyl phosphate

Degradation of nucleotides:ReactionInhibitorDisease treated with inhibitor

Xanthine oxidase

Inhibitor: allopurinol

Disease: Gout

Helicase (DnaB protein)

Unwinds DNA

Primase (DnaG protein)

Synthesizes RNA primers

Single–stranded DNA–binding protein (SSB)

Binds single–stranded DNA

RNA polymerase

Facilitates DnaA activity (DnaA – Recognizes ori sequence)

DNA topoisomerase II

Separates new and original strand in replication

DNA ligase

Links okazaki fragments

Dam methylase

Methylates (5')GATC sequences at ori

Which activity does DNA polymerase III have?

5'–3' Elongation activity3'–5' Exonuclease activity

Which activity does DNA polymerase I have?

5'–3' Elongation activity5'–3' Exonuclease activity

DNA polymerase III function

New strand elongation

DNA polymerase I function

Fills gaps

Enzymes needed for Human Mismatch repair

Dam methylase

MutH, MutL, MutS proteins

DNA helicase II

SSB

DNA polymerase III

Exonuclease I, VII, X

RecJ nuclease

DNA ligase

Function of exonuclease in DNA repair

Removes abnormal region

Enzymes needed for Base excision repair

DNA glycosylases

AP endonucleases

DNA polymerase I

DNA ligase

Function of base excision repair

Removal of damaged region and replacement by new DNA

Function of DNA glycosylase

Removes damaged base at AP–site

Type of damage for nucleotide excision repair

DNA lesions that cause large structural changes. E.g. pyrimidine dimers

Nucleotide excision repair enzymes

ABC exinuclease

DNA polymerase I

DNA ligase

Reaction impaired in Phenylketonuria

Phenylalanine hydroxylase

Phenylalanine → Tyrosine

Reactions impaired in Maple syrup urine disease

reactions catalyced by branched chained 𝛂-ketogluterate dehydrogenase complex

Reactions impaired in Tyrosinemia type I

Fumarylacetoacetate

Fumarylacetoacetate → Fumarate + acetoacetate

Reactions impaired in Tyrosinemia type II

Tyrosine aminotransferase

Reactions impaired in Tyrosinemia type III

Hydroxyphenylpyruvate dioxygenase

Hydroxyphenylpyruvate → Homogenisate

Reactions impaired in Citrullinemia type I

Argininosuccinate synthetase

Citrulline + Aspartate → Argininosuccinate

Reactions impaired in Homocystinuria

Cystathione beta–synthase

Cysteine + Serine → cystathione

Reactions impaired in (Hyper)argininemia

Arginase

Arginine → ornithine + urea

Reactions impaired in Lesch–Nyhan syndrome

____ Phosphoribosyltransferase

Adenine + PRPP → AMP + PPi

Hypoxanthine + PRPP → IMP + PPi

Guanine + PRPP → GMP + PPi

Reactions impaired in Arginosuccinate lyase deficiency

Argininosuccinate lyase

Arginosuccinate ⇋ Arginine + Fumarate

Reactions impaired in beta–ketothiolase deficiency

Acyl–Coa acetyltransferase

Ketoacyl–CoA → Acyl–CoA + Acetyl–CoA

Reactions impaired in Methylmalonic acidemia

Methylmalonyl–CoA mutase

Methylmalonyl–Coa → Succinyl–CoA

Reactions impaired in propionic acidemia

Propionyl–CoA carboxylase

Propionyl–CoA → Methylmalonyl–CoA

Reactions that leads to the formation of galactose metabolite potentially causing cataract

Aldose reductase with galactose

Galactose → Galactitol

Name the enzymes that their defect can lead to galactosemia

Gal–1–P Uridyltransferase

Galactokinase

UDP–Gal–4 epimerase

What are the sources of propionyl–CoA in methylmalonic acidemia?

Amino acids

Odd chained fatty acids

Propionate

List the defected carboxylase enzymes inmultiple carboxylase deficiency and biotinidase deficiency

Pyruvate carboxylase

Propionyl–CoA carboxylase

Acetyl–Coa carboxylase

Methylcrotonyl–Coa carboxylase

List the possible causes of permanent congenital hypothyreosis?

Thyroid gland dysgenesis

Defects in thyroid hormone synthesis or secretion

Defects in thyroid hormone transport

Central hypothyroidism

Proteins required to initiate replication in prokaryotes

DnaA protein

DnaB protein (Helicase)

DnaC protein

HU (Histone–like protein)

Primase (DnaG protein)

SSB

RNA polymerase

DNA gyrase (DNA topoisomerase II)

Dam methylase

Proteins at prokaryotic replication fork

SSB

DnaB protein (helicase)

Primase (DnaG protein)

DNA polymerase III

DNA polymerase I

DNA ligase

DNA gyrase (DNA topoisomerase II)

Direct repair

DNA photylases

O6–methylguanine–DNA methyltransferase

AlkB protein

Type of damage for mismatch repair

Mismatches

Typoe of damage for base excision repair

Abnormal bases (uracil, hypoxanthine, xanthine), alkylated bases

Type of damage for Direct repair

DNA photylases:

* Pyrimidine dimers

O6–Methylguanine–DNA methyltransferase:

* O6–MethylguanineAlkB

protein:

* 1–Methylguanine
* 3–methylcytosine

Endonuclease

Cleaves inside DNA

Exonuclease

Cleaves on either 5' or 3' end

Exinuclease

Special endonuclease. Cleaves twice – is a part of nucleotide excision repair (ABC exinuclease)

Which metabolites are needed for the AlkB function?

Succinyl–Coaalpha–ketoglutarate

DNA and RNA polymerase: Similarities

Direction of synthesis: 5'–3'Mechanism of elongation

Hydrolysis of pyrophosphate

Processivity

What is special for RNA polymerase?

No polyA og polyG

Don't need a primer

No nuclease activity

Template: one strand of DNA, certain genes

What is the replication fork?

The sites where DNA synthesis occurs

What is another name for DNA gyrase, and where are they found?

Topoisomerase II

Only prokaryotes

Which DNA polymerases have proofreading ability?

All of them

What kind of activity is proofreading activity?

Nuclease activity

What is a protein with no enzymatic activity?

SSB

What is a nucleotide polymerase in the replication fork that doesn't have proofreading ability/nuclease activity?

Primase – RNA polymerase

Which molecule is responsible when there is a methylation of a cytosine group, and what kind of repair is it?

AlkB protein

Direct repair

Which molecule is responsible when there is a methylation of a guanine group, and what kind of repair is it?

O6–Methylguanine–DNA methyltransferase

Point mutation

Endonuclease

Cleaves inside

Exonuclease

Cleaves either at 5' or 3' end

Exinuclease

Special endonuclease

Cleaves twice – part of nucleotide excision repair

Which metabolites are needed for Alk–B protein process?

Succinyl–CoA and alpha–ketoglutarate. The protein needs an acceptor of the methyl group. Direct repair enzyme.

What is the direction of synthesis in transcription?

5'–3'

What determines transcription start sites?

Promoter regions

What are the prokaryotic promoter regions?

–35–10 (Pribnow box)+1 (transcription start site)