Usmle - Biochem 3/4

Front 1

Rate-limiting step of de novo purine synthesis:

Back 1

Glutamine-PRPP amidotransferase

Front 2

Rate-limiting step of Urea cycle

Back 2

Carbamoyl phosphate synthetase I

Front 3

Rate-limiting step of Fatty acid synthesis

Back 3

Acetyl-CoA carboxylase

Front 4

Rate-limiting step of Fatty acid oxidation

Back 4

Carnitine acyltransferase I

Front 5

What's the difference between the actions of biotin and folic acid?

Back 5

Biotin is a cofactor in carboxylation reactions -- it adds CO2

THF is methyl group donor -- it adds CH3

Front 6

What is the difference between the activity of NADH and NADPH?

Back 6

NADH is usually involved in catabolic processes, i.e. Glycolysis and the TCA

NADPH is usually involved in anabolic processes, like steroid and fatty acid synthesis.

Front 7

HMP Shunt:

(1) What does it do?
(2) Describe the most prominent associated pathology.

Back 7

NADPH is made by the HMP shunt, AKA the pentose-5-phosphate pathway.

A small fraction of the Glucose-6P that's made in the first step of glycolysis gets shunted off to this pathway to restore NADP+ to NADPH.

Hint 7

G6PD is the rate-limiting step of the shunt. When it is defective, NADPH deficiency occurs which is minor in most tissues, but not in the erythrocytes, where the shunt is the only source of NADPH.

Result: oxidative/radical damage to RBCs and hemolytic anemia.

Front 8

How do hexokinase and glucokinase differ?
(1) General description
(2) Kinetics

Back 8

Both of these enzymes phosphorylate glucose as part of the first step of glycolysis.

Hexokinase is found in all cells and specializes in operating in a low glucose environment to provide a small amount of glucose for each cell's needs.

Glucokinase is found in the liver, and specializes in working in a hi glucose environment to rapidly phosphorylate lots of glucose, providing glycogen storage for the whole body.

and is inhibited by the presence of glucose 6-P. This allows individual cells to burn only as much glucose as they need.

Glucokinase is found in the liver, and is not; this allows the organ to function as a glycolytic machine for the rest of the body.

Hint 8

Hexokinase has a hi affinity for glucose and a LOW K_m, so it can operate in low glucose environments.

It also has a low V_m, so that regardless of the environment, it doesn't make a lot

Glucokinase has a LOW substrate affinity and a HI K_m, but a very hi V_max, so it works best where there's lots of glucose, and makes stuff for the whole body.

Front 9

(1) What is the rate-limiting step of glycolysis, and (2) how is it regulated?

Back 9

Fructose-6P + ATP --PFK-1--> Fructose-1,6-bisphosphate

Hint 9

As the rate-limiting enzyme, PFK-1 is:

Downregulated by ATP, Citrate

Upregulated by AMP, fructose-2,6-BP

Front 10

Which two steps of glycolysis consume ATP?

Back 10

Glucose --Gluco/Hexokinase--> G-6P

Fructose-6P --PFK-1--> Fructose-1,6-bisphosphate

Front 11

In which two steps does glycolysis produce ATP?

Back 11

#1: yields 2 ATP

1,3-bisphosphoglycerate --phosphoglycerate kinase--> 3-phosphoglycerate

#2: also yields 2 ATP

Phosphoenolpyruvate--Pyruvate kinase--> Pyruvate

Front 12

How do blood sugar levels interact with the rate-limiting step of glycolysis?
(main idea)

Back 12

Background:

2 enzymes act on the substrate of hte rate-limiting reaction: PFK-1 and PFK-2

PFK-1 is responsible for the main substrate.

**In the presence of insulin, PFK-2 is activated.
**PFK2's activity effectively induces PFK-1 (and therefore glycolysis).

Front 13

(1) What is the mechanism by which insulin interacts with the rate of glycolysis?

(2) How about glucagon?

Back 13

Hi blood sugar --> hi insulin --> decreased cAMP --> dephosphorylation of PFK-2 gives it a kinase activity --> increased production of Fructose-2,6-bisphospate --> increased PFK activity --> increased glycolysis.

