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Step 1 Miscellanous > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is the structure of a nucleosome, what links them together, and what amino acids are they rich in?

A

Octamer of histones, linked together by H1 histone to form the “beads” of nucleosomes with DNA twice wrapped around them. They are rich in positively charged lysine and arginine -> stabilize negatively charged DNA

H1 = 1inker histone

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2
Q

How does mismatch repair occur in bacterial DNA replication?

A

DNA is normally methylated at specific C and A sites

Newly replicated strand will not be methylated. Any mismatches can be repaired via mismatch repair enzymes using the methylated strand as a template (repair of hemimethylated DNA)

Prior to cell division, the new strand will finally be methylated via Dam methylase.

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3
Q

Where is DNA typically directly methylated in order to mute DNA? Are these common sites?

A

CpG islands (C-phosphodiesterbond-G)

Note that these CpG islands are actually pretty rare in eukaryotic DNA because they are unstable.

This is because methylcytosine is easily deaminated to thymine, which is again transcriptionally active.

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4
Q

Can regions of methylated histones be activated? How is this reversible compared to DNA methylation?

A

Sometimes yes, depending on the location of histone methylation. However, it tends to reversibly repress DNA transcription.

DNA methylation is much more permanent than histone methylation.

Note that we want to acetylate histones in order to activate gene transcription.

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5
Q

What amino acids are necessary for purine synthesis?

What other cofactor is required?

A

GAG =
Glycine - entire amino acid is donated
Aspartate - nitrogen donor
Glutamine - 2x nitrogen donor

N10-formyl-Tetrahydrofolate is also required for the addition of two carbons

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6
Q

How are cytosine, uracil, and thymine structurally related?

A

Cytosine deamination makes uracil
Uracil methylation makes thymine

Obviously, as stated before, methyl-Cytosine deamination makes thymine.

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7
Q

How is each nucleotide added as DNA polymerase moves along?

A

5’ end of nucleotide to be added has triphosphate on it

3’ end of elongating cleaves and attaches between the alpha and the beta phosphate, leaving pyrophosphate behind.

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8
Q

What does deamination of adenine vs adenosine make?

A

Adenine -> hypoxanthine

Adenosine -> inosine

Remember:
Inosine = hypoxathine + deoxyribose sugar
Inosine is a nucleoSide
With phosphaTe, it would be a nucleoTide

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9
Q

What amino acids / carbons are used in the pyrimidine synthesis pathway?

A

Amino acid:
Aspartate - the entire thing
Glutamine + HCO3-: nitrogen used by carbamoyl phosphate synthetase 2 to make carbamoyl phosphate

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10
Q

What enzyme is used to synthesize orotic acid from aspartate + carbamoyl phosphate and what blocks this?

A

Dihydroorotate dehydrogenase

Blocked by leflunomide

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11
Q

What is the enzymatic cause of orotic aciduria?

A

Defective UMP Synthase:

Orotic acid + PRPP cannot be combined to make UMP, so orotic acid acid accumulates.

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12
Q

What condition must orotic aciduria be told apart from and how is this done?

A

Ornithine transcarbamoylase deficiency, where excess carbamoyl phosphate is shunted into pyrimidine synthesis -> orotic acid also accumulates.

Difference:
Orotic aciduria actually causes impaired pyrimidine synthesis -> megaloblastic anemia will occur.

OTCase deficiency causes impaired urea cycle -> hyperammonemia and decreased BUN.

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13
Q

Is orotic aciduria or OTCase deficiency more common?

A

OTCase deficiency is -> it is X-linked

Orotic aciduria is autosomal recessive.

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14
Q

Give the inhibitor of human, bacterial, and protozoan dihydrofolate reductase?

A

Human - methotrexate
Bacterial - Trimethoprim
Protozoan - Pyrimethamine - (T. gondii)

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15
Q

What antiviral agent is very similar to mycophenolate mofetil in mechanism of action?

A

Ribavirin - Guanine nucleoside analog which functions to inhibit IMP dehydrogenase

-> Thus acts to inhibit DNA / RNA synthesis

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16
Q

What is the function of HGPRT?

A

Hypoxanthine-Guanine PRPP transferase

Hypoxanthine -> IMP. IMP can be aminated to AMP.

Guanine -> GMP.

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17
Q

What is guanine deaminated to?

A

Xanthine, which can be broken down by xanthine oxidase to uric acid.

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18
Q

How is Lesch-Nyhan inherited and what are the clinical findings? Treatment?

A 
X-linked, HGPRT deficiency 
H = hyperuricemia 
G = gout 
P = Pissed off (aggression / self-mutilation)
R = Retardation 
T = dysTonia

Treatment is allopurinol to prevent gout

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19
Q

What are the two amino acids do not have a degenerate / redundant code?

A

Methionine and tryptophan

Met = AUG start codon

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20
Q

What bases is the origin of replication rich in?

A

Just like promoters, TATA boxes which are less sticky than C/G are where origins of replication are.

There are multiple in eukaryotes and single in prokaryotes.

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21
Q

What are the causes of the progerias Werner’s and Bloom’s syndrome?

A

Autosomal recessive mutations in helicase (DNA unwinding enzyme at the replication fork)

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22
Q

What DNA replication enzyme are fluroquinolones actually disrupting?

A

DNA topoisomerases II and IV

-> topoisomerase II is also called “DNA gyrase”

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23
Q

How is DNA polymerase III different from DNA polymerase I?

A

DNA polymerase III - much faster, has 3’ to 5’ exonuclease activity (can go backwards to repair), but no 5’ to 3’ exonuclease activity when it is replicating.

DNA polymerase I - slower, but possesses 5’ to 3’ exonuclease activity -> ability to remove RNA primer in the forward direction

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24
Q

Why are telomeres added? Where are they added?

A

Added to the 3’ ends of chromosomes (with matching complementary DNA obviously) -> added so that when DNA polymerase starts synthesizing 5’ to 3’ it’s not losing any of its important genetic information when then required primer is excised, cutting some off on the 5’ end (template was the 3’ end of the parent gene).

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25
Q

What is transition vs transversion point mutation?

A

Transition - purine to purine or pyrimidine to pyrimidine Transversion - purine to pyrimidine or pyrimidine to purine

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26
Q

What is a common cause of a DNA mutation within the coding region which ends up being silent?

A

Mutation in the third nucleotide of a codon, which is a wobble codon for the same amino acid
-> can still affect gene transcription depending on presence of similar amounts of tRNA for that codon or not.

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27
Q

Explain how glucose interacts with the lac operon.

A

When glucose is low -> cAMP rises (similar to how glucagon causes a rise in cAMP when glucose is low)

cAMP -> binds catabolite activator protein (CAP).

CAP binds the activator / enhancer site -> activity of promoter is enhanced.

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28
Q

What protein codes for the repressor protein of the lac operon and how is it deactivated?

A

LacI codes for the repressor. Binding of allolactose will cause dissociation of the repressor from the operator sequence -> transcription of lac operon can commmence.

-> transcription can only occur at all when there is lactose present to force repressor to unbind the operator.

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29
Q

What are the proteins of the Lac operon?

A

LacZ, LacY, and LacA

LacZ = beta galactosidase
LacY = galactose permease
LacA = galactose acetylase
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30
Q

When does nucleotide excision repair occur and how does it happen?

A

Happens in the G1 phase of the cell cycle only
-> specific endonucleases cleave around thymidine dimers, think DNA polymerase / ligase fill the gap.

Defective in xeroderma pigmentosum.

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31
Q

When is base excision repair needed and how does it work?

A

Needed whenever a base is damaged, most often deamination or depurination. Occurs throughout cell cycle

GEL PLease

Glycosylase -> cleaves off bad base from nucleotide.
Endonuclease -> cleaves phosphodiester backbone from 5’ end
Lyase -> cleaves 3’ end
Polymerase -> fills the gap
Ligase -> seals it

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32
Q

What DNA repair mechanism is defective in Lynch Syndrome? What phase of the cell cycle is it supposed to occur in?

