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Biochemistry Flashcards

1
Q

Chromatin structure

A

DNA loops twice around the histone OCTAMER to form a nucleosome (BEADS ON A STRING)

H1 histone binds to linker DNA

Euchromatin = less condensed
Heterochromatin = condensed  (more methylation and less acetylation)
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2
Q

Charge of DNA

A

(+) due to lysine and arginine “its a (+) experience at dLA”

(-) Phosphate groups

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3
Q

DNA methylation

Histone Methylation

Histone acetylation

A

DNA is methylated in imprinting ( DNA/histone epigenetic process that silences an allele without changing the DNA sequence)

Methylation of a gene promoter (CpG islands) typically represses gene transcription.

Histone methylation - reversible transcriptional suppression. But can also activate depending on where the methyl group is.

Histone acetylation - relaxes DNA coiling and active DNA

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4
Q

Nucleotides

A

note: Nucleosides lack a phosphate but a nucleotide has a phosphate thats linked by a phosphodiester bond 3’-5’

more G-C bonds = higher melting temp

PURe As 2 Gold Rings - purines are adenine and guanine which has 2 rings

CUT 1 slice of Py - pyrimidines are cytosine, uracil, and thymine which have 1 ring

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5
Q

Deamination products of nucleotides

A

Deamination is the process of losing a amino group

Cytosine –> uracil
Adenine –> hypoxanthine
Guanine –> xanthine
5-methylcytosine –> thymine

methylation of uracil makes thymine

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6
Q

AA necessary for purine synthesis

A

Cats purr until they GAG (glycine, aspartate,glutamine)

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7
Q

Purine synthesis

A

Ribose 5-P —– phosphoribosyl pyrophosphate (PRPP) synthase —> PRPP —> IMP –> AMP or GMP

de novo requires aspartate, glycine, glutamine, and THF

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8
Q

Pyrimidine base production

A

Requires aspartate
CPS= carbamoyl phosphate synthetase

CPS1 = m1tochondria (ureal cycle). Deficiency causes hyperammonemia)
CPS2=cyTWOsol

Glutamine + CO2 —CPS2 and 2ATP–>carbamoyl phosphate

Carbamoyl phosphate + aspartate –> orotic acid

orotic acid + PRPP –> UMP (step is impaired in orotic aciduria)

UMP –> UDP –> dUDP OR CTP

UDP –ribonucleotide reductase —> dUDP –> dUMP –thymidylate synthase and THF —> dTMP + DHF

DHF is replenished via dihydrofolate reductase to reform THF which is used to make more dTMP

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9
Q

A major cause of autosomal recessive SCID( severe combined immunodeficiency)

A

SCID - Disturbed development of functional T and B cells

Adenosine Deaminase Deficiency (ADA deficiency) - ADA is required for degradation of adensosine and deoxyadensosine. If deficient we have increase in dATP nucleotide which causes lymphotoxicity.

Adenosine –ADA–> Inosine –> –> uric acid –> excreted

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10
Q

Purine salvage

A

refer to picture

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11
Q

Patient presents with hyperuricemia (orange “sand” in diaper), gout, is pissed off/aggressive, self mutilation, retardation/intellectual disability, dystonia

A

Lesch-Nyhan syndrome is xlinked recessive

Defective purine salvage due to absent HGPRT (hypoxanthine guanine phosphoribosyl transferase) which is needed to convert hypoxanthine to IMP and guanine to GMP.