Hint 13

Low blood sugar --> hi glucagon --> hi cAMP in cells --> PFK-2 is phosphorylated and given a phosphatase activity --> PFK-2 reconverts Fructose-2,6-bisphosphate to fructose-6P --> Fructose-2,6-Bisphosphate levels decrease and PFK-1 is downregulated --> Glycolysis stops.

Front 14

What cofactors are required for pyruvate processing enzymes to function?

Back 14

1. Pyrophosphate (Thamine/TTP)
2. FAD (B2, riboflavin)
3. NAD (B3, niacin)
4. CoA (B5, pantothenate)
5. Lipoic Acid

Hint 14

We treat the enzyme complex responsible for pyruvate processing as though it were a single enzyme, pyruvate dehydrogenase, but obviously it's 3 enzymes. Don't worry about them.

Front 15

Pyruvate Dehydrogenase Deficiency
Etiology & Presentation

Back 15

Causes:
1. Genetic deficiency
2. Cofactor deficiency (i.e. B1 def in alcoholism)

Hint 15

Presentation:

Neurological defects

Front 16

So we've made pyruvate from glucose. What are the 4 things we can do with it?

Back 16

Can be made into:

1. A.Coa for the TCA

2. Lactic acid fermentation

3. Oxaloacetate for either Gluconeogenesis or TCA

4. We can package waste NH3 from the periphery into it, turning it into alanine.
[This is then shipped back to the liver for entry into the Urea Cycle.]

Front 17

What are the products of one turn of the TCA Cycle?

Back 17

For each turn of the cycle, we burn 1 A.CoA. The net output is:

3 NADH
1 FADH2

1 GTP
2 CO2

= 12 ATP

Front 18

What are the enzymes of the TCA cycle?

Back 18

Citrate Is Krebs Starting Substrate For Making Oxaloacetate!!

Citrate
Isocitrate
α-ketoglutarate
Succinyl CoA
Succinate
Fumarate
Malate
Oxaloacetate

Front 19

Where and how is α-ketoglutarate metabolized?

Back 19

α-ketoglutarate is a metabolite of the TCA cycle:

α-KG --α-KG dehydrogenase--> Succinyl CoA

Hint 19

α-ketoglutarate dehydrogenase is interesting because it is just like pyruvate dehydrogenase!

It's a complex of 3 enzymes with the same 5 cofactors: B1, B2, B3, B5, lipoic acid.

Front 20

How does arsenic affect cellular metabolism?

Back 20

Arsenic inhibits lipoic acid from acting as a cofactor in pyruvate dehydrogenase.

The result is neurological problems, lactic acidosis

Front 21

Arsenic poisoning
Presentation:

Back 21

This type of toxicity presents with vomitting, rice-water stools, and garlic breath.

Front 22

How does NADH made in the cytoplasm during glycolysis get restored to NAD+, so glycolysis can continue?

Back 22

NAD+ and NADH CANNOT cross the inner mitochondrial membrane!

Instead, oxaloacetate is converted to a non-TCA substrate -- aspartate -- which crosses through a channel.

Hint 22

1. Oxaloacetate --> Aspartate
2. Aspartate crosses opposite glutamine
3. Aspartate is reconverted to oxaloacetate in the cytoplasm
4. OAA accepts H:- from NADH, becoming malate
5. Malate crosses back into matrix to be reused by TCA

Front 23

List the basic amino acids.

Back 23

Lysine
Arginine
Histidine

(all positively charged in serum)

Front 24

List the acidic amino acids.

Back 24

Aspartate
Glutamate
(both negatively charged in serum)

Front 25

Histone Structure

Back 25

Tetramers of H2A, H2B, H3, and H4 proteins form nucleosome core.

DNA wraps twice around each core.

H1 proteins are not in the nucleosome core, but rather tie the nucleosome beads together.

Front 26

What are the two functions of methylation DNA methylation?

Back 26

(1) Template strand cytosine and adenine residues are methylated, indicating to DNA polymerase which strand is the template for repairs.

(2) Hypermethylation: CpG islands of DNA tend to become hypermethylated, inactivating transcription.
-- CpG islands are associated with the promoters for housekeeping genes that we want to express at low basal rates.