A

Also known as hereditary nonpolyposis colorectal cancer (HNPCC) -> Defective mismatch repair in G2 phase of cell cycle.

Deficiency will result in higher mutations due to slippage of DNA polymerase in DNA replication, leading to more microsatellite instability with frameshift mutations and duplications

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33
Q

Give three conditions in which nonhomologous DNA end joining (double-strand DNA repair) is defective?

A
  1. Ataxia-telangiectasia
  2. BRCA1 mutation
  3. Fanconi anemia
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34
Q

What are the symptoms of Fanconi anemia?

A
  1. Aplastic anemia, increased risk of tumors / leukemia
  2. Cafe-au-lait spots
  3. Short stature, hypoplastic thumb, radial defects
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35
Q

Why would fMet stimulate neutrophil chemotaxis?

A

Only in prokaryotes does the start codon methionine (AUG) actually get formylated. In human, seeing fMet actually stimulates neutrophils to come in and fight a bacterial infection.

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36
Q

What sequence is in eukaryotes and prokaryotes is responsible for ribosome binding to start translation? How does this sequence start in eukaryotes?

A

Prokaryotes - Shine-Dalgarno sequence

Eukaryotes - Kozak sequence
-> GCCGCC-AUG

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37
Q

At what sites do activator proteins and repressor proteins bind on the DNA? Where can these be located? How do they work?

A

Activator -> binds enhancer sequence
Repressor -> binds silencer sequence

These can be located upstream, downstream, or within the introns of the gene

The activator / repressor proteins bend the DNA to interact with the RNA polymerase II on the promoter, modifying transcription

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38
Q

What sequences does RNA polymerase II bind within the promoter, which is upstream the gene of interest?

A

CAAT and TATA boxes

-> areas which easily dissociate.

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39
Q

How many RNA polymerases are in eukaryotes and what are their functions? Where do they function?

A

3 RNA polymerases
Numbered in the same sequence as their functional products rRNA -> mRNA -> tRNA
rRNA = RNA polymerase I - functions only in nucleolus
mRNA = RNA polymerase II
tRNA = RNA polymerase III

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40
Q

What is the only piece of rRNA made outside the nucleolus?

A

5S rRNA, transcribed by RNA polymerase III

-> essential component of the 60S ribosome

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41
Q

What RNA polymerase is in prokaryotes and what inhibits it?

A

Only one RNA polymerase which carries out all the functions

-> Rifampin blocks DNA-dependent RNA polymerase

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42
Q

What is the original RNA transcript which is made by RNA polymerase 2, and what three things must be done within the nucleus before the final mature mRNA is released?

A

hnRNA (heterogenous nuclear RNA)

  1. Addition of 7-methylguanosine cap at 5’ end (protect from exonuclease digestion)
  2. Polyadenylation of 3’ end by about 200 A’s
  3. Splicing out of introns (occurs concurrently with 1/2)
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43
Q

How is the poly A tail made?

A

Requires a Poly-A polymerase (RNA polymerase which does not required a template), which uses the AAUAAA polyadenylation signal at the end of the 3’ mRNA to latch on.

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44
Q

What is the function of P bodies and where are they located?

A

Cytoplasmic processing bodies (P bodies)

Function in mRNA quality control and storage, which contain exonucleases, decapping enzymes, and microRNAs. They may be stored here for future translation

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45
Q

What proteins are responsible for intron splicing in eukaryotes and what is the intermediate structure called?

A

Small nuclear ribonuclear proteins (snRNPs) -> intermediate is a lariat structure (loop) formed by 3 phosphodiester bonds (one of which is via the 2’ hydroxyl of an adenine)

3’-OH of 5’ end, upstream a guanine base, attacks the 5’ phosphate downstream another guanine base to splice out the lariat intermediate, which stays in loop form.

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46
Q

Give two disorders with auto-antibodies to snRNPs?

A

SLE = anti-Smith = a snRNP

Mixed connective tissue disease = anti U1-RNP

These are involved in splicing out introns via a lariat intermediate.

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47
Q

How do you remember snRNP vs miRNA?

A

snRNP - small nuclear -> must be occurring in the nucleus, has some function in processing the mRNA -> splices out introns

microRNA -> clearly doesn’t say it’s nuclear, thus it’s probably in the cytoplasm.
-> interacting in the cytoplasm -> silencing of mRNA.

Great, now you can’t get snRNP / miRNA confused.

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48
Q

How do microRNAs work? How about silencing RNA?

A

Typically bind the 3’ untranslated region of specific mRNAs, targeting them for degradation or translational repression (often used by cancers to repress tumor suppressors)

This is in contrast to siRNA (silencing) which forms dsRNA in the translated region and blocks translation.

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49
Q

How is the amino acid attached to tRNAs? What is the sequence?

A

Attached via 3’ hydroxyl of adenine in the sequence: 5’-CCA-3’

CCA = Can Carry Amino (acids)

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50
Q

What are the two other main arms of tRNAs (other than acceptor stem for amino acid and the anticodon loop)? What is their function? What special amino acids do they contain?

A

T-arm = Tethers tRNA molecule to ribosome, contains CYT - cytosine, pseudouridine, and ribothymidine

D-arm = Detects the aminoacyl-tRNA synthetase, contains Dihydrouridine

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51
Q

How are tRNAs charged? What substrate is required?

A

Each amino acid has its own tRNA synthetase

Amino acid is bound to the enzyme by adenine in the active site, converts ATP to PPi and aminoacyl-AMP

Amino acid is transferred from aminoacyl-AMP to 3’ hydroxyl of acceptor arm of tRNA. Correct amino acid is determined by a single or few bases in the tRNA -> not necessarily corresponding to a single arm.

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52
Q

What failsafes / ways to check are in place to prevent the wrong amino acid from binding the tRNA? What happens if the wrong amino acid is in the active site?

A
  1. Steric hinderance of fitting into the active site
  2. tRNA incoming does not match the amino acid in the active site.
  3. Chemically related amino acids have an alternate hydrolysis site in enzyme which preferentially hydrolyzes the closely confused amino acid.

In all cases, aminoacyl-AMP is hydrolyzed.

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53
Q

What happens if the tRNA is charged with the wrong amino acid?

A

tRNA reads usual codon but inserts the wrong amino acid.

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54
Q

What is the energy source for initiation, elongation, and termination?

A

GTP (for Gripping and Going places)

ATP = Activation only

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55
Q

How does initiation occur (in prokaryotes)?

A

Initiation factors stabilize the small subunit (30S in bacteria) on the Shine-Dalgarno sequence. First tRNA carrying fMet binds the start codon, and IF-2 has GTP bound which is hydrolyzed to bring the large subunit (50S) in contact with the mRNA. fMET tRNA will be in the P site at this point.

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56
Q

What are the three sites on the ribosome?

A

APE
A = Aminoacyl site
P = Peptidyl site
E = Exit site

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57
Q

What catalyzes peptide bond formation and how does the ribosome move forward?

A

The ribozyme (23S of small subunit in prokaryotes)

Amino acid in A site attacks carbonyl in P site to form peptide bond.

Peptide always stays in P site, and the leaning of the tRNAs draws them one site forward, while moving mRNA one codon along

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58
Q

How does termination occur?

A

Release factor binds a stop codon (UGA, UAA, UAG), hydrolyzing bond in P site, causing dissociation of ribosome.

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59
Q

How do cell cycle inhibitors work? Give an example of one and what induces it?

A

They inactivate the cyclin / CDK complexes or inhibit their formation in the first place (directly / indirectly)

Example: p21 -> inactivates CDKs, which leads to hypophosphorylation and activation of Rb

-> induced by p53 when DNA damage is seen

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60
Q

Where does N-glycosylation occur and how does it occur?

