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Step 1 > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Codon that signals initiation of protein synthesis

A

AUG

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2
Q

Stop codons

A

UAA
UAG
UGA

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3
Q

Southern blot detects

A

DNA

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4
Q

Northern blot detects

A

RNA

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5
Q

Western blot detects

A

Protein

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6
Q

Dot (slot) detects

A

RNA, DNA or protein

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7
Q

Purine types and number of rings that they have:

A

Adenine
Guanine

2 rings

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8
Q

Pyrimidines types and number of rings that they have:

A

Cytosine
Uracil

One ring

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9
Q

A-T form __ bonds between them:

A

Two hydrogen bonds

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10
Q

G-C form __ bonds between them:

A

Three hydrogen bonds

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11
Q

Chemotherapeutic agents that target S phase:

A

Interfere with DNA Synthesis:

Methotrexate (ectopic pregnancy; dihydrofolate reductase, no thymine + leucovorin)
Capecitadine->5-flurouracil (pyrimidine analog, no thymine)
Cytarabine (AML; pyrimidine analog)
Clabribine (Hairy cell; purine analog). Claudio is a pure hairy man
Azathioprine->6-mercaptopurine (Ulcerative colitis; purine analog)
Hydroxyurea (ribonucleotide reductase)

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12
Q

Chemotherapeutic agents that targets G2 phase:

A

Bleomycin (forms free radicals that breaks DNA)

Bortezomib

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13
Q

Chemotherapeutic agents that target M phase:

A

Interfere with microtubules:

Vincristine
Vinblastine
Paclitaxel
Erlibutin

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14
Q

Non cell-cycle specific chemotherapeutic agents:

A 
Affect replication by:
Alkaliting (cross link DNA):
Cyclophosphamide (+ mesna)
Cisplatin (+ amifostine)
Busulfan (ablate marrow)
Carmustine (glioblastoma)
Procarbazine

Intercalating (intercalate within DNA chains):
Doxorubicin (+ dexrazoxane)
Daunorubicin (+ dexrazoxane)
Dactinomycin

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15
Q

Chemotherapeutic agents that target the jump between S and G2 phase:

A

Etoposide, tenitopiside (inhibit topoisomerase 2)

Iridotecan, topotecan (inhibit topoisomerase 1)

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16
Q

Eucromatine (from less to more condensed)

A

10 nm chromatin

30 nm chromatin

Loops of 30 nm chromatin attached to scaffolding proteins

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17
Q

Is heterochromatin condensated or non condensated?

A

Highly condensed

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18
Q

Leading strand characteristics:

A

Continuous

Moving into/ toward the replication fork

5’—>3’

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19
Q

Lagging strand characteristics:

A

Discontinuos, series of Okazaki fragments

Moving away from the replication fork

3’—>5’ toward the replication fork

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20
Q

Nalidixic acid mechanism of action:

A

It is a synthetic quinolone that inhibits DNA gyrase

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21
Q

DNA polymerase gamma function:

A

Replicates mitochondrial DNA

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22
Q

Single-stranded DNA-binding protein (SSB) function:

A

Stabilization of unwound template strands

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23
Q

Fluorquinolones mechanism of action:

A

Inhibit tropoisomerases 2 (DNA gyrase) and 4

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24
Q

Inactivation or deletion of p53 gene is associated with:

A

Li Fraumeni syndrome and solid tumors

SBLA: sarcoma, breast, brain, leukemia, adrenal

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25
Q

Most DNA repair occurs in ____ phase

A

G1

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26
Q

Which enzyme is deficient in xeroderma pigmentosa?

A

Excinuclease (excision endonuclease, an UV specific endonuclease) enzyme deficiency

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27
Q

Lynch syndrome (Hereditary nonpolyposis colorectal cancer) usually results from which mutation and which tumors are associated with it?

A

Autosomal dominant sd. due to a mutation in genes hML!!H1 and hMS!!H2! Love 1st Sex 2nd!
Increased risk of Colon (proximal colon is always involved), Endometroid (before 50), Ovary and STOMACH ca. CEOS of Merry Lynch
Dx: tumor cells on w. have microsatellite instability on GATA sequence on Ch7 (normally used for testing)

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28
Q

Mechanism of action of Rifampin:

A

Inhibiting prokaryotic RNA polymerase

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29
Q

Mechanism of action of Actinomycin D:

A 
Chemotherapeutic drug (antitumor antibiotic) also called dactinomycin
Binds DNA to prevent transcription, it intercalates DNA
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30
Q

Alpha-amanitin (in certain mushrooms) acts

A

Inhibiting eukaryotic RNA polymerase 2!!

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31
Q

A cistron is

A

A gene

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32
Q

Hogness box
Pribnow box
are…

A

The TATA box

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33
Q

Two example sequences of promoter regions are:

A 
CAAT box (80 bases upstream) and TATA box (25 bases upstream)
Binding site for general transcription factors and RNA polymerase 2
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34
Q

Missense mutation definition:

A

Change leads to a new amino acid

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35
Q

Nonsense mutation definition:

A

Change leads to a stop codon

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36
Q

Frame-shift versus in-frame mutation:

A

Frameshift: non triple number of nucleotides are deleted (Duchenne) or inserted (Tay-Sachs) so all aa after the mutation are messed up

In frame: nucleotide substitution (Becker) triplet deletion (CF) or insertion (Huntington, Spinobulbar muscular atrophy)

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37
Q

When does Gray baby syndrome occurs?

A

In babies with not enough UDP-glucuronyl transferase to metabolize chloramphenicol or inadequate renal excretion

If untreated they die from cardiovascular collapse

Chloramphenicol can also cause aplastic anemia and thrombocytopenia

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38
Q

Cystic fibrosis is normally consequence of

A

The deletion of phenylalanine at position 580 and generates improper folding

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39
Q

Klein-Waardenburg syndrome is due to

A

A mutation in a PAX gene

Presents with partial albinism+deafness+aniridia

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40
Q

Menkes disease is due to

A

A deficient collagen cross-linking due to Cu deficiency (mutation in gene ATP7A)

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41
Q

Sensitivity and specificity of ELISA are:

A

Sensitivity: high
Specificity: low

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42
Q

Kwashiorkor is due to and presents with:

A

Protein malnutrition. Presents with edema

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43
Q

Marasmus is due to and presents with:

A

Chronic deficiency of calories. Does not present with edema

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44
Q

What do statins inhibit in cholesterol synthesis?