Accumulation of xanthine results in excess uric acid and de novo purine synthesis (from new rather than via salvage pathway)

Orange sand is sodium urate crystals

H-yperuricemia/uric acid accumulates in the brain
G-out
P-issed off/self mutilation/aggression
R-etardation
T-dysTonia
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12
Q

Exception to the genetic code features

A

unambiguous

degenerate/redundant ( methionine/AUG and tryptophan/UGG are only encoded by 1 codon)

commaless/nonoverlapping ( Except in some viruses)

universal (except in mitochondria of humans)

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13
Q

Promoters and origin of replication is rich in

A

AT sequences (i.e. TATA box regions)

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14
Q

DNA topoisomerase

A

Creates a single or double stranded break in the helix to add or remove supercoils

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15
Q

Primase

A

RNA primer for DNA pol III

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16
Q

DNA polymerase III

A

Prokaryotes only

has 3’–>5’ exonuclease activity which proofreads

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17
Q

DNA polymerase I

A

prokaryotes only

same as DNA pol III, exonuclease activity

degrade RNA primer and adds DNA

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18
Q

Telomerase

A

Eukaryotes only

reverse transcriptase/RNA dependent DNA polymerase

adds DNA : TTAGGG to 3’ end of chromosomes

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19
Q

Transition vs transversion

A

DNA mutation that is purine to purine vs purine to pyr (viceversa)

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20
Q

What DNA mutation causes sickle cell disease

A

Missense mutation where glutamic acid is replaced with valine

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21
Q

Nonsense mutation

A

early stop codon ( UAG, UAA, UGA) –> nonfunctional protein

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22
Q

What DNA mutation causes Duchenne muscular dystrophy

A

Frameshift mutation affecting the DMD gene

Lacks functional dystrophin gene and cannot stabilize/protect mm fibers

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23
Q

What DNA mutation causes Tay Sachs disease

A

Frameshift mutation

lack enzyme that breaks down fatty substance gangliosides which then build up in th brain and destroy the nervous system (motor deficit, blind, deaf)

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24
Q

LAC operon

A

glucose is the preferred metabolic substrate in E. Coli. If glucose is absent but lactose available then lac operon is activated to switch to lactose metabolism.

low glucose –> increase in adenylate cylase activity –> increase generation of cAMP from ATP –> activation of catabolite activator protein (CAP) –> increases transcription

High lactose –> unbind repressor protein from repressor/operator site –> increases trancription

allolactose is an inducer that inactivates repressor

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25
Q

Xeroderma pigmentosum

A

autosomal recessive

defect in nucleotide excision repair during G1 phase- cannot repair DNA pyrimidine dimers caused by UV exposure

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26
Q

Base excision repair

A

Important in spontaneous/toxic deamination

Base specific Glycosylase removes altered base and creates AP site (apurinic/apyrimidinic)

AP endonuclease cleaves the 5’ end

Lyase cleases the 3’ end

DNA pol Beta fills gap

Ligase seals it

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27
Q

Lynch syndrome

A

Due to problem in mismatch repair during S phase

autosomal dominant

HNPCC- hereditary nonpolyposis colorectal cancer

Colon and endometrial cancers most common

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28
Q

Defect in ataxia telangiectasia and fanconi anemia

A

Defective nonhomologous end joining )bringint ogether 2 ends of DNA fragments to repair double stranded breaks. No requirement for homology. Some DNA lost

ataxia telangiectasia is progressive difficulty with coordinating movements

Fanconi anemia is impaired bone marrow function

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29
Q

Defect in BRCA1 mutation

A

homologous recombination - repair damaged strand sing a complementary strand from the intact homologous dsDNA as a template

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30
Q

mRNA start codon

A

AUG or rarely GUG

AUG - methionine in euk
AUG - N-formylmethionine(fmet) in prok

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31
Q

RNA polymerases (euk)

A

RNA I: rRNA (MOST common)
RNA II: mRNA
RNA III: tRNA

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32
Q

alpha- amanitin found in death cap mushrooms

A

Amanita phalloides mushrooms

inhibit RNA pol II (mRNA) and cause severe hepatotoxicity

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33
Q

RNA polymerase (prok)

A

one RNA pol makes 3 kinds of RNA

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34
Q

mRNA

A

DNA transcribed into hnRNA which is spliced into mRNA which is translated into proteins

capped with 7’-methylguanosine cap, spliced at 5’ then 3’, and poly A tailed transcript produced in the nucleus and then translated in the cytosol

polyadenylation signal = AAUAAA. Addition of 200 As at 3’ end

Exons are EXPRESSED

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35
Q

microRNAs

A

noncoding RNA molecules that posttranscriptionally regulate gene expression by targeting the 3’ untranslated region