A

Occurs in the Rough ER, where a preformed oligosaccharide is transferred from dolichol phosphate to an asparagine (N) side chain of the protein to be N-glycosylated

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61
Q

Where does O-glycosylation occur and how does it occur?

A

Occurs in the gOlgi, where a sugar is transferred via a threonine or serine side chain and the sugars are added on one at a time (Dol-P not involved)

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62
Q

Where are peptide neurotransmittered synthesized in neurons?

A

Nissl bodies (RER in neurons)

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63
Q

Are goblet cells rich in mucin?

A

Yes -> mucinogen is a glycoprotein

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64
Q

What organelle does drug detoxification occur in?

A

Smooth ER

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65
Q

What causes I-cell disease and what are its symptoms very similar to?

A

I = inclusion cell disease, mucolipidosis type 2

Lysosomal storage disease due to failure of Golgi to phosphorylate mannose residues -> no mannose-6-phosphate -> acid hydrolases will end up extracellularly (diagnostic in plasma)

Appears exactly like Hurler syndrome -> course facial features, corneal clouding, restricted joint movement

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66
Q

What is the function of the signal recognition particle (SRP)?

A

Recognizes the signal sequence on nascent proteins from free ribosomes and causes translational arrest. Then drags them to the rough ER, allowing synthesis to continue through translocon channel (needed for RER-destined proteins)

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67
Q

What proteins mediate the trafficking of vesicles from the rough ER to the cis-Golgi?

A

Rough ER -> cis-Golgi = anterograde = COPII
cis-Golgi -> Rough ER = retrograde = COPI

II steps forward, I step back, a terrible, terrible mnemonic since you’ll remember it wrong like this.

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68
Q

What are plasmalogens? What is their physiologic significance?

A

Phospholipids with an ether backbone, similar to phosphoglycerols, which are synthesized in the peroxisome

Significance -> important phospholipid in myelin, explains why peroxisome dysfunction leads to neurologic disease

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69
Q

Give two diseases which are caused by autosomal recessive mutation in proteins required for peroxisome biogenesis? Symptoms?

A

Neurologic symptoms -> due to accumulation of branched FA called phytanic acid

  1. Zellweger syndrome - seizures, hypotonia, hepatomegaly
  2. Refsum disease - Night blindness, ataxia, shortening of 4th toe
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70
Q

What X-linked disease is caused by a peroxisomal defect?

A

X-linked adrenoleukodystrophy, due to lack of VLCFA transporter for perioxisomes

  • > nerve demyelination = CNS problems, coma, death
  • > Important cause of adrenal sufficiency -> Addison’s disease
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71
Q

How is the proteasome involved in Parkinson’s disease? In the viral response?

A

Parkinson’s disease - Autosomal recessive form with absence of E3 ubiquitin ligase

Viral response - Viral proteins made in the cell are degraded by the proteasome, transported by TAP1/TAP2 before being expressed on MHC Class 1 in the RER.

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72
Q

What are the functions of microfilaments vs microtubules vs intermediate filaments?

A

Microfilaments - muscle contraction, cytokinesis, i.e. actin

Intermediate filaments - maintain cell structure, i.e. keratin, desmin, neurofilaments, GFAP

Microtubules - movement (cilia, flagella, axonal trafficking), cell division (mitotic spindle)

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73
Q

What directions do dynein and kinesin help transport?

A 
Kinesin = anterograde = kinetically forward = - to + 
Dynein = retrograde, towards nucleus = + to -
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74
Q

How does GTP binding interact with tubulin stability?

A

GTP-bound tubulin promotes polymerization. Hydrolysis of GTP makes GDP-tubulin, which depolymerizes. If addition of GTP-tubulin is faster than GTP hydrolysis, then the microtubule grows. Otherwise, it shrinks

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75
Q

What anchors cilia into cell membrane? What is its microtubular structure?

A

The basal body, comprised of 9 triple microtubules (versus 9 doublets + a 2 singlet arrangement of cilia).

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76
Q

How does Kartagener syndrome cause fertility dysfunction in females?

A

Lack of dynein arms -> dysfunctional fallopian tube cilia

-> increased risk of ectopic pregnancy

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77
Q

What does the Na/K ATPase do when phosphorylated / dephosphorylated during a single cycle? What drug other than digoxin inhibits this pump?

A

Phosphorylated - pumps 3Na+ out
Dephosphorylation - pump 2 K+ in

Ouabain inhibits K+ binding site, and is another cardiac glycoside

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78
Q

What is the next step after synthesis of preprocollagen? What disease is this deficient in?

A

Hydroxylation of lysine / proline -> Required vitamin C -> vitamin C deficiency will cause scurvy
-> if hydroxyproline / hydroxylysine aren’t present, the triple helical structure of procollagen does not form properly #6719

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79
Q

After hydroxylation, how does preprocollagen become procollagen? What disease is marked by failure of procollagen formation?

A

N and O glycoylation occurs in the ER and Golgi, respectively, after which hydrogen and disulfide bonds help create the triple helix, with disorganized ends of procollagen still attached

Osteogenesis imperfecta -> failure to make triple helices of 3 alpha procollagen chains due to replacement of Gly in Gly-X-Y with a bulky amino acid

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80
Q

What gets exocytosed in collagen synthesis? What happens next? What disease is caused if this cannot occur?

A

Procollagen

Next: terminal regions are cleaved to insoluble tropocollagen by procollagen peptidase

If procollagen peptidase is absent -> Ehlers-Danlos syndrome

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81
Q

How is tropocollagen converted to collagen? What enzyme is required?

A

Via staggering and covalent lysine-hydroxylysine linkages by lysyl oxidase -> lysyl oxidase requires copper

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82
Q

What two diseases are characterized by failure to crosslink tropocollagen?

A

Ehlers-Danlos (there are many variants)

Menkes disease -> impaired copper absorption and transport (required for lysyl oxidase activity)

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83
Q

What are the clinical features of Osteogenesis imperfecta and what is it commonly confused with?

A

Impaired Type 1 collagen synthesis:

BITE
Bones - multiple fractures
I = Eye -> blue sclera from choroidal veins showing (translucent connective tissue)
T = Teeth, abnormal dentin
E = Ears, hearing loss, due to abnormal ossicles

Confused with child abuse -> look for ITE signs

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84
Q

What is the usual cause of osteogenesis imperfecta?

A

Autosomal dominant disorder due to decreased production of otherwise normal Type I collagen

As we’ve said before though, it can also be caused by problems forming triple helix in procollagen due to bulky amino acids. There are many causes.

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85
Q

What are the three presentations of Ehlers-Danlos syndrome, which is most common, and which is most severe?

A

Hypermobility Type - Most common, hyperextensible skin and hypermobile joints

Classical Type - also joint and skin symptoms, with easy bruising, due to Type V collagen mutation

Vascular Type - Type III collagen defect, more severe, vascular and organ rupture, with aortic aneurysms (Ehlers-Danlos Type IV)

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86
Q

How is Menke’s disease inherited, and what are its clinical features?

A

X-linked recessive -> impaired copper absorption and transport with failed collagen production due to decreased lysyl oxidase activity (copper cofactor)

Brittle, kinky hair, growth retardation, hypotonia in boys
-> “Menkes kinky hair syndrome”

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87
Q

How does Menke’s disease relate to Wilson’s disease?

A

Menke’s disease - ATP7A defect - X-linked -> impaired Copper absorption from small intestine

Wilson’s disease - ATP7B defect - Chromosome 13 -> impaired transport of copper from hepatocytes into bile or into apoceruloplasmin, the primary carrier to other tissues.

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88
Q

What is the function of ceruloplasmin?