A

3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase

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45
Q

Name 4 facts about the action of Methotrexate

A
  • Antineoplastic
  • Interferes with DNA replication in phase S
  • Competitively inhibits dihydrofolate reductase
  • Deprives the cell of active folate
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46
Q

Competitive inhibitors effect in Km and Vmax:

A

Increase Km

Do not change Vmax

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47
Q

Noncompetitive inhibitors effect in Km and Vmax:

A

Decrease Vmax

Do not change Km

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48
Q

GLUT 1 and 3 have a ____ affinity for glucose

A

High

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49
Q

GLUT 2 has a ____ affinity for glucose

A

Low

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50
Q

GLUT 1 and 3 are in

A

Most tissues

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51
Q

GLUT 2 is in

A

The liver and pancreatic beta-islets

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52
Q

GLUT 4 is in

A

Skeletal muscle and adipose tissue

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53
Q

Pyruvate kinase deficiency is associated with

A

Ch1
Hemolytic anemia
Increased 2,3-BPG, low O2 affinity for Hb, high O2 in tissues
Burr cells (echinocytes)
No heinz bodies
Autosomal recessive ♂and♀ (DD. with G6PD that is X-linked ♂ recessive and will have heinz bodies)

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54
Q

Hexokinase/Glucokinase acts

A

In glycolysis

Phosphorylating glucose to trap it in the cell

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55
Q

Heinz bodies are characteristic from

A

G6PDH deficiency

Glutathione reductase deficiency

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56
Q

Galactosemia is due to a deficit of one of 2 enzymes:

A

Galactokinase or

Galactose 1-phosphate uridyltransferase

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57
Q

Clinical picture of galactosemia:

A 
Newborn
Cataracts
Jaundice
Hyperbilirrubinemia
Vomiting and diarrhea
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58
Q

Hereditary fructose intolerance is a deficiency of the enzyme:

A

Aldolase B

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59
Q

Clinical picture of hereditary fructose intolerance:

A 
Starts when baby stops breast feeding
Vomiting
Lethargy
Liver damage, hyperbilirubinemia
Hypoglycemia
Hyperuricemia
Renal proximal tubule defect (Fancony)
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60
Q

Thiamine is

A

Vitamine B1

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61
Q

Thiamine (vit B1) deficiency may lead to

A

Beriberi
or
Wernike-Korsakoff syndrome (confusion, ataxia, ophthalmoplegia)

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62
Q

Clinical picture of Wernike-Korsakoff syndrome:

A 
Alcoholic
Ataxia
Ophthalmoplegia, nystagmus
Memory loss and confabulation
Cerebral hemorrhage
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63
Q

McArdle disease is a deficiency of

A

Muscle glycogen phosphorylase

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64
Q

Clinical picture of McArdle disease:

A

Weak, initial exercise intolerance with cramps
Recovery or ‘second wind’
Possible myoglobinuria
No lactic ac. in venous blood

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65
Q

Pompe disease is a deficiency of:

A

Lysosomal alpha1,4-glucosidase

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66
Q

Clinical picture of Pompe disease:

A

Cardiomegaly
Muscle weakness
Death in 2 years

Due to accumulation of glycogen-like material in endosomes

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67
Q

Function of chylomicrons

A

Transport triglycerides and cholesterol from intestine to tissues

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68
Q

Function of VLDL

A

Transport triglycerides from liver to tissues

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69
Q

Function of IDL

A

Pick up cholesterol from HDL to form LDL

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70
Q

Function of LDL

A

IDL remnant, takes cholesterol from the liver to the peripheral tissues

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71
Q

Function of HDL

A

Takes cholesterol from peripheral tissues to the liver (reverse cholesterol transport)

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72
Q

Clinical picture of Medium Chain Acyl-Coa Dehydrogenase (MCAD) Deficiency:

A

Fasting hypoglycemia
Lethargy, coma
C8-C10 acyl carnitines in blood
Episodes after fasting/illness

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73
Q

Tay-Sachs disease is a deficiency of _____ and _____ is accumulated

A

Hexosaminidase A deficiency

Ganglioside GM2 accumulation

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74
Q

Gaucher disease is a deficiency of_____ and _____ is accumulated

A

Glucocerebrosidase deficiency

Glucocerebroside accumulation

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75
Q

Niemann-Pick disease is a deficiency of_____ and _____ is accumulated

A

Sphingomyelinase deficiency

Sphingomyelin accumulation

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76
Q

The most common disorder in the urea cicle is:

A

Ornithine transcarbamoylase deficiency

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77
Q

Phenylketonuria is a deficiency of:

A

Enzyme Phenylalanine hydroxylase

Or cofactor Tetrahydrobiopterin (BH4)

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78
Q

Clinical picture of phenylketonuria:

A

Musty odor
Mental retardation
Pale skin, eye and white hair
Pallor of cathecholaminergic brain structures

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79
Q

Alkaptonuria is a deficiency of the enzyme:

A

Homogentisate oxidase, that converts tyrosine to fumarate

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80
Q

Clinical picture of Alkaptonuria:

A

Urine becomes dark
Ochronosis (dark cartilage)
Arthritis

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81
Q

Maple syrup urine disease is a deficiency of:

A

Branched-chain ketoacid dehydrogenase enzyme

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82
Q

Clinical picture of maple syrup urine disease:

A 
Urine smells like maple syrup
Mental retardation
Abnormal muscle tone
Ketones
Metabolic acidosis
Hyperammonemia because urea cycle is blocked
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83
Q

Homocystinuria is due to:

A

Cystathionine synthase enzyme deficiency or affinity loss (B6)

Methionine synthase= homocysteine methyl transferase=Methylenetetrahydrofolate reductase deficiency (B12, folic acid)

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84
Q

Clinical picture of homocystinuria:

A 
Deep vein thrombosis
Atherosclerosis 
Early stroke and MI
Ectopic lens (luxates down and in)
Marfan-like habitus (loose slender fingers)
Mental retardation
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85
Q

Pyridoxine is:

A

Vitamin B6

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86
Q

Orotic aciduria can be a deficiency of the enzyme ____ or ____

A

Ornithine transcarbamoylase or OTC (generates hyperammonemia). Carbamoyl phosphate accumulates and backs up to orotic acid. You cannot form citruline

Uridine monophosphate synthase or UMP synthase (generates megaloblastic anemia) because orotic acid accumulates

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87
Q

Lesch-Nyhan syndrome is a deficiency of ___ and the enz. ___ is overactive:

A

Deficiency of HGPRT enzyme (purine salvage)
You cannot form GMP and IMP so PRPP accumulates and you have an overactive PRPP amidotransferase (de novo purine synthesis)

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88
Q

Clinical picture of Lesch-Nyhan syndrome:

A

Orange crystals in diapers
Spastic cerebral palsy
Self mutilation
Hyperuricemia

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89
Q

Histone acetylation forms

A

Euchromatin; Acetylation makes the DNA Active

Deacetylation is the opposite and mutes the DNA

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90
Q

Methylation of DNA forms

A

Heterochromatin; Methylation Mutes the DNA
Hypomethylation is little methylation
Hypermethylation is a lot of methylation

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91
Q

Mechanism of action of streptomycin:

A

Binds 30S ribosomal subunit impairing the initiation of protein synthesis

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92
Q

Tocopherol is vitamin

A

E

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93
Q

Galactosyl beta-1,4-glucose is also called

A

Lactose

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94
Q

RNA polymerase I mainly produces:

A

Ribosomal RNA

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95
Q

RNA polymerase II mainly produces:

A

Messenger RNA

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96
Q

RNA polymerase III mainly produces:

A

Transfer RNA

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97
Q

Tetracycline acts:

A

Binding to the 30S subunit of microbial ribosomes preventing the attachment of tRNA (prevents protein synthesis)

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98
Q

Previous administration to which drugs is needed to do a TB test in the treatment of rheumatoid arthritis:

A

TNF-α inhibitors:

Etarnercept 
Infliximab 
Adalimumab
Certolizumab
Golimumab

They can also cause drug-induced lupus

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99
Q

The enzyme defective in PKU is:

A

Phenylalanine hydroxylase

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100
Q

Mode of inheritance of Lech Nyhan disease:

A

X-linked recessive

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101
Q

Mode of inheritance of Marfan sd:

A

Autosomal dominant

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102
Q

The enzyme lysyl oxidase requires as a cofactor:

A

Cu

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103
Q

Coenzymes that pyruvate dehydrogenase need to work:

A

Tender Loving Care For Nancy:

Thiamine pyrophosphate (from thiamine)
Lipoic acid
Coenzyme A (from pantothenic ac)
FAD (from riboFlavin, B2 as FAD gives 2 ATPs)
NAD (from Niacin, B3 as NAD gives 3 ATPs)

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104
Q

Enzymes that require thiamine pyrophosphate (coming from thiamine, B1) to work:

A

Be APT for thiamine:
Branched chain ketoacid dehydrogenase (Val, Iso->propionyl-CoA; Leu->acetyl-CoA)
Alpha-ketoglutarate dehydrogenase (Alpha-KG->succinyl-CoA)
Pyruvate dehydrogenase (pyruvate->acetyl-CoA)
Transketolase (Ribose5-P->glycolysis)

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105
Q

3 main features of G6PD deficiency are:

A

Immunodeficiency
Heinz bodies
Hemolytic anemia

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106
Q

Adenyl cyclase is inhibited by:

A

The alpha part of the Gprot Gi

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107
Q

Liver phosphodiesterase is inhibited by:

A

Methylxanthines

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5
Perfectly
108
Q

Phosphofructokinase-2 is inhibited by:

A

Glucagon phosphorylation

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109
Q

Na/K ATPase is inhibited by:

A

Ouabain

Digoxin

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110
Q

Effect of competitive inhibitors in the Linewaver-Bruk plot:

A

The lines cross

111
Q

Effect of non-competitive inhibitors in the Linewaver-Bruk plot:

A

The lines don’t cross

112
Q

Hypoglycemia + hypoketosis indicate:

A

Beta-oxidation defect (more frequently MCAD deficiency)

113
Q

The ABC carboxylases (that need ATP, biotin (B7 raw🥚) and CO2 to work)

A

PAPa:
Pyruvate carboxylase (gluconeogenesis: pyruvate->oxalacetate)
Acetyl-CoA carboxylase (FA synthesis: acetyl-CoA->malonyl-CoA)
Propionyl-CoA carboxylase (FA oxidation: propionyl-CoA->methylmalonyl-CoA; VOMIT pathway)

114
Q

Vitamin K depending enzyme:

A

Gamma-Glutamyl-carboxylase

115
Q

Differential diagnosis between Hurler and Hunter disease:

A

On Hurler disease the is corneal clouding

116
Q

Name the two obliged activators of enzymes:

A

Acetyl-CoA (for pyruvate carboxylase in gluconeogenesis)

N-acetylglutamate (for carbamoyl phosphate synthetase I in the urea cycle)

117
Q

Tender Loving Care For Nancy enzymes:

A

Pyruvate dehydrogenase
Alpha ketoglutarate dehydrogenase
Branched-chain Ketoacid dehydrogenase

118
Q

Which 5 things generate propionyl-CoA:

A 
VOMIT
Valine
Odd-chain fatty acids 
Methionine 
Isoleucine 
Threonine
119
Q

Black urine is an indicator of the illness:

A

Alcaptonuria

120
Q

Pink/red urine is an indicator of the illness:

A

Porphyria

121
Q

Brown urine is an indicator of the illness:

A

It is an indicator of hyperbilirubinemia

↑ urobilinogen: hemolysis (not unconjugated! because it is fat soluble)
↑ conjugated bilirubin: hepatitis, obstruction

122
Q

Caramel/burnt orange urine is an indicator of the illness:

A

Maple syrup urine disease

123
Q

Enzymes that require the coenzyme form of B12:

A

Methylmalonyl-CoA mutase (peripheral neuropathy-> subacute degeneration)
Homocysteine methyl transferase=methionine synthase (homocysteinemia and macrocytic anemia)

124
Q

Enzymes that require the coenzyme form of folic acid:

A 
Thymidylate synthase (macrocytic anemia) 
Homocysteine methyl transferase (homocysteinemia)
125
Q

Enzymes that require the coenzyme form of pyridoxine B6:

A

Cystathione synthase (homocysteinemia and homocystine in urine)
ALA synthase (sideroblastic anemia)
DOPA decarboxylase
ALT, AST

126
Q

6 mercaptopurine mechanism of action:

A

Inhibits amidotransferase in purine synthesis

127
Q

Direction of DNA synthesis:

A

5’ to 3’

128
Q

Protein defective in Marfan sd:

A

Fibrillin-1 (an extracellular glycoprotein that acts as a scaffold for elastin)

129
Q

Reaction catalyzed by light exposure in the skin:

A

Conversion of 7-dehydrocholesterol to cholecalciferol (vit D3)

130
Q

Substances that bind a Janus kinase/STAT messenger system:

A

Growth hormone
Prolactin
Erythropoietin
And cytokines (interferon and interleukin)

131
Q

What activates prot. kinase C?

A

IP3 (by increasing intracellular calcium) and DAG

132
Q

Elements of the PIP2 (phosphatidylinositol) system:

A 
Gq protein 
Phospholipase C
IP3 (Ca2+)
DAG
Prot. Kinase C
133
Q

The PIP2 (phosphatidylinositol) system is activated by:

A

Vasopressin

Epinephrine (alpha 1)

134
Q

Elements of the cAMP system:

A 
Gs or Gi protein 
Adenyl cyclase 
cAMP (degraded by PDE)
Prot. Kinase A
CREB (at the gene level)
135
Q

The cAMP system is activated by:

A

Glucagon
Epinephrine (beta->Gs)
Epinephrine (alpha 2->Gi)

136
Q

Cytochrome P450 inducers:

A

Barb’s funny mom refuses greasy carb shakes: Phenobarbital (barbiturates), phenytoin, modafinil, rifampin, griseofulvin, carbamazepine, St. John’s wort

Alcohol (chronic)

137
Q

Cytochrome P450 inhibitors:

A

Gee queen GRACE IS inhibit: Gemfibrozil, quinidine, grapefruit juice, ritoNAVIR (protease inhibitors), AZOLes, cimetidine, eryTHROMYCIN (macrolides except azithromycin), isoniazid, sulfanilamides

Alcohol (acute)
Amiodarone 
Diltiazem, verapamil 
Quinolones (ciproFLOXACIN)
SSRIs (fluoxetine)
Cyclosporine
138
Q

Which are the only purely ketogenic aa?

A

Lysine and Leucine

139
Q

Biochemical processes that occur within the mitochondria:

A

Beta-oxidation of FA
TCA cycle
Carboxylation of pyruvate in gluconeogenesis
Transcarbamylation of ornithine in urea cycle

140
Q

Biochemical processes that occur within the cytoplasm:

A

Glycolysis
FA synthesis
Pentode-phosphate pathway
Urea cycle (except OTC)

141
Q

Hallmarks of Tay-Sachs disease:

A

Psychomotor retardation, no splenomegaly

142
Q

Hallmarks of Gaucher disease:

A

Crumpled paper inclusions, bone problems and pancytopenia

143
Q

Hallmarks of Niemann-Pick disease:

A

Foamy bubbly macrophages and splenomegaly

144
Q

Characteristics of riboflavin (B2) deficiency:

A 
Cheilosis or stomatitis (cracking lips and mouth corners)
Glossitis (magenta tongue)
Seborrheic dermatitis 
Eye changes 
Rare
145
Q

Drugs metabolized by cytochrome P450 (affected by inhibitors and activators):

A

Antiepileptics, theophylline, warfarin

146
Q

Substances that bind intracellular receptors with DNA-binding domains; zinc fingers:

A

Steroid hormones: testosterone, estrogen, cortisol, aldo…
Thyroid hormone
Vit. A and D

147
Q

Substances that bind ligand-gated ion channels:

A

Neurotransmitters (Ach, 5HT, NMDA, GABA)

148
Q

Substances that bind a tyrosine kinase system:

A

Transmembrane TK receptor: Insulin and all growth factors (insulin-like GF)
Transmembrane receptor for JAK-STAT pathway: cytokines, INFs, PRL, poietins, GH!!!

Insulin and GF do not activate JAK-STAT and vice-versa!

149
Q

Substances that bind a G-prot coupled receptor:

A

Epinephrine (Gq, Gi and Gs)
Glucagon (Gi and Gs)
Ca2+ to regulate PTH (Gq)

150
Q

Which pathway is inhibited by ethanol metabolism?

A

Gluconeogenesis

151
Q

Which is the most damaging free radical? Example of what generates it:

A

Hydroxyl (OH), generated by Fe

152
Q

Which enzyme convents oxygen in superoxide (O2-) free radical?

A

NADPH oxidase

153
Q

What are the 4 mechanisms of the body to get rid of free radicals?

A

Antioxidants vit A,C,E
Superoxide dismutase (for superoxide)
Glutathione peroxidase (for hydroxyl, especially in RBSs needs HMP shunt)
Catalase (for hydrogen peroxidase)

154
Q

Where do you get exposed to carbon tetrachloride and what does it cause?

A

Dry cleaning industry
Causes fatty liver and necrosis
It is oxidized by P450 and becomes toxic causing free radical injury and lipid peroxidation

155
Q

Cofactors needed for wound healing and why:

A 
Vit C (needed for HYDROXYLATION of Pro and Lys of pro-collagen)
Copper (needed for cross-linking of pro-collagen) 
Zinc (needed for collagen type 3—>1)
156
Q

Last step of heme synthesis enzyme and location:

A

Ferrochelase converts protoporphyrin to heme adding Fe to it. It occurs on the mitochondria

157
Q

Glycine is an important component of:

A

Collagen (Gly-X-Y); it creates “kinks” in the aa sequence that are needed to correctly form the SECONDARY structure
Heme (+ Succinyl-CoA)

158
Q

Important role of Alanine:

A

Activates gluconeogenesis

159
Q

When is Proline hydroxylation deficient?

A

In scurvy (no Vit C)

160
Q

Phenylalanine and Tyrosine are important components of:

A

Catecholamines
Melanine
T3 and T4

161
Q

Tryptophan is an important component of?