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36
Q

tRNA structure

A

T arm (ribothymidine, pseudouridine, cytidine sequence) allows it to tether to the ribosome

D arm detects - (dihydrouridine residues) necessary for tRNA recognition by correct aminoacyl-tRNA synthetase

anticodon loop

acceptor stem - CCA at 3’ end which then is covalently bound to the AA

aminoacyl-tRNA synthetase - 1 per AA, uses ATP to match

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37
Q

Protein synthesis initiation

A

euk initiation factors (eIFs) identify either the 5’ cap or an internal ribosome entry site (IRES) at 5’-UTR–> help assemble 40S ribosomal subunit with initiator tRNA

Released when the mRNA and the ribosomal 60s subunit assemble with the complex

uses GTP

EUK: 40S + 60S –> 80S (EVEN)
PROK: 30S + 50S –> 70S (Odd)

tRNA charged with ATP
tRNA grips and translocates with GTP

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38
Q

Protein synthesis elongation

A

A site - incomin aminoacyl tRNA
P site - accomodates growing peptide
E site - holds empty tRNA as it exits

aminoacyl-tRNA binds to A site –> rRNA (ribozyme) catalyzes the peptide bond and transfers growing polypeptide to AA in A site

ribsome advances 3 spaces –> peptidyl tRNA now in P site

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39
Q

Protein synthesis termination

A

release factor recognizes stop codon

requires GTP to release

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40
Q

Cell cycle

A

regulated by cyclins, cyclin-dependent kinases (CDKs), and tumor suppressors

M phase –> G1(growth) or G0 –> S (DNA synthesis) –> G2

cyclin-CDK complexes must be activated/deactivated at appropriate times for cell cycle progression

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41
Q

tumor suppressors

A

P53–> induces P21 –> inhibits CDK –> hypophosphorylation of Rb/activates Rb –> inhibits G1-S progression

Defect can cause Li- fraumeni syndrome ( predisposition ot wide range of cancers)

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42
Q

growth factors

A

bind tyrosine kinase receptors to transition the cell from G1 to S phase

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43
Q

Cell types

A

permanent - G0
Stable/quiescent - G0 then to G1 when stimulated
Labile - never G0. always G1 (MOST affected in chemo)

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44
Q

RER vs SER

A

RER- secretory protein synthesis

SER- steroid synthesis and detox

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45
Q

Function of the Golgi

A

Modified N-oligosaccharides on asparagine
Adds O-oligosaccharides on serine and threomine
Adds mannose-6-phosphate to proteins for trafficking to lysososmes

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46
Q

Pt presents with coarse facial features, gingival hyperplasia, clouded corneas, restricted joint movements, claw hand deformities, kyphoscoliosis, and high plasma levels of lysosomal enzymes

A

I-Cell disease/ inclusion cell disease/ mucolipidosis type II - an inherited lysosomal storage disorder

defect in N-acetylglucosaminyl-1-phosphotransferase prevent phosphorylation of mannose residues and therefore a decrease in mannose-6-phosphate –> proteins excreted rather than delivered to lysosomes

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47
Q

Signal recognition particle (SRP)

A

traffics protein from the ribosome to the RER. if absent then protein accumulates in the cytosol

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48
Q

Vesicular trafficking proteins

A

COPI: golgi to golgi (retrograde). cis-Golgi to ER
COPII: ER –> cis-golgi (anterograde)

“two steps FORWARD.. 1 step BACK”

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49
Q

Peroxisome

A
  • beta oxidation of very long chain FA
  • alpha oxidation
  • catabolism of branched FA, AA, and ethanol
  • synthesis of cholesterol, bile acids, and plasmalogens
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50
Q