A
  1. Copper carrier
  2. Free radical scavenger
  3. Facilitates iron metabolism -> via copper-dependent oxidase activity.

Iron can only be carried be transferrin in the Ferric state (Fe+3). Scavenges an electron for this purpose. Also helps facilitate storage of iron in ferritin as well.
-> reason why it’s a positive acute phase protein.

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89
Q

What amino acids predominate in elastin? What spinous ligament is elastin a major part of?

A

Same as collagen -> proline, glycine, and lysine, but they are not hydroxylated

A major part of ligamentum flavum

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90
Q

Where is elastin cross-linked and what accounts for its elastic properties?

A

Cross-linked extracellularly via lysyl oxidase -> lysine residues will form desmosine / isodesmosine heterocyclic structures

Elastic due to valine-rich hydrophobic domains.

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91
Q

How does UVA contribute to wrinkles?

A

Generates free radicals which decrease collagen production -> wrinkles of aging due to decreased collagen and elastin production, allowing tonic contraction to have a greater effect (less ECM)

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92
Q

How is the subluxation of the lenses in marfinoid syndrome of homocystinuria told apart from Marfan syndrome?

A

Homocystinuria - downward (may be nasal or temporal) Marfan syndrome - upward (may be nasal or temporal)

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93
Q

What is defective in Marfan syndrome? Inheritance?

A

Autosomal dominant mutation in fibrillin1 gene on chromosome 15, which is the glycoprotein which surrounds elastin.

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94
Q

What are the relative temperatures of Denaturation, Annealing, and Elongation in PCR?

A

Denaturation ~ 95 degrees C
Annealing (of primers) ~ 55 degrees C
Elongation ~ 72 degrees C, a little hotter for the polymerase to run

95
Q

How does a general southern / northern / western blot work?

A

Run the substance of interest through a gel, then blot the gel with a membrane, and use a labelled probe to detect the substance w/ respect to its presence and how far it migrated.

96
Q

What is the mnemonic for knowing which blotting procedure is using what? And what probes are used to detect these?

A

Substances for each technique SNoW DRoP
Southern - DNA, probe = cDNA
Northern - RNA, probe = DNA or RNA
Western - Protein, probe = antibody

97
Q

How does a southwestern blot work?

A

Like it sounds, you detect a protein (DNA-binding protein / transcription factor, western portion) using an oligonucleotide probe of DNA which it would normally bind (the southern portion)

98
Q

What is used to confirm an HIV diagnosis after ELISA (the more sensitive test, but can give false +)?

A

Checking if patient has antibodies to protein components of HIV virus, via Western blot. Put the patient’s serum on Western blot of HIV proteins, and use a probe to detect patient’s antibodies to the relevant components antigens.

99
Q

How does flow cytometry work and when is it typically used?

A

Can detect protein antigens on cells (i.e. CD4 and CD3 markers) via tagging those cells with fluorescent antibodies specific to those antigens, and measuring the fluorescent properties of cells in a sample one at a time -> able to get an exact count of CD4+ cells or CD3+ cells in a sample -> commonly used in hematalogic abnormalities

100
Q

What are the applications of microarrays?

A

They are plentiful -> profiling gene expression of thousands of genes simultaneously, detecting single nucleotide polymorphisms (SNPs) and copy number variants as well (array-CGH). Done by attaching nucleic acid probes onto a chip and measuring amount of hybridization.

101
Q

How would a 22q11 deletion appear on a FISH?

A

Probe would fluoresce on the one normal copy of chromosome 22, but would be absent on the second chromosome (where the microdeletion occurred)

102
Q

What is a direct vs indirect ELISA?

A

Direct ELISA - primary antibody has the enzyme attached. Primary antibody may be directed against a specific antigen (i.e. HBsAg) or an antibody (I.e. anti-HBs)

Indirect ELISA - primary antibody binds the specific antigen. Secondary antibody binds the primary antibody. Secondary antibody has the enzyme attached.

Enzyme is used for a detectable color change.

103
Q

What phase of the cell cycle is karyotyping done at?

A

Cells are arrested at metaphase via application of colchicine.

104
Q

How is cloning of a gene generally done?

A

Eukaryotic mRNA is isolated and then exposed to reverse transcriptase to get cDNA without any introns -> can be inserted into a plasmid with an antibiotic marker to confirm the plasmid was properly uptaken.

105
Q

What is the usage of a Cre-lox system?

A

Can manipulate genes at specific development timepoints via a Cre recombinase, which is easily controlled via inserting specific Lox sequences around the gene of interest.
-> good for studying a gene which is likely to cause death if globally expressed, so basically you can control when the gene is expressed during embryonic life by determine when the Cre recombinase is expressed

106
Q

What is a dominant negative mutation? Give an example.

A

A nonfunctional protein interferes with the function of wild type
i.e. a malfunctioning transcription factor prevents the binding of the working, wild type transcription factor

107
Q

What is McCune-Albright Syndrome a clinical example of in genetics? Give the clinical triad which accompanies it.

A

Somatic mosaicism -> post-zygotic mutation in G-protein signalling, would be lethal if occurring in whole body.
Similar disruption as in pseudohypoparathyroidism, which causes Albright Hereditary Osteodystrophy.

Triad:

  1. Polyostotic fibrous dysplasias
  2. Cafe-au-lait spots, often unilateral (mosaicism)
  3. Endocrinopathy -> usually precocious puberty due to increased E2 or T secretion
108
Q

What is locus vs allelic heterogeneity?

A

Locus heterogeneity - mutations at different loci produce a similar phenotype (i.e. multiple genes can cause Ehlers-Danlos syndrome)

Allelic heterogeneity - Different mutations of the same locus can produce the same phenotype (i.e. Marfan syndrome, Beta-thalassemia -> mutation can be in splice sites or promoter sequences)

109
Q

In what stage of meiosis does heterodisomy and isodisomy occur via uniparental disomy?

A 
heterodIsomy = Meiosis I 
IsodIsomy = Meiosis II

If you think about why, having a nondisjunction in meiosis II means that the sister chromatids are inherited together. In Meiosis I, it would mean that homologous chromosomes are inherited together then segregated in meiosis II.

110
Q

When should you really be considering UPD?

A

When a child has an autosomal recessive condition and only one parent was a carrier

111
Q

Calculate the carrier rate in females of an X-linked recessive disease with a 1/5000 rate in males. Disease rate in females?

A

1/5000 = q, since they only have one chromosome.

2pq = carrier rate 
2(~1)(1/5000) = 1/2500

Disease rate = (1/5000)^2

112
Q

Does 15q11 maternal uniparental disomy cause Prader-Willi or Angelman syndrome?

A

Causes Prader-Willi

Think “Padre-Willi” -> the paternal genes are what are expressed, and must be mutated or deleted for this condition occur.
-> Since the gene is normally maternally imprinted, maternal UPD will lead to no paternal pattern of gene expression, resulting in disease

113
Q

What gene must be lost to cause Angelman syndrome?

A

15q11 maternal genes are lost, can happen in paternal UPD since the gene is paternally imprinted.

114
Q

What are the symptoms of Prader-Willi syndrome?

A

Ghrelin defect -> hyperphagia, obesity, intellectual disability, hypogonadism, hypotonia (like Down syndrome)

115
Q

What are the symptoms of Angelman syndrome?

A

Happy puppet - inappropriate laughter and need to be held up due to seizures and ataxia

116
Q

What causes hypophosphatemic rickets and how is it inherited?

A

X-linked dominant
Caused by increased phosphate wasting at proximal tubule due to lack of PHEX protein which degrades FGF23 -> increased FGF23-mediated phosphate wasting

Results in rickets-like presentation

117
Q

Give another example of a condition affecting the kidney which is X-linked dominant?