A

Serotonin
Niacin
Melatonin

162
Q

Which aa becomes essential in PKU? And which one needs to be lowered?

A

Tyrosine and they need to eat less Phenylalanine (because phenylalanine-hydroxilase doesn’t work)

163
Q

Lysine is an important component of:

A

Collagen (needs Cu for hydroxylation)

Histones

164
Q

Arginine is an important component of:

A

Urea and creatinine!! Pee!!
NO
Histones

165
Q

Glutamate is an important component of:

A

GABA
Glutathione
Accepts NH3 and forms Glutamine to transport it
Incorporated in the first reaction of de novo pyrimidine synthesis (2ATPs, CO2 and glutamine)

166
Q

Important role of Cysteine:

A

It has a sulfhydryl group that forms disulfide bounds which helps forming protein tertiary structure
Sulfhydryl group are deadly

167
Q

How can you diagnose thiamine (B1) deficiency?

A

Baseline erythrocyte transketolase activity (assume in alcoholic or malnourished)

168
Q

Where do the primers have to bind in PCR?

A

Both the forward and reverse primers have to bind to the 3’ sequence of both the coding and the template strand

169
Q

Tissues that cannot use ketonic bodies as energy source:

A

RBCs and liver

170
Q

What molecule attaches to misfolded proteins to promote their destruction?

A

Ubiquitin

171
Q

Which enzyme converts NE to Epi in the adrenal medulla?

A

Phenylethanolamine-N-methyltransferase (PNMT)

Upregulated by cortisol

172
Q

Pellagra is due to a deficiency of which vitamin?

A

B3, niacin

173
Q

Why do fibrates cause cholesterol gallstones?

A

Because they inhibit cholesterol 7alpha hydroxylase so decrease bile acid production

174
Q

Enz. deficient and hallmarks of Von Gierke disease:

A 
Glucose-6-phosphatase 
Severe hypoglycemia (with hepatomegaly, high cortisol and hyperlipidemia)
175
Q

Enz. deficient and hallmarks of Pompe disease:

A

Acid alpha 1,4-glucosidase on the lysosomes

Cardiomegaly (also hypotonia, macroglossia and hepatomegaly)

176
Q

Why do you get anticipation?

A

Due to a further expansion of trinucleotide repeats during SPERMATOGENESIS

177
Q

What is the most frequent cause of homocysteinuria? Which aa becomes essential?

A

Cystathionine synthase deficiency

Cysteine becomes essential

178
Q

Which aa becomes essential in phenylketonuria?

A

Tyrosine

179
Q

Clinical picture of lead poisoning:

A 
High protoporphyrin
Abdominal pain
Constipation
Neurophychiatric symptoms 
Microcytic anemia (basophilic stippling and ring sideroblasts)
Blue lines in gums 
Lead lines in bone Rx
Wrist and foot drop
180
Q

What enzyme in the body has reverse transcriptase activity?

A

Telomerase

181
Q

Which enzyme is deficient in I cell disease? What it’s its function?

A

N-acetylglucosaminyl-l-Phosphotransferase

Phosphorylates manoses in lysosomal proteins so they go inside the lysosomes

182
Q

Name 4 important X-linked recessive diseases:

A

Homozygous women are also symptomatic and Turner X0

Duchenne, Becker
Lesch-Nyhan
G6PD deficiency
Hemophilia A and B

Menkes
OTC deficiency
SCID due to IL2 receptor deficit
Red-green color blindness
Fabry, Hunter
Wiskott-Aldrich, Burton
Ocular albinism
183
Q

Name 3 important X-linked dominant diseases:

A

Heterozygous women can be also symptomatic but milder (X inactivation)

Hypophosphatemic rickets (Vit D resistance)
Fragile X
Alport
Rett (retarded ataxic girls, boys die -de novo bc no kids-)

184
Q

Name 4 important mitochondrial inherited diseases and their molecular basis:

A 
Leber optic neuropathy
Leigh sd (subacute necrotizing encephalopathy)

Due to oxidative phosphorylation defects

MELAS (encephalopathy, lactic acidosis, stoke-like)
Myoclonic epilepsy with ragged red muscle fibers

Due to a tRNA defect

185
Q

Substances to avoid in G6PD deficiency:

A 
TMP/SMX
Nitrofurantoin 
Floxacines (fluorquinolones)
Isoniazid 
Dapsone 
Quinine 
Fava beans
186
Q

Fabri disease is a deficiency of _____ and _____ is accumulated

A

Alpha-galactosidase A

Globotriaosylceramide/ ceramide trihexoside

187
Q

Ilnesses due to splicing problems:

A

The problem is on the mRNA intron not in the coding exon

Tay Sachs (most frequently due to frameshift)
Gaucher
Beta-thalassemia 
Lupus
Marfan
188
Q

To which portion of the tRNA does the aa bind?

A

It binds to the CCA portion at the 3’ end

189
Q

What vitamin abnormality can cause pseudotumor cerebri? What else can it cause?

A

Vit A toxicity

Also causes arthralgias, alopecia, dermatitis and hepatomegaly

190
Q

Clinical picture of arginase deficiency:

A

Normally symptoms after an insult:
Spasticity
Unsteady gait
Vomiting

Low serum urea and high arginine

191
Q

Clinical picture of I cell disease:

A

Coarse face
Gingival hyperplasia
Cloudy cornea
Problems moving joints, deformities and scoliosis

192
Q

What is the function of the 5’ 7-methylguanosine cap of mRNA?

A

Needed to be recognized by initiation factors in the ribosome

193
Q

What is the function of the 3’ poly A tail of mRNA?

A

Avoid mRNA degradation by ribonucleases and allow it to leave the nucleus

Gets inserted into AAUAAA sequence

194
Q

Which enzyme is defective in McArdle’s?