Zellweger syndrome

A

autosomal recessive

cerebrohepatorenal syndrome- caused by decreased peroxisome causing accumulation of lipids which impairs normal function of multiple organ systems

mutated PEX gene

hypotonia, seizures, hepatomegaly, early death

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51
Q

refsum disease

A

autosomal recessive

disorder of alpha oxidation in peroxisome

phytanic acid not metabolized to pristanic acid

scaly skin, cataracts,night blindness, shortening of 4th toe, epiphyseal dysplasia

tx with diet

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52
Q

adrenoleukodystrophy

A

xlinked recessive

disorder of beta oxidation in peroxisome –> build up of VLCFA (very long chain FA) in ADRENAL glands, white matter of brain (LEUKO), testes.

adrenal gland crisis, coma, and death

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53
Q

proteasome

A

barrel shaped protein complex that degreades damaged or ubiquitin-tagged proteins

implicated in parkinsons

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54
Q

microtubule

A

helical array of polymerized heterodimers of alpha and beta tubulin

each dimer has 2GTP bound

Positive end goes to the periphery
Negative end goes to the nucleus

dynein- retrograde to microtubule ( + –> -)
Kinesin- anterograde to microtuule (- –> +)

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55
Q

cilia structure

A

9 doublet + 2 singlet arrangement of microtubules

basal body (base of cilium below cell membrane) consists of 9 microtubule triplet with no central microtubule

axonemal dynein - ATPase that links peripheral 9 doublets and causes bending of cilium

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56
Q

pt presenting with decreased Male/Female fertility due to immotile sperm and dysfunctional fallopian tube cilia

A

kartagener syndrome (primary ciliary dyskinesia)

“kartagener’s restaurant - take out only. theres no dynein “dine in””

can also cause bronchiectasis, recurrent sinusitis, chronic ear infections, conductive hearing loss, and situs inversus

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57
Q

N-K ATPase

A

1 ATP
3 Na out (phosphorylated)
2 K in (dephosphorylated)
ATP site on cytosolic side

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58
Q

Collagen

A

Type 1 - bONE
- decrease in osteogenesis imprefecta type 1
Type 2 - carTWOlage
Type 3 - reticulin - blood vessels
- decrease in Ehlers Danlos syndrome, vascular type
type 4 - floor (basement membrane)
- Alport syndrome ( kidney dz, hematuria, hearing
loss, eye abnormalities)
- goodpasture syndrome ( targeted by
autoantibodies, autoimmune dz where attack
basement membrane of kidneys and lungs)

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59
Q

Collagen synthesis

A

Collagen is 1/3 glycine

1) synthesis - pro alpha chain backbone [ Gly-X-Y] . X and Y are proline or lysine
2) hydroxylation of proline and lysine. This requires vitamin C. This is why a vitamin C deficiency causes scruvy
3) Glycosylation of hydroxylysine residues and formation of procollagen via H and disulfide bonds –> procollage is a triple helix of alpha chains. If cant form triple helix –> osteogenesis imperfecta
4) exocytosis of procollagen
5) cleavage of procollage at C and N terminals –> tropocollagen which is isnsoluble. Problems with cleavage causes Ehlers Danlos syndrome
6) formation of cross links between tropocollagen molecules by covalent lysine-hydroxylysine cross-linkage (by copper containing lysyl oxidase) to make colalgen fibrils. Problems with crosslinking causes ehlers danlos syndrome and menkes diseases (x linked recessive, impaired copper absorption and transport due to defective Menkes protein (ATP7A). Leads to decreased activity of lysyl oxidase and defective colalgen)

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60
Q

osteogenesis imperfecta

A

most commonly COL1A1 and COL1A2
autosomal dominant

patients that cant BITE
B- bones have multiple fractures
I- eyes have blue sclera
T- teeth have dental imperfections to due lack of dentin
E- Ear/hearing loss due to abnormal oscicles

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61
Q

Ehlers Danlos syndrome

A

hyperextensible skin, hypermobile joints, and tendeny to bleed (Easy bruising)