A

Alport syndrome -> due to a mutation in Type IV collagen
-> due to a structural protein. Explains why it’s dominant

Can’t see, can’t pee (glomerulonephritis), can’t hear a bee

118
Q

What is the inheritance pattern of Sturge-Weber syndrome?

A

Non-inherited, sporadic mutation of neural crest derivatives due to somatic mosiacism -> activating mutation in one copy of GNAQ gene

119
Q

What is the inheritence pattern of Ocular albinism?

A

X-linked

You would know all the other ones

120
Q

What is the newborn screening test for cystic fibrosis (CF)?

A

Immunoreactive trypsinogen -> trypsinogen in the blood.

Trypsinogen will be elevated in the serum of CF patients since excretory ducts are blocked by thick mucus.

121
Q

Why does subfertility happen in women with CF?

A

Abnormally thick cervical mucus

122
Q

What nasal finding is common in children with cystic fibrosis?

A

Nasal polyps - Caused by repeated bouts of edema / inflammation due to rhinitis

123
Q

What will venous lactate levels after exercise testing show in glycogenoses vs mitochondrial disease?

A

Glycogenoses, except Pompe’s disease -> deceased rise in blood lactate, as all available glucose is fully used, and no more can be broken down from glycogen

Mitochondrial disease - elevated blood lactate, as problems with oxidative phosphorylation force all energy generation via anaerobic glycolysis

124
Q

What are the clinical features of Duchenne? Are there any CNS symptoms?

A

Patients present by age 5 with waddling gait due to pelvic girdle muscle weakness -> lordosis. Calf muscles shorten with pseudohypertrophy. Become wheelchair dependent by age 12. Cognitive impairment is common as dystrophin is needed for neuronal maintenance.

Death occurs due to respiratory compromise / infection / dilated cardiomyopathy

125
Q

What are the clinical features of Becker? Are there any CNS symptoms?

A

Adolescent onset -> most not wheelchair bound until age 16. No cognitive deficits, and less tendency to form contractures of muscle since breakdown is less severe.

126
Q

What is the most common form of muscular dystrophy in adults? What causes it?

A

Myotonic dystrophy type 1

- expanded CTG repeat in DMPK gene

127
Q

What are the relevant symptoms of myotonic dystrophy type 1?

A

CTG - cataracts, toupee (frontal balding), gonadal atrophy

Myotonia - inability to relax muscles after vigorous effort - i.e. handshake
Muscular dystrophy
EKG changes - heart block leads to arrhythmias

128
Q

How do patients with myotonic dystrophy look? What is a common treatment required in this condition?

A

They have a “hatchet face” appearance -> muscle loss in temporal face + frontal balding makes face look elongated

Need for pacemaker is common -> PR interval elongation progresses to heartblock

129
Q

What causes fragile X syndrome? When is someone at risk?

A

> 200 trinucleotide repeats CGG in the FMR1 gene. This will cause stopping of translation (intronic region), due to gene hypermethylation.

> 55 repeats is considered “premutation”, and there is repeat instability when this is maternally transmitted.

130
Q

Is fragile X dominant or recessive? What heart condition is associated?

A

X-linked dominant

Associated with mitral valve prolapse

131
Q

What are the most important clinical signs of Down syndrome?

A
  1. Hypotonia (at birth) with IUGR**
  2. Single transverse palmar crease (only 5% chance in a normal person)
  3. Oblique palpebral fissues
  4. Clinodactyly - short, curved 5th finger
  5. Intellectual disability
  6. Congenital heart disease - AV septal defect
  7. Brushfield spots - in the iris
  8. Hirschsprung disease
  9. Increased risk of Alzheimer’s, ALL (>5), AML (<5)
132
Q

What is used for first trimester chromosomal abnormality screening? What would be found in abnormal?

A

PaPP-A - Pregnancy-associated plasma protein A - decreased in all chromosomal abnormalities

hCG - human chorionic gonadotropin - DECREASED in all chromosomal abnormalities, but INCREASED in Down’s syndrome

Nuchal translucency - thickness behind fetus’ neck - increased in all chromosomal abnormalities

133
Q

What is MSAFP and when is it increased vs decreased?

A

Maternal Serum AlphaFeto Protein

Increased in Neural Tube Defects (along with acetylcholinesterase)
Decreased in Down Syndrome

134
Q

What are typical quad test findings for a Down syndrome baby?

A

MSAFP - low
hCG - high
estriol - low (fetal-placenta unit not well intact)
inhibin A - high (produced in placenta)

135
Q

What are the ultrasound findings for a baby with Down syndrome?

A
  1. Nuchal translucency is increased (skin of neck separation from underlying tissue)
  2. Hypoplastic Nasal bone - reduced in length or absent
  3. AV cardiac defect
  4. Duodenal atresia - DOUBLE BUBBLE sign
136
Q

What is the mneumonic for Edward syndrome?

A

PRINCE Edward (trisomy 18) = election age

P = prominent occiput
R = Rocker-bottom feet
I = intellectual disability
N = nondisjunction
C = Clenched fists (overlapping fingers)
E = Low-set ears

Remember also microcephaly with micrognathia and congenital heart disease

137
Q

What is the mneumonic for Patau syndrome? What trisomy is it?

A

Patau = Trisomy 13 = Puberty

6 P’s:

  1. cleft Palate / liP
  2. holoProsencephaly
  3. Polydactyly
  4. cutis aPlasia - missing skin on scalp
  5. Polycystic kidney
  6. microPhthalmia w/ possible proboscis (due to holoprosencephaly)
  7. omPhalocele
138
Q

What are the clinical features of Velocardiofacial syndrome?

A

One possible 22q11 syndrome

Velopharyngeal incompetence = cleft palate (not cleft lip)

Cardio = cardiac defects

Facial = facial dysmorphism, prominent nose, upslanted palpebral fissues, small, abnormal ears.

139
Q

What causes Williams syndrome and what are the characteristic features?

A

Chromosome 7 microdeletion, including elastin gene -> same chromosome as CF

Elastin problems: Elfin faces, supravalvular aortic stenosis
Hypercalcemia (opposite of DiGeorge)
Extreme friendliness to strangers (remember Dr. Sandall telling me about this)

140
Q

What is the 5p microdeletion syndrome and its clinical signs/symptoms?

A

Cri du chat = cry of the cat

High-pitching meowing or crying, microcephaly, intellectual disability, ventricular septal defect (VSD)

141
Q

What two mechanisms contribute to pancytopenia in Gaucher’s disease?

A
  1. Splenic enlargement with crumpled tissue paper macrophages -> increased phagocytosis / hypersplenism
  2. Bone marrow infiltration with macrophages -> also contributes to compression of blood supply and avascular necrosis of femur
142
Q

What is the medical use of mineral oil and its possible major side effect?

A

Bulk-forming laxative

May cause a fat-soluble vitamin deficiency by holding onto fat-soluble vitamins in the GI tract

143
Q

What vitamin deficiency causes Bitot spots?

A

Vitamin A - due to keratinization of conjunctival epithelium

144
Q

What are the normal ways in which vitamin A exerts its effect, and what tissues are highly dependent in light of this?

A
  1. It binds nuclear hormone DNA-binding receptors (RAR / RXR heterodimers) to influence gene expression
    - > most critical for differentiation of mucus-secreting epithelium
  2. Also is a component of Rhodopsin which is needed for seeing in low light
  3. Immune system -> increased susceptibility to infection
145
Q

What three major enzymes is thiamine (B1) a cofactor for? What other function does it have?

A

Think ATP
A: alpha-ketoglutarate dehydrogenase (TCA cycle)
T: Transketolase - pentose phosphate pathway
P: pyruvate dehydrogenase (along with flavin and NAD, 1-2-3)

+ Branched chain alpha ketoacid dehydrogenase

Also plays a role in neural conditions (WK syndrome)

146
Q

What are the two forms of B1 deficiency that is not WK syndrome and what causes each of them?