A

Muscle glycogen phosphorylase or myophosphorylase

195
Q

Clinical picture and reaction involved in pyruvate kinase deficiency:

A

Hemolytic anemia with high 2,3-BPG

Phosphoenolpyruvate cannot be converted to pyruvate so cells that rely on glycolysis like RBCs lyse

196
Q

Clinical picture and reaction involved in pyruvate dehydrogenase deficiency:

A

Neurologic deficits, lactic acidosis, high alanine, X-linked.
Do not give glucose! Gets better with ketogenic diet (low carb, high FAT and ketogenic aa, thiamine, lipoid ac and carnitine)
Pyruvate cannot be converted to Acetyl CoA so it cannot go to Krebs cycle

197
Q

Enzymes activated allosterically by AMP:

A

PFK-1 in glycolysis

Glycogen phosphorylase in glycogenolysis

198
Q

Enzymes activated by insulin:

A

Glucokinase and PFK-2 in liver glycolysis
Glycogen synthase in glycogenesis
Acetyl-CoA carboxylase in FA synthesis
HMG-CoA reductase in cholesterol synthesis

199
Q

Enzymes activated by glucagon and Epi:

A

Glycogen phosphorylase in glycogenolysis

PEP carboxylase in liver gluconeogenesis

200
Q

Name 4 important autosomal dominant diseases:

A 
Familial hypercholesterolemia (LDL receptor)
Neurofibromatosis type 1
Marfan
Acute intermittent porphyria
201
Q

Enzymes inhibited by allopurinol:

A 
Xanthine oxidase
PRPP amidotransferase (also inhibited by azatioprine=6-mercaptopurine)
202
Q

What is the mutation in Marfan? and in Fragile X?

A

Marfan: FBN1 (bueno)

Fragile X: FMR1 (Fragilex Mental Retardation)

203
Q

What is the difference between variable expressivity and incomplete penetrance?

A

Variable expressivity patients with the same genotype present differently in incomplete penetrance some patients with the bad genotype are not sick at all

204
Q

What aa is precursor of 5HT? and of Epi?

A

Tryptophan: 5TH
Tyrosine: DOPA, DA, NE, Epi

205
Q

Function and cofactor for phenyetanolamine-N-methyltransferase:

A

Converts NE to Epi in the cytoplasm
Upregulated by cortisol
Needs SAM

206
Q

What is pleiotropy?

A

When one mutation causes different problems in different organs like blue sclera and fractures in OI

207
Q

Mode of inheritance of OI:

A

Autosomal dominant

208
Q

What organs handle galactose? and fructose? What enzyme defect causes a lot and little problems in their metabolism?

A

Glactose: Liver and brain lactating mama; lactase =) =) kinase =) Gal 1P uridyltransferase =(
Fructose: Liver and kidney; kinase =) aldolase B =(

209
Q

Cathecholamine synthesis pathway:

A 
Phenylalanine
(Phenylalanine hydroxylase, THB)
Tyrosine
(Tyrosine hydroxylase, THB)
DOPA
(DOPA decarboxylase or aa decarboxylase, B6)
DA
(DA beta-hydroxylase, VitC/Cu)
NE
(Phenylalanine-N-methyltransferase, SAM)
Epi

Summary of cofactors
THB → THB → B6 → VitC/Cu → SAM
TTBCS teeete becese…

210
Q

Name 3 uncouplers and explain their mechanism:

A

Allow electron flow and O2 consumption but uncouple it to ATP generation, give the energy as heat

2,4-DNP (Dinitrophenol)
High dose aspirin
Thermogenin in brown adipose tissue

211
Q

Which cellular process is defective in xeroderma pigmentosum?

A

Nucleotide excision repair, G1

212
Q

Which cellular process is defective in BRAC1 and what ca. generates?

A

Homologous recombination

Breast, ovarian and prostate

213
Q

Which cellular process is defective in Lycnh sd. and what ca. generates?

A

Mismatch base repair, G2
If you cannot correct mismatched bases you get microsatellite instability

Colon (HNPCC), endometrium, ovary, stomach, brain and thyroid

214
Q

Which cellular process is defective in ataxia-telangiectasia?

A

ATM gene 3 functions:

Check point detecting (p53) double-stranded breaks-> ca.

Serine/threonine kinase activity with MHEJ to repair the double-stranded breaks (nonhomologous end joining) and generate VDJ recombination-> lymphopenia

Old mytochondria death

215
Q

Ways to activate and mute DNA:

A

Mute: DNA and histone methylation, histone deacetylation

Active: histone acetylation

Same for DNA and histones

216
Q

What is deficient in hyperchylomicronemia?

A

LPL enz or it’s cofactor in the lipoprotein Apo C2

217
Q

What is deficient in hypercholesterolemia?

A

LDL receptors or it’s ligand in LDL ApoB-100

218
Q

What is deficient in abetalipoproteinemia?

A

ApoB-48 and ApoB-100

219
Q

What part of Hb is affected in thalassemia? and in porphyria?

A

Heme in porphyria

Globin in thalassemia

220
Q

What is coding introns or exons?

A

Exons are coding introns are spliced out!

221
Q

Examples of transcription factors (DNA-binding proteins) and which kind of proteins use to bind DNA?

A

Lipid soluble hormone receptors that display Zinc fingers to bind HRE
PPARs (peroxisome proliferator-activated receptors) that display Zinc fingers to bind CRE

The most common way to bind DNA is though Zn fingers, the exceptions are:

Water soluble hormones receptors ↑cAMP and bind to CREB that display Leucine zippers to bind PPREs. C-Jun and c-Fos also work tough leucine zippers

Inflammation activates NFkB that displays Rel domains that activate JAK-STAT to bind kB elements

During development we activate Homeodomain proteins (HoX, PAX) that display HeliX-turn-helix

222
Q

Zinc deficiency may lead to:

A 
Alopecia
Poor wound healing
Stomatitis
Low immunity
Hypogonadism
Anosmia
Cirrhosis

Associated with acrodermatitis enteropatica

223
Q

Hyperamonemia can be a deficiency of the enzyme ____ or ____

A

Carbamoyl phosphate synthetase 1. You cannot from Carbamoyl phosphate

Ornithine transcarbamoylase or OTC. Carbamoyl phosphate accumulates and backs up to orotic acid. You cannot form citruline

224
Q

Metabolic changes done by alcohol:

A

↑NADH so:
Lactic acidosis bc pyruvate converts into lactate
Blocks gluconeogenesis bc OOA goes back to malate
Ketoacidosis bc Acetyl-CoA goes into ketones rather than to TCA
Steatosis bc DHAP and Acetyl-CoA from glycolysis go to FA synthesis

225
Q

Why do we need NADPH for?