Most common type is hypermobile joint type

Classic type: joint and skin symptoms caused by mutation in type V collagen (COL5A1 and COL5A2)

Vascular type: type 3 procollagen deficiency (COL3A1 and COL3A2)

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62
Q

Pt presents with brittly kinky hair, growth retardation, and hypotonia

A

Menkes disease

x linked recessive

impaired copper absorption and transport due to defective Menkes protein (ATP7A). Leads to decreased activity of lysyl oxidase which needs copper as a cofactor –> defective collagen

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63
Q

Elastin

A

rich in nonhydroxylated proline, glycine, and lysine

crosslinking gives it its elastic properties

alpha1-antitrypsin 1 inhibits elastase and therefore elastin breakdown –> deficiency causes emphysema due to unopposed elastase activity

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64
Q

Marfan syndrome

A

MarFAN syndrome

autosomal dominant

FBN1 gene on chromosome 15 –> defective fibrillin ( a glycoprotein that forms sheats around elastin)

Skeletan, heart, and eyes

FAN - subluxation of lenses typically upwards and temporally. As if looking upward at a ceiling fan

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65
Q

PCR

A

denature by heating to 95
Anneal by cooling to 55. Add primers, a heat stable DNA polymerase like Taq and dNTPs
Elongonation by increase temp to 72 and DNA poly attache s to dNTPs to the strand

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66
Q

Blotting

A

SNoW DRoP

Southern - DNA
Northern - RNA
Western - Protein
Southwestern - DNA binding proteins

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67
Q

Flow cytometry

A

cells are tagged with antibodies specific to surface or intracellular proteins. Antibodies are then tagged with a unique fluorescent dye. Sample is analyzed one cell at a time by focusing a laser on the cell and measuring light scatter and intensity of fluorescence

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68
Q

Micro arrays

A

thousands of nucleic acid sequences are arranged in grids on glass or silicon. DNA or RNA probes are hybridized to the chip and a scanner detects the relative amounts of complementary binding

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69
Q

enzyme linked immunosorbent assay (ELISA)

A

immunologic test

Direct ELISA - a specific antigen
Indirect ELISA- antibody

antibody linked to an enzyme. added substrate reacts with enzyme and produces a detectable signal

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70
Q

Cas9/CRISPR

A

a genome editing tool derived from bacteria that allows removing, adding, or altering sections of the DNA sequence

Cas9 - endonuclease
gRNA - guide RNA sequence that binds to the complementary target DNA sequence

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71
Q

fluorescence in situ hybdrization

A

similar to karyotyping. except fluorescent DNA or RNA probes bind to specific gene ites of interest on chromsoomes. Each color represents a chromosome specific probe.

Detects microdeletions, translocation, duplications

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72
Q

Cre-lox system

A

can inducibly manipulate genes at specific developmental points

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73
Q

RNA interference

A

dsRNA is synthesized that is complementary to the mRNA sequence of interest.

Transfected into human cells, dsRNA separates and promotes degradation of target mRNA, “knocking down” gene expression

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74
Q

incomplete penetrance

A

% penetrance x probability of inheriting genotype = risk of expressing phenotype i.e. BRCA1

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75
Q

pleiotropy

A

one gene contributed to multiple phenotypic effects i.e. phenylketonuria

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76
Q

anticipation

A

increasing severity or earlier onset of disease in succeeding generations i.e. huntingtons

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77
Q

McCune Albright syndrome

A

Mosaicism example. lethal if affecting all cells. But survivable in patients with mosaicism

due to mutation affecting G protein signaling

Unilateral cafe-au-late spots with ragged edges

polyostotic fibrous dysplasia - bone replaced with collagen and fibroblasts

one endocrinopathy (i.e. precocious puberty)

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78
Q

Locus heterogeneity
Allelic heterogeneity
Heteroplasmy

A

locus heterogeneity - mutations at different loci can produce a similar phenotype (albinism)

Allelic heterogeneity - different mutations in the same locus produce the same phenotype (beta thalassemia)

Heteroplasmy - both normal and mutated mtDNA

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79
Q

Uniparental disomy

A

euploid/correct number of chromosomes

offspring gets 2 copies from 1 parent and no copies from other parent.