A

Dry beriberi - due to impaired glucose metabolism -> peripheral polyneuropathy with myelin degeneration and symmetrical numbness / muscle wasting

Wet beriberi - abnormal ATP synthesis affects cardiac function -> peripheral vasodilation and high output myocardial failure (dilated cardiomyopathy) causing peripheral edema

147
Q

How is B1 deficiency definitively diagnosed?

A

Increased RBC transketolase activity following B1 administration.

148
Q

What types of reactions and B2, B3, and B6 used for?

A

B2 - riboflavin: Prosthetic molecular group in flavoproteins (FMN, FAD) -> i.e. succinate dehydrogenase

B3 - niacin: Component of NAD / NADP

B6 - pyridoxine: cofactor for transamination / decarboxylation reactions, glycogen synthesis, and synthesis of melanin / monoamine neurotransmitters, and heme synthesis (ALA synthase)

149
Q

What are the features of riboflavin deficiency?

A

2 C’s of B2
1. Cheilosis - cracking at side of mouth
2. Corneal vascularization
+
3. Glossitis - cyanotic color of tongue (cannot turn over the keratinized epithelium of tongue fast enough)
4. Dermatitis - greasy, scaling skin of face / genitalia

-> last two are common features of all B vitamin deficiencies

150
Q

What syndrome is caused by B3 deficiency?

A 
3 D's of B3 (niacin)
Pellagra:
Diarrhea - GI epithelium
Dermatitis - skin epithelium
Dementia - nervous system

Dermatitis - especially affects sun-exposed areas (“Casal necklace” and hyperpigmentation of sun-exposed limbs)

151
Q

What are possible causes of niacin deficiency and how is it made?

A

Made from tryptophan, requires cofactors B2 and B6 for synthesis

  1. Malignant carcinoid syndrome - decreased tryptophan levels due to usage to make serotonin
  2. Isoniazid - decreases B6 levels
  3. Hartnup disease
152
Q

What causes Hartnup disease and what symptoms will precipitate?

A

Autosomal recessive disorder causing deficiency of neutral amino acid reuptake in kidney proximal tubules and enterocytes. -> aminoaciduria and decreased gut absorption -> manifests primarily as tryptophan deficiency leading to pellagra-like symptoms

  • > also causes cerebellar atxia
  • > treat with high protein diet and nicotinic acid (niacin)
153
Q

What is vitamin B5 an essential component of?

A

Coenzyme A
-> needed for acyl transfers and fatty acid synthesis

Deficiency is rare

154
Q

What does B6 deficiency cause?

A

Neuropathy / hyperirritability / convulsions due to loss of neurotransmitters / function in energy storage

Sideroblastic anemia (ALA synthase)

Also same symptoms as B2 deficiency: Dermatitis, cheilosis, glossitis

155
Q

What cofactor does glycogen phosphorylase use?

A

B6!

156
Q

What is the function of methylmalonyl-CoA mutase?

A

Converts methylmalonic acid to succinyl-COA
-> requires B12

remember that methylmalonic acid is made from propionyl-CoA (odd chain FA pathway) via help of biotin for a carboxylation rxn

157
Q

Why is vitamin B12 dependent on folate?

A

B12-dependent synthesis of methionine from homocysteine (methionine synthase) requires a methyl from methyl-tetrahydrofolate

-> note that methionine deficiency can cause secondary folate deficiency (methyl trap theory)

158
Q

What is folate specifically required for?

A

Synthesis of purines and methylation of dUMP to dTMP

159
Q

What happens to homocysteine levels in B9 vs B12 deficiency?

A

Levels increase in both deficiencies

160
Q

What are the two substrates of ALA synthase?

A

Glycine + Succinyl-CoA

-> this is the B6-dependent reaction

161
Q

What are the two main adverse effects possible with vitamin C overdose?

A
  1. Calcium oxalate nephrolithiasis - vitamin C is broken down and excreted as oxalic acid, can cause kidney stones
  2. Iron toxicity - in those predisposed, since it helps reduce iron to its ferric form for better absorption.
162
Q

What is Moller-Barlow disease?

A

Scurvy in children leading to increased cartilage and bowing, like Rickets, due to DECREASED osteoid production

163
Q

What are the deficiency syndromes involving vitamin E? Include one adult and one neonatal syndrome.

A
  1. Degeneration of long peripheral axons, dorsal column, and spinocerebellar myelin degeneration (neuropathy appearing similar to B12 deficiency)
  2. Hemolysis / anemia -> especially infants exposed to oxidative stress of oxygen therapy as newborns
    - > also associated with acanthocytosis. Makes sense because vitamin E deficiency is also seen in abetalipoproteinemia
164
Q

What can zinc deficiency cause?

A

Hypogonadism and short stature, impaired immune response (zinf fingers motif), delayed wound healing (needed for collagenase for granulation tissue), hypogeusia (impaired taste acuity), CNS damage, and baldness

-> acrodermatitis enteropathica

165
Q

How does kwashiorkor occur / what are the physical manifestations?

A

Adequate caloric intake with deficient protein intake -> visceral compartment wasting

Physical - loss of endogenous protein synthesis results in:
Edema - loss of albumin
Hepatomegaly - fatty change due to apolipoprotein synthesis decrease

166
Q

How does the metabolic state in kwashiorkor contribute to its more fulminant course? What induces further cellular damage?

A

Induction of a HYPERmetabolic state -> nonphysiologic adaption to starving -> further cellular catabolism of low fuel stores

Often another nutritional deficiency (vitamin E deficiency) is present with infection -> oxidative cellular damage is common

167
Q

What other symptoms are present in kwashiorkor? How does this present in hospitalized patients?

A

Loss of appetite (patient feels ill), hair / skin changes are present (due to oxidative damage) including dermatosis, and mental changes

-> impaired wound healing in hospitalized patients is common

168
Q

Why does alcoholism cause fasting hypoglycemia?

A

Pushes oxaloacetate to malate due to increased NADH levels. -> need oxaloacetate from pyruvate via pyruvate carboxylase

Also, DHAP is pushed to glycerol 3 phosphate from increased NADH levels.

169
Q

Why does alcoholism cause ketoacidosis and hepatosteatosis longterm?

A

Increased NADH levels disfavor TCA production of NADH -> increased usage of acetyl-CoA for ketogenesis and lipogenesis

170
Q

What two enzymes does citrate activate?

A
  1. Acetyl-CoA carboxylase -> rate-limiting step of fatty acid synthesis
  2. Fructose-1,6-bisphosphatase -> rate limiting step of gluconeogenesis
    - > Indicates high energy charge, want to build glucose + fatty acids
171
Q

What is the rate limiting step of pyrimidine synthesis and what upregulates / downregulates it?

A

CPS 2

  • upregulated by ATP (have alot of charge, want to make pyrimidines to match purines) and PRPP (have sugar to hold)
  • downregulated by UTP -> excess pyrimidines
172
Q

What is the rate limiting step of purine synthesis and what upregulates / downregulates it?

A

Glutamine-PRPP amidotranserase

Downregulated by all purines -> IMP (deaminated adenosine), AMP, GMP

173
Q

What makes N-acetylglutamate and what does it do?

A

NAG synthesis -> activated by high arginine (high nitrogen status)

Acetyl-CoA + Glutamate -> N-acetylglutamate

Upregulates CPS1

174
Q

What is the rate-limiting step of fatty acid oxidation?

A

Carnitine acyltransferase I -> the speed at which you can get fatty acids into the mitochondria

Downregulated by malonyl-CoA

175
Q

What effect does thyroxine have on HMG-CoA reductase?

A

Despite the fact that hyperthyroidism causes hypocholesterolemia, it increases its activity. You can think about this as increased cholesterol production and turnover in general -> other mediators such as peripheral lipoprotein usage account for its hypocholesterolemia.