A

Glutathione reProduction
FA and cholesterol Production
Oxidative burst

226
Q

What is the best test to dx: triplet expansion, translocations, aneuploidy, inheritance patterns, large genes defects?

A

Southern blot/PCR: triplet expansion
FISH: translocations, microdeletions
Karyotype: aneuploidy, large deletions
Linkage: ancestry, marfan and congenital adrenal hyperplasia
Multiplex probe hybridization: genes that can be mutated in different sites like dystrophin

227
Q

What are the functions of eukaryotic DNA polymerase δ, α, β, ε and γ?

A

Δ(δ) and α to make DNA. δ elongates the Okazaki fragments
β and ε to repair errors
γ mitochondrial DNA

228
Q

Which DNA polymerases can degrade both thymine and demethylated thymine?

A

demethylated thymine=uracil=RNA
thymine=DNA

Just the ones that remove the primer:
DNA polymerase 1 in prokaryotes
RNAhase in eukaryotes

229
Q

What is the AAUAAA sequence function?

A

Signal in the hnRNA for Poly(A)polymerase to add the poly A tail

230
Q

What is the AGGU sequence function?

A

Signal at the hnRNA exon/intron junction for the spliceosome to splice

231
Q

What is the TATA, CAAT or GC boxes function?

A

Signal at the promoter region of the DNA for GENERAL transcription factors to bind and start transcription

232
Q

What is the response elements/enhancer regions function?

A

Signal at the DNA for SPECIFIC transcription factors to bind and start transcription

233
Q

What is the TTAGGG sequence function?

A

Signal at the telomeres of chromosomes for telomerase to add DNA

234
Q

Enzyme affected in lead poisoning and in sideroblastic anemia:

A

Both have ringed sideroblasts in the marrow (heme accumulates in mitochondria) and basophilic stippling in the smear (RNA aggregates)

Lead: inhibits ferrochelatase and ALA dehydratase
Sideroblastic: ALA synthase (rate limiting)

235
Q

What vitamins do the dehydrogenases need to work?

A 
Niacin B3
But:
Branched chain ketoacid dehydrogenase 
Alpha-ketoglutarate dehydrogenase 
Pyruvate dehydrogenase
That also require B1, B2, B3 and B5

Succinate dehydrogenase or complex 2 in e- transport chain needs B2 and does need B3

236
Q

Which enzyme needs only B1 to work?

A

Trasketo1ase; is the one tested on an alcoholic because it is selective for B1 and because it is cytoplasmic and therefore in the RBCs (the others are mitochondrial)

237
Q

What vitamin is needed for adding or removing CoA?

A

PEntothenic acid of B5

238
Q

What vitamins do the carboxylases need to work?

A

Biotin B7, ATP and CO2
Acetyl-CoA carboxylase
Pyruvate carboxylase
Propionyl-CoA carboxylase

239
Q

What is methyl-THF and how are its levels in B9 and B12 deficiency?

A

Unusable folate after it is used
↓ in B9 deficiency
↑ in B12 deficiency

240
Q

What vitamin is needed for adding or removing methyl groups?

A

Cobalamin B12

241
Q

Which vitamin deficiency gives you hemolytic anemia?

A

Vit E deficiency because it causes membrane damage leading to thorny RBCs and breakdown

Also neuropathy, ataxia and retinitis pigmentosum

242
Q

Name 7 medical conditions with polygenic inheritance:

A 
Androgenetic alopecia
Epilepsy
Glaucoma
HT
Ischemic heart disease
Schizophrenia
DM2
Spina bifida

*Here the recurrence risk depends on the number of affected relatives

243
Q

Name 4 examples of transcription factors:

A 
C-myc (Burkitt)
MYCL1=L-myc (lung)
N-myc (neuroblastoma)
C-jun
C-fos
CREB
244
Q

Name the 9 hydrophobic essential aa:

A 
Glycine (tiniest), proline (collagen)
Alanine (starvation)
Valine, leucine, Isoleucine (branched chain)
Phenylalanine, tyrosine (PKU)
Tryptophan (5-HT, niacin)
245
Q

Name the 8 intermediate substrates in the Krebs cycle:

A

Citrate Is Krebs’ Starting Substrate For Making Oxalacetate:

Citrate
Isocitrate
α-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Malate
Oxalacetate
246
Q

Glycogen regulation by hormones and substrates:

A

↑ Glycogen synthase:
Insulin (liver and muscle)
Glucose 6P
Cortisol

↓ Glycogen phosphorylase:
Insulin (liver and muscle)
Glucose 6P
ATP

↑ Glycogen phosphorylase:
Epi beta (liver and muscle) alpha 1 (only liver)
Glucagon (only liver)
Ca inside the m. (synchronization of exercise and energy)

↓ Glycogen synthase:
Epi beta (liver and muscle)
Glucagon (only liver)

247
Q

Important roles of Aspartate:

A

Carries ammonia at the beginning of the urea cycle

Incorporated in de novo pyrimidine synthesis

248
Q

Which 3 compounds require tetrahydrobiopterin for their synthesis?

A

Tyrosine
DOPA, DA, NE, Epi; low DA leads to hyperprolactinemia
Serotonin

249
Q

What type of mutation causes a temperature-sensitive repression of the tryptophan operon in E. coli?

A

Missense, are the only mutations that are mild enough that can be only apparent under certain environmental conditions, in this case are called conditional mutations

Mutants of Escherichia coli exhibiting temperature-sensitive repression of the tryptophan operon because of a MISSENSE mutation that alters the tryptophanyl transfer ribonucleic acid (tRNA) synthetase

250
Q

Which aa is needed for collagen and elastin cross-linking? Why is cross-linking important?

A

Lysine (Lysyl oxidase and Cu make covalent lysine-hydroxylysine cross-linkage)

Cross-linking is needed for elasticity and reinforcement

251
Q

Define positive and negative nitrogen balance:

A

Negative: CATAbolism; burns, injuries, fevers, Kawashkior, hypothyroidism, wasting and fasting. The amount of nitrogen excreted is greater than the amount ingested.

Positive: ANAbolism; growth, hypothyroidism, tissue repair, and pregnancy. The amount of nitrogen excreted is less than the amount ingested.