Heterodisomy - meiosis I error (heterozygous)
IsodIsomy - meiosis II error (homozygous)

in pt with recessive disorder when only one parent is a carrier.

I.e. angelman syndrome and prader willi

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80
Q

Hardy-weinberg

A

X linked recessive disease in males = q
in females = q^2

  • no mutations at locus
  • natural selection is not occuring
  • completely random mating
  • no net migration
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81
Q

Pt presents with hyperphagia, obesity, intellectual disability, hypogonadism, and hypotonia

A

Uniparental disomy –> Prader-Willi Snydrome

paternal allele is deleted or mutated on chromosome 15
Mother is silenced

82
Q

Pt has inappropriate laughter (happy puppet), seizures, ataxia, and severe intellectual disability

A

Uniparental disomy –> angelman syndrome

Maternal UBE3A gene is deleted or mutated
Paternal is silenced

83
Q

X linked recessive vs dominant

A

mostly sons affected and skips generations
vs
both parents can transmit. Mothers to 50% of sons and daughters. Fathers to all daughters no sons. (i.e. hypophosphatemic rickets- vit D resistant rickets. Increased phosphate wasting results in ricket like presentation, fragile X, alport syndrome

84
Q

mitochondrial inheritence

A

mom to son or daughters

mitochondrial myopathies - myopathy, lactic acidosis, and CNS disease. secondary to failure in oxidative phosphorylation. MM fibers often show ragged red fibers due to accumulation of diseased mitochondria.

leber hereditary optic neuropathy - cell death in optic nerve neurons

85
Q

Cystic Fibrosis

A

autosomal recessive

CFTR gene on chromosome 7

deletion of Phe508

decrease in Cl- secretion and H20 secretion. Increased intracellular Cl- causes compensatory increase in Na reabsorption via epithelial Na channels. Futher increases H20 reabsorption –> thick mucus secreted into lungs and GI tract

pilocarpine induced swear test is diagnostic. Newborn screening with increased immunoreactive trypsinogen. meconium ileus in children. infetility in men because have absent vas deferens

contraction alkalosis and hypokalemia

early infanct - s aureus
adolescence - p aeruginosa

86
Q

x linked recessive disorders

A

Oblivious Female Will Often Give Her Boys Her x-Linked Disorders

O-ornithine transcarbamylase deficiency
F-Fabry disease
W-wiskott aldrich syndrome
O-ocular albinism
G-6PD deficiency
H-hunter syndrome
B-Bruton agammaglobulinemia
H-hemophilia A and B
L-lesch0nyhan syndrome
D-Duchenne and becker muscular dystrophy
87
Q

Duchenne muscular dystrophy

A

Frameshift mutation in DMD–> absent dystrophin protein –> myofiber damage over time

onset before 5 yo

begins in pelvic girdle mm and progresses superioly

pseudohypertrophy of calve mm - fibrofatty replacement of mm

dilated cardiomyopathy is common cause of death

Gowers sign

88
Q

Beckers muscular dystrophy

A

non-frameshift deletions in dystrophin gene

X-linked

adolescent onset

89
Q

Pt presents with myotonia, mm wasting, cataracts, testicular atrophy, frontal balding, arrhythmia

“hatchet face” due to atrophy of temporalis mm and dropping mouth due to weakness of facial mm

A

Myotonic type 1

autosomal dominant

CTG repeat expansion in the DMPK gene

C- cataracts
T-toupe
G-gonadal arophy

90
Q

pt is a 3 yo girl that has regression in her motor,verbal, and cognitive abilities. Also has wringing of her hands

A

Rett syndrome (RETTurn aka regression)

MECP2 on X chromosome

typically 1-4 yo girls because boys die in utero

motor,verbal, and cognitive abilities are regressing. Ataxia, seizures, growth failure, and stereotyped handwringing