Front 27

Role of acetylation in gene expression.

Back 27

This modification, performed by histone acetyltransferases (HATs), loosens DNA from heterochromatin to euchromatin, increasing transcription.

Front 28

Distinct characteristics of the 5 nucleotides:

Back 28

Cytosine: ammonia group
Uracil: ketone
Thymine: methylated

Adenine: ammonia group
Guanine: ketone + ammonia group

Front 29

What simple pyrimidine modification is frequently responsible for mutations, and how is it repaired?

Back 29

Cytosine deaminates to uracil spontaneously and at a constant rate.
-- C ==> U, resulting in an AT mismatch
-- Repaired by BER

Front 30

How do healthy cells combat skin cancers?

Back 30

This mutation is combated with Nucleotide Excision Repair.

1. In NER, excision endonuclease detects the dimer b/c the shape is distorted, and nicks the damaged strand on both sides of the lesion, perhaps several bases down.

2. Exonucleases remove the fragment

3. DNA Polymerase I replaces the missing fragment, and DNA Ligase ligates it into the strand.

Hint 30

Thymidine dimer formation is the most common cause of skin cancers, i.e.:
-- Melanoma
-- Basal cell carcinoma
-- Squamous cell carcinoma

Front 31

What simple purine modification is responsible for mutations, and how does it happen?

Back 31

Methylation of Guanine by alkylating agents, i.e. cytoxan, results in it's mismatch with thymine.

-- G-->C
-- met-G-->T

Front 32

State Mechanism of de novo purine synthesis. Note requirements for production of both bases.

Back 32

1. Ribose 5-phosphate --PRPP Synthetase--> PRPP

2. PRPP + NH3 from glutamine ---> 5-Phosphoribosylamine -->-->--> Inosine monophosphate (IMP)

3a. IMP + aspartate & GTP ---> AMP
3b. IMP + NAD & ATP --> GMP

Hint 32

**Guanosine requires ATP and NAD+ for its generation.

**Adenosine requires GTP for its generation.

Front 33

What is the committed step of de novo purine synthesis?

Back 33

PRPP + NH3 from glutamate ---> 5-ribosylamine + PPi

Front 34

What is the rate-limiting step in de novo purine synthesis?

Back 34

Ribose-5-phosphate ---PRPP Synthetase--> PRPP

Front 35

What is the major difference between purine and pyrimidine synthesis?

Back 35

In purine synthesis we start with a ribose backbone and build a base to it.
-- *Inosine*

In pyrimidine synthesis we make a temporary base and add the backbone to it, then modify the base.
-- **Orotic Acid**

Front 36

What is the major difference between purine and pyrimidine synthesis?

Back 36

In purine synthesis we start with a ribose backbone and build a base to it.
-- *Inosine*

In pyrimidine synthesis we make a temporary base and add the backbone to it, then modify the base.
-- **Orotic Acid**

Front 37

Hydroxyurea
MoA & Indications

Back 37

Inhibits thymine production by inhibiting ribonucleotide reductase

Hint 37

Indications:

Chemotherapeutic agent used to keep white count low in AML.

Front 38

Hydroxyurea
MoA & Indications

Back 38

Inhibits thymine production by inhibiting ribonucleotide reductase

Hint 38

Indications:

Chemotherapeutic agent used to keep white count low in AML.

Front 39

6-mercaptopurine
MoA and Ind

Back 39

A false purine analogue that both:

(1) inhibits production of real purines via feedback inhibition

(2) gets incorporated into DNA, terminating DNA synthesis.

Hint 39

Maintenance therapy for children with ALL.
Often given as azothioprine, a precursor.

Front 40

6-mercaptopurine
MoA and Ind

Back 40

A false purine analogue that both:

(1) inhibits production of real purines via feedback inhibition

(2) gets incorporated into DNA, terminating DNA synthesis.

Hint 40

Maintenance therapy for children with ALL.
Often given as azothioprine, a precursor.

Front 41

5-fluorouracil
MoA & Ind

Back 41

Tumor cells convert it to a false fdUMP, which irreversibly inhibits thymidylate synthase.