252
Q

Which aa is a precursor for thyroid hormone?

A

Phenylalanine

253
Q

Which type of mutation do you get with a single nucleotide or base deletion?

A

Frameshift mutation

254
Q

Where is the receptor for the signal recognition particle?

A

On the RER; if there is a problem in the signal recognition particle protein accumulates in the cytoplasm and never goes to the RER

255
Q

What is the clinical consequence of eating a lot of carrots?

A

Increased β-carotenes in the diet cause the skin to turn yellow (hypercarotenemia) but the sclera remains white (vs jaundice)

256
Q

Name a possible mechanism of resistance to restriction endonuclases:

A

Hypermethylation; methylase methylates DNA making the DNA resistant to restriction endonucleases

257
Q

Which enzyme becomes essential to make nucleotides in G6PD?

A

Transketolase

258
Q

Define genetic polymorphism:

A

A single nucleotide substitution that is present in at least 1% of the population

259
Q

Phases of collagen synthesis and illnesses that interfere with them (5):

A

Procollagen synthesis (impaired synthesis of osteoid by osteoblasts): Osteogenesis imperfecta and alport

Proline and lysine hydroxylation: Scurvy; ultimately essential for triple helix formation

Hydroxylysine glycosylation

Triple helix assembly by hydrogen bonds: Osteogenesis imperfecta

Exocytosis

Cleavage of N and C regions: Ehlers-DaNlos

Cross-linking by lysyl oxidase: Menkes and Ehlers-DaNlos

260
Q

Reactions canalized by 21 alpha hydroxylase, 11 beta hydroxylase and 17 hydroxypregnenolone:

A

21: progesterone →11-deoxycorticosterone and 17-hydroxyprogesterone →11-deoxycortisol
11: 11-deoxycorticosterone →corticosterone and 11-deoxycortisol →cortisol
17: pregnenolone →17-hydroxypregnenolone and progesterone →17-hydroxyprogesterone

21 puts the 11
11 takes out the 11
17 puts the 17

261
Q

What is the diagnosis of a kid with neurologic defects, high lactate and high alanine in blood?
What if he also has fasting hypoglycemia and ketoacidosis?

A

Pyruvate dehydrogenase deficiency, X-linked

Pyruvate carboxylase deficiency, autosomal recessive (rare)

262
Q

Which mutations alter RNA or cDNA length?

A

ONLY Frameshift/In frame because nucleotides are deleted or inserted!!

Nonsense, missense, conservative or silent mutations do not affect mRNA or cDNA length because they are substitutions! some will affect protein length but not mRNA length!

263
Q

What makes elastin elastic?

A

Cross-linking

264
Q

How are proteins needed for apoptosis transcribed if you are breaking up the cell?

A

Internal ribosome entry site; the internal ribosome entry site sequence (in the 5’UTR) makes that the eukaryotic ribosome binds mRNA and translation can happen in the middle of the mRNA sequence

265
Q

Steps on a PCR (6):

A

Heating (95deg) → Dematuration → Cooling → Primers binding → Re-warming (72deg) → DNA polymerase binds more DNA

266
Q

How do you explain that a normal mom has a baby with achondroplasia?

A

90% of the mutations are DE NOVO, 10% are inherited

267
Q

How do you calculate carrier frequency based on incidence?

A

q=√incidence
carrier frequency=2!!!!!pq
DO NOT FORGET THE 2

268
Q

When does the nondisjunction that causes Down syndrome occur?

A

On anaphase 1 or 2 of meiosis

269
Q

Which enzyme is missing in the zona glomerulosa preventing the synthesis of cortisol and androgen?

A

17-hydroxylase that catalyzes the conversion of progesterone →17-hydroxyprogesterone

270
Q

Name the 8 intermediate substrates in the urea cycle:

A

Ordinarily, Careless Crappers Are Also Frivolous About Urination

Ornithine + Carbamoyl phosphate →Citrulline + Aspartate →Argininosuccinate - Fumarate →Arginine - Urea →Ornithine

271
Q

Which DNA damage do ionizing and UV radiation cause?

A

Ionizing = free radical formation double stand DNA breaks, fixed by NONhomologous recombination (not working in ataxia-telangiectasia)

Non ionizing (UVB) = DNA damage by formation of pyrimidine dimers, fixed by NUCLEOTIDE excision repair (not working in xeroderma pigmentosum)

272
Q

What is the mode of inheritance of both Friedreich ataxia and ataxia telangiectasia?

A

Autosomal recessive

Friedreich, chromosome 9. Hammer toes, sensory loss
Telangiectasia, chromosome 11. Inmunodeficiency

273
Q

Which processes occur inside and outside the cell in collagen synthesis? In which illnesses are each of them defective?

A

Inside, RER:

Procollagen synthesis: Defective in osteogenesis imperfecta (impaired synthesis of osteoid=bone matrix by osteoblasts) and Alport

Proline and lysine HYDROXYLATION in porcollagen: requires Vit. C, defective in Scurvy; ultimately essential for triple helix formation

HYDROxylysine glycosylation=disulfide bond formation

Triple helix assembly by HYDROgen bonds: Osteogenesis imperfecta (impaired synthesis of osteoid=bone matrix by osteoblasts)

Outside:

CUTting of disulfide bonds, cleavage of N and C regions: Ehlers-DaNlos

CrOss-Linking of pro-collagen by lysyl oxidase: requires CU, defective in Menkes

274
Q

Why is fructose metabolized faster than glucose and galactose?
Why to treat Von Gierke you can eat glucose and corn but NOT fructose or galactose?
Why to treat some gluconeogenesis diseases you can eat galactose?

A

Fructose is closer to pyruvate in glycolysis so it is metabolized and sends energy to the TCA cycle faster than glucose and galactose

Fructose and galactose require an intact Glucose-6-phosphatase to increase the glucemia therefore in Von Gierke you can eat glucose and corn but NOT fructose or galactose

Galactose enters gluconeogenesis at one of it’s latest steps trough Galactokinase → Galactose 1-phosphate uridyltransferase. So you can have a gluconeogenesis disease where the hypoglycemia is corrected by eating galactose and not glycerol or fructose (because glycerol and fructose enter gluconeogenesis a lot later)

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