176
Q

Where does ketogenesis occur and what is the rate-limiting step? How does it occur?What is the precursor to each of these processes?

A

Ketogenesis occurs in mitochondria

-> Acetoacetyl-CoA -> HMG-CoA via HMG CoA synthase is rate-limiting

HMG-CoA lyase cleaves HMG-CoA to Acetyl-CoA + Acetoacetate, the principle ketone body which is sometimes reduced to B-hydroxybutyrate

177
Q

Why can’t the liver use ketone bodies?

A

It lacks thiophorase, which is required to add a CoA group to Acetoacetate to make Acetoacetyl-CoA so it is usable for energy
-> two molecules of acetyl-CoA can be liberated to feed the TCA cycle in these conditions

178
Q

How is cholesterol synthesis initiated?

A

Still needs Acetoacetyl-CoA -> HMG-CoA via HMG-CoA synthase in the mitochondria, but HMG-CoA is exported in the cytoplasm and made into mevalonate via HMG-CoA reductase, the rate-limiting step which is inhibited by statins

179
Q

How much ATP is made via a molecule of glucose and why does it depend on which pathway it uses (malate-aspartate vs Glycerol-3-phosphate pathway)?

A

32 ATP if via malate-aspartate shuttle
-> shuttle only available in liver / muscle

30 ATP if via Glycerol-3-phosphate dehydrogenase electron shuttle
-> only available in skeletal muscle

The malate aspartate shuttle can bring NADH from the cytosol to the mitochondria and use complex one, whereas G3PDH bypasses complex one -> 1 less ATP per NADH formed from glycolysis.

Remember that two ATP are formed directly from anaerobic glycolysis.

180
Q

What effect does arsenic have on glycolysis?

A
  1. Results in no net ATP production, since it leads to the bypassing of glyceraldehyde-3-phosphate -> 3-phosphoglycerate
  2. Binds lipoic acid, inhibits PDH, and alpha-ketoglutarate DH
181
Q

Why does Fructose-6-phosphate inhibit glucokinase?

A

Presence of high levels of Fructose-6-phosphate in the cell rather than Glucose-1-phosphate indicates the cell is trying to do Gluconeogenesis, not Glycolysis

Thus, we don’t want glucokinase to be holding Glucose-6-phosphate in the cell if gluconeogenesis is occurring in the tissues.

This is in contrast to Glucose-6-phosphate directly inhibiting hexokinase, which is present in muscle (aka you don’t want to have glucose in muscle than you need)

182
Q

What amino acid acts as a downstream effector to inhibit pyruvate kinase (PEP -> pyruvate)?

A

Alanine, since we don’t want to make more pyruvate if we already have so much that we’re oversaturated with alanine

183
Q

What two enzymes are very structurally and functionally similar to pyruvate dehydrogenase?

A
  1. Alpha-ketoglutarate DH (TCA cycle)

2. Branched-chain amino acid DH

184
Q

Where is CO2 lost starting from pyruvate?

A

Pyruvate dehydrogenase - minus CO2, plus NADH
Isocitrate DH - minus CO2, plus NADH
alpha-ketoglutarate DH - minus CO2, plus NADH

185
Q

What cofactors are used by alanine aminotransferase?

A

B6 only - allows amino groups to be carried to the liver from muscle

186
Q

What’s the uncoupler in brown fat called?

A

Thermogenin

187
Q

What are the four irreversible enzymes of gluconeogenesis?

A

Pathway Produces Fresh Glucose

Pyruvate carboxylase
PEP carboxykinase
Fructose-1,6-bisphosphatase
Glucose-6-phosphatase

188
Q

Why can’t muscles do gluconeogenesis?

A

It lacks glucose-6-phosphatase -> cannot release glucose once it’s form.

Can occur in kidney and small intestine tho

189
Q

Can fatty acids be used for gluconeogenesis?

A

Only odd-chain ones, which will produce propionyl-CoA as their final product -> can enter TCA cycle as succinyl-CoA and serve as a glucose source (requires B12 with a methylmalonyl-CoA intermediate)

Even chain ones won’t produce any propionyl-CoA

Glycerol component of the triglycerides is also gluconeogenic substrate -> via glycerol kinase

190
Q

What causes essential fructosuria and what are the symptoms?

A

Defect in fructokinase, which normally makes F1P

No symptoms due to fructose not being trapped in cells
Fructose appears in blood / urine

-> hexokinase phosphorylates fructose directly in these individuals (does not happen normally)

191
Q

What causes fructose intolerance? What accumulates?

A

Remember FAB GUT

Deficiency of aldolase B, which converted Fructose-1-phosphate to DHAP and glyceraldehyde (vs aldolase A which converts F-1,6-BP to DHAP and glyceraldehyde-3-P)

Accumulates fructose-1-phosphate

192
Q

What causes onset of symptoms of fructose intolerance? What are they?

A

High fructose or sucrose (fructose + glucose) foods, appearing when food is introduced in diet -> treatment is to avoid

Due to usage of phosphate in cell, impairs gluconeogenesis -> hypoglycemia, vomiting.

Jaundice / cirrhosis from fructose buildup in liver.

193
Q

How do Galactose vs Fructose conditions differ in terms of time of onset and severity?

A

Galactose buildup -> more severe, due to alcohol pathway
Galactose conditions -> appear sooner, because lactose is in breast milk.

Fructose is not until baby is weaned onto real foods later.

194
Q

What is the cause of classic galactosemia? What are the main presenting symptoms? Which one is shared with galactokinase deficiency?

A

Typically Galactose-1-phosphate uridyltransferase deficiency

Symptoms: 
E. coli sepsis 
Hepatomegaly 
Failure to thrive 
Infantile cataracts (Also shared with galactokinase deficiency)
195
Q

Why do infantile cataracts occur in galactokinase deficiency?

A

Galactose is converted to galactilol via aldose reductase, which accumulates in lens of the eye

196
Q

What tissues are most susceptible to sorbitol accumulation and why?

A

Tissues which have an aldose reductase to make sorbitol, but not sorbitol dehydrogenase to make sorbitol -> fructose are susceptible

These include: Lens, Retina, Kidneys, Schwann cells (LuRKS)

-> also get free radical damage anyway as NADPH is ultimately made into NADH from the two enzyme pathway -> more ROS moved towards ETC

Also sorbitol is bad because it’s osmotically active

197
Q

What are two acute treatments for hyperammonemia (not lactulose + rifaximin)?

A

benzoate + phenylbutyrate -> forming products which are renally excreted

198
Q

What is the only urea cycle enzyme defect which is not associated with hyperammonemia?

A

Arginase deficiency

199
Q

What is the Cahill cycle?

A

Way of disposing of nitrogen, pyruvate accepts amino group to make alanine in muscle. Alanine transported to liver for urea cycle, with pyruvate made back to glucose for shipment back to muscle.

This is similar to the Cori cycle, in which lactate release by muscles into blood undergoes gluconeogenesis in the liver and repackaging

200
Q

What is melatonin formed from?

A

Tryptophan (turkey makes you tired), downstream from serotonin synthesis

201
Q

What’s the rate-limiting step in dopamine synthesis and what cofactor is needed?

A

Tyrosine hydroxylase

Requires BH4 as a cofactor (as does phenylalanine hydroxylase, upstream)

202
Q

What hormone is required for upregulation of phenylethanolamine-N-methyltransferase?

A

Cortisol! And that’s good because it’s produced in the zona fascicula and blood vessels carry high concentrations of it to the adrenal medulla when ACTH is high

203
Q

What are the clinical features of PKU and why?

A

Severe intellectual disability, seizures, eczema, fair skin and hair color. This is because Tyrosine is needed to make T3/T4, NE / E / Dopamine, and melanin pigment

204
Q

How is PKU detected in newborns?