91
Q

pt presents with enlarged testes, long face, large jaw, large everted ears, autism, and a mitral valve prolapse

A

Fragile X syndrome

X lined dominany

CGG repeat during oogenesis in FMR1 gene –> hypermethylated –> decreased expression

Most common cause of inherited intellectual disability
2nd most common genetically associated mental deficiency (after Downs)

C - chin protruding
G - Giant
G - Gonads

92
Q

Trinucleotide repeat expansion diseases

A

Tri HUNTING for My FRAGILE cage-FREE eggs (X)

1) Huntington disease (AD)- CAG repeat.
C-CAUDATE
A- decreased ACH and
G-GABA

2)Myotonic dystrophy (AD) - CTG repeat
C- Cataracts
T-Toupee
G-Gonadal atrophy

3) Fragile X (XD) - CGG
C-chin protruding
G-giant
G-gonads

4) Friedreich ataxia (AR) - GAA
ataxic GAAit

93
Q

Downs Syndrome

A

trisomy 21 (mostly due to meiotic nondisjunction, if robertsonian translocation then due to chromosomes 14 and 21)

5 A's of Downs syndrome
 A- advanced maternal age
A- Atresia (duodenal)
A- AV septal defect
A- Alzheimer disease early onset (chromosome 21 codes for amyloid precursor protein)
A-AML/ALL
94
Q

Edwards syndrome

A

trisomy 18

PRINCE edward died at age 1

P-prominent occiput
R-rocker bottom feet
I-Intellectual disability
N-nondisjunction
C-clenched fists (with overlapping fingers)
E- Ears are low set

also: micrognathia (small jaw)

95
Q

Patau syndrome

A

trisomy 13

think P=puberty=age 13

Cleft lip/palate, holoprosencephaly, polydactyly,cutis aplasia, polycystic kidney disease

death by age 1

96
Q

Serum markers for Trisomy 21,18,13

A

first trimester: All low EXCEPT for 21 the beta-hCG is high

second trimester: All low except in 21 the beta-HCG and inhibin A are high. Everything normal in 13

97
Q

Robertsonian translocation

A

long arms of 2 acrocentric chromosomes fuse at the centromere and the 2 short arms are lost

98
Q

Cri-du-chat syndrome

A

congenital deletion on the short arm of chromosome 5

“cry of the 5 cats”

high pitches crying/meowing and cardiac abnormalities (VSD)

99
Q

Williams syndrome

A

congenital microdeletion of long arm of chromosome 7

includes elastin gene

elfin facies, hypercalcemia (increased sensitivity to vit D), extreme friendiness with strangers

I watched WILL ferrel in Elf SEVEN times and he was FRIENDLY

100
Q

22q11 deletion syndromes

A

Digeorge syndrome - thymic, parathyroid, and cardiac defects

Velocardiofacial syndrome - palate, facial, and cardiac defects

due to aberrant develpment of 3rd and 4th branchial (pharyngeal) pouches

CATCH 22
C- cleft palate
A-abnormal fascies
T-thymic dysplasia
C-cardiac defects
H-hypocalcemia secondary to parathyroid aplasia
101
Q

fat soluble vitamins

A

ADEK

102
Q

water soluble vitamins

A 
B1 (thiamine -->TPP)
B2 (riboflavin --> FAD,FMN)
B3 (niacin --> NAD+)
B5 (pantothenic acid --> CoA)
B6 (pyridoxine --> PLP)
B7 (biotin)
B9 (folate)
B12 (cobalamin)
C (ascorbic acid)

All wash out of body except B12 (stored in liver for 3-4 yrs) and B9 (stored in liver for 3-4 months)

coenzymes or precursors

deficiency: dermatitis, glossitis, diarrhea

103
Q

Vitamin A

A

retinol

  • Constinuent of visual pigments
  • Essential for normal differentiation of pancreatic and mucus secreting cells
  • Prevents squamous metaplasia

Treats measles
Retin-A - wrinkles and acne med
Isotretinoin