This blocks thymidine synthesis, resulting in a thymidine-less death.

Front 42

Mechanism of Pyrimidine Synthesis:

Back 42

1a. As with purine synthesis, we make PRPP from Ribose-5-phosphate.

1b. CO2 + Gln + ATP ---CPT II---> Carbamoyl Phosphate

2. Carbamoyl Phosphate -->-->--> Orotic Acid

3. Orotic Acid + PRPP ---> UMP

4a. UMP ---> dUMP (or fdUMP in chemo)

4b. UMP ---ribonucleotide reductase---> CTP

5a. dUMP ---Thymidylate synthase + met-THF---> dTMP

Front 43

Causes of orotic aciduria.

Back 43

(1) Inability to convert orotic acid to UMP caused by autosomal recessive deficiency in either:
-- orotic acid phosphoribosyltransferase
-- orotidine 5'-phosphate decarboxylase

Front 44

Presentation of orotic aciduria

Back 44

Symptoms seen in infancy:

1. Increased orotic acid in urine
2. Megaloblastic anemia
3. Failure to thrive

Front 45

Clinical findings in orotic aciduria:

Back 45

Symptoms seen in infancy:

1. Increased orotic acid in urine
2. Megaloblastic anemia
3. Failure to thrive

Front 46

What is the committed step of pyrimidine synthesis?

Back 46

Gln + CO2 + 2ATP ---CPT II---> Carbamoyl phosphate

The production of carbamoyl phosphate is the committed and rate-limiting step of pyrimidine synthesis.

Front 47

2 Purine Breakdown Pathways:

Back 47

(1)
1. AMP ---AMP deaminase---> IMP
2. IMP ---> Inosine
3. Inosine ---> Hypoxanthine
4. Hypoxanthine ---Xanthine oxidase---> Xanthine
5. Xanthine ---Xanthine oxidase---> Uric Acid

(2)
1. AMP ---> Adenosine
2. Adenosine ---Adenosine Deaminase---> Inosine
3, 4, 5: same as above

Front 48

SCID
Path & Presentation:

Back 48

Adenosine deaminase (ADA) deficiency results in:

1) Buildup of ATP b/c we can't break it down. ATP buildup downregulates ribonucleotide reductase, resulting in decreased DNA synthesis.

2) inability to break down adenosine into inosine. Buildup of adenosine is toxic to B and T lymphocytes.

Hint 48

Presentation: Bubble boy

Front 49

Lesch-Nyhan syndrome
Path & Presentation:

Back 49

Path:
Caused by X-linked Recessive deficiency of HGPRT, which converts both hypoxanthine and guanine to IMP.

Results:
(1) Hypoxanthine buildup ---> excess uric acid production
(2) Guanine buildup ---> excess uric acid production.

Hint 49

Presentation:
MR, aggression, self-mutilation, choreoathetosis, hyperuricemia and gout.

Front 50

DNA Polymerase I

Back 50

Prokaryotic only. Degrades RNA primer and fills gaps.

Front 51

DNA Polymerase III

Back 51

*Prokaryotes only*. Elongates leading strand by adding deoxynucleotides until it reaches primer of preceding fragment, then falls off.

Front 52

What pathology results from loss of nonhomologous end joining?

Back 52

Ataxia telangiectasia: disease consisting of cerebellar ataxia, dilation of blood vessels in skin and eyes, and immunodeficiency of T and B cell origin.

Front 53

Which carbon on an incoming nucleotide bears the triphosphate?

Back 53

The 5' carbon bears the triphosphate.

The 3' carbon has the hydroxyl group on which the next nucleotide is attached.

Front 54

Stop and Start Codons:

Back 54

Start: AUG (codes for methionine)

End:
UGA U Go Away
UAA U Are Away
UAG U Are Gone

Front 55

What is the role of promoters and enhancers?

Back 55

Promoters are sequences of DNA upstream from that are bound by RNA Polymerase and other TF's.

Enhancers are DNA sequences that bind TFs to enhance transcription.
*They may be upstream, downstream, or IN an INTRON of the gene they enhance!*