A

Phenylpyruvic acid in newborn urine (urinary excretion by minor pathways)

205
Q

What condition does congenital deficiency of homogentisate oxidase cause? How is it inherited?

A

Alkaptonuria -> accumulation of homogentisic acid in tissue, in conversion of tyrosine to fumurate

Autosomal recessive - loss of homogentistate dioxygenase

206
Q

What are the three enzymatic causes of homocystinuria?

A
  1. Cystathione synthase deficiency
  2. Decreased affinity of cystathione synthase for B6 cofactor (treat by increasing intake)
  3. Methionine synthase deficiency - supplement methionine
207
Q

What causes Cystinuria and what is its primary complication?

A

Defect in renal PCT amino acid transporter of COLA -> Cystine, ornithine, lysine, arginine

Excess cystine in urine (2 cysteines connected by disulfide bond) forms HEXAGONAL cystine stones.

208
Q

What test is diagnostic of cystinuria?

A

Cyanide-nitroprusside test

209
Q

How does the debranching enzyme work?

A

Once you reach a “limit dextran” with 4 sugars left on a branch

  1. Glucosyltransferase domain moves 3 of the remaining 4 sugars on a branch to the adjacent (mainstem) branch
  2. The last sugar has an alpha1-6 bond, which is cleaved by glucosidase domain of the debranching enzyme

-> this enzyme is defective in Cori disease

210
Q

What are the clinical features of von Gierke disease?

A

Hepatomegaly and renomegaly (from glycogen accumulation)

Severe fasting hypoglycemia

Increased blood lactate -> glucose accumulates and is pushed to lactate

Marked lipidemia / ketosis, can cause eruptive xanthomas in face and buttocks

211
Q

What are the clinical findings in Pompe disease?

A

Cardiomegaly is major issue, along with hepatomegaly, hypotonia, and muscle wasting. Progressive hypertrophic cardiomyopathy.

-> death occurs early due to heart failure

212
Q

What type of disease is McArdle and why? What enzyme is missing?

A

Myopathic GSD

  • Glycogen phosphorylase in (M)uscle is absent, which breaks off alpha 1-4 bonds until down to the last 4 sugars on the branch
  • Only affects muscle because the liver glycogen phosphorylase is present
  • glycogen accumulates in muscle cells which cannot be broken down into glucose-1-phosphate
213
Q

How will patients present clinically with McArdle?

A

Muscle cramps due to lack of energy in muscles working. There will be no rise in blood lactate with exercise (no glucose available)

Leads to Myoglobinuria -> use of protein as energy source
-> possible rhabdomyolysis and acute renal failure
-> will have a second burst of energy during exercise due to increased blood flow and increased glucose delivery to muscles
(liver glycogen phosphorylase is intact)

214
Q

Why is there a cherry-red spot in GM2 gangliosidoses? What disease does GM2 ganglioside accumulate it?

A

Because the macula is the lowest concentration of neurons -> has the lowest amount of glycosphingolipids accumulating as a result of enzyme deficiencies

Accumulates in Tay-Sachs disease - deficiency of Hexosaminidase A

215
Q

What enzyme is defective in Fabry disease and what substrate accumulates?

A

alpha-galactosidase A

-> accumulates Gb3 or ceramide trihexose

216
Q

What is the triad of early symptoms to remember as early manifestations of Fabry disease?

A
  1. Angiokeratomas - spotty skin lesions (red, punctate) due to dilation of capillaries
  2. Hypohidrosis - decreased sweating ability
  3. Acroparesthesia - peripheral neuropathy causing pain in hands / feet
217
Q

What are the late symptoms of Fabry disease?

A
  1. Progressive renal failure (podocytes accumulate Gb3, leading to proteinuria)
  2. Cardiovascular disease
  3. Cerebrovascular disease (strokes)
    - > vascular damage.
218
Q

What are the common features of Hurler syndrome?

A

Airway destruction, dwarfing, coarse facial features, buildup of GAGs in heart, hepatosplenomegaly

  • *corneal clouding**
  • *Alder-Reilly anomaly** - azurophilic granules in neutrophils / monocytes
219
Q

Where does fatty acid synthesis occur?

A
  1. Liver
  2. Adipose tissue
  3. Lactating mammary glands (makes medium chain fatty acids for the baby)
220
Q

Why does ketoacidosis occur in both alcoholism and diabetes?

A

Alcoholism - excess NADH shunts oxaloacetate to malate DKA - oxaloacetate is depleted for gluconeogenesis -> acetyl-CoA builds up from inability to use TCA cycle -> production of ketone bodies

221
Q

How soon into starvation are glycogen stores exhausted? Why does protein and not just fat need to be broken down during starvation?

A

About 1 day

Even though most of the body can run on ketone bodies, protein needs to be broken down for glucose use by RBCs -> lack mitochondria and thus cannot use ketones

222
Q

What is the function of LCAT? What is needed to active it?

A

LCAT = Lecithin cholesterol acyltransferase
Esterifies plasma cholesterol released from tissues so they can be uptaken by HDL (so they will be hydrophobic enough)

Needs Lipoprotein A-1 to activate it.
A1 = Activates

Apo-AI is considered the principle protein in HDL

223
Q

What is the function of Apolipoprotein C-II and what particles is it present on?

A

VLDL, HDL, Chylomicrons -> “C”ofactor for “C”leavage -> required for activity of vascular endothelial lipoprotein lipase (LPL) to free fatty acids from VLDL / chylomicrons for tissue uptake

224
Q

What is the function of B100?

A

Packaged with VLDL by liver, it will also be present in IDL and LDL.

Function: Binds the LDL receptor on liver (since no Apo-E is present). The liver scavenger receptor is the apo B/E receptor

225
Q

What is the function of hepatic triglyceride lipase?

A

Degrades the remaining triglycerides in chylomicrons -> chlyomicron remnants, as well as IDL -> LDL

226
Q

What are the clinical features of homozygous FH?

A

Same features as heterozygous form (xanthelasmas, xanthomas, arcus corneae) +

  1. Early life CHD + hypercholesterolemia (cholesterol 700+)
  2. Early MI’s
  3. Plantar xanthomas! unique for homozyogous -> knees, elbows, areas of skin trauma
227
Q

What is familial combined hyperlipidemia?

A

An autosomal dominant inheritance of moderate elevations of triglycerides and total cholesterol
-> unknown genetic cause, but is demonstrable clinically

228
Q

What are the clinical features of familial combined hyperlipidemia?

A

Premature CHD w/ family history of premature CHD

Xanthomas and xanthelasmas will be ABSENT

-> associated with obesity, glucose intolerance, diabetes

229
Q

What is the pathognomonic feature of dysbetalipoproteinemia?

A

Palmar xanthomas
-> think of xanthomas which make an E shape on the creases of the palms
ApoE = 3 (looks like roman numeral 3), and E on the palms

230
Q

What other problems will dysbetalipoproteinemia have other than palmar xanthomas?

A

Premature atherosclerosis (greatly increased cholesterol) and tuberous xanthomas (large bullous vesicles on elbows due to increased triglycerides)

231
Q

Is there increased risk of atherosclerosis in hyperchylomicronemia (Type I familial)? What can be seen in the supernatant of the blood?

A

The supernatant is creamy due to increased triglycerides

Atherosclerosis risk is NOT increased

232
Q

How does insulin affect lipoprotein lipase?

A

Stimualtes it -> in order for adipocytes to take up free fatty acids

233
Q

How does alcohol affect HDL levels?

A

It actually increases it (Similar to estrogens), but not good since triglycerides will also be incresaed.

234
Q

Why do elevated triglycerides cause acute pancreatitis?

A

Chylomicrons obstruct capillaries and lead to local activation of LPL -> fatty acids become cytotoxic to pancreatic exocrine cells and induce pancreatic inflammation

Step 1 Miscellanous (40 decks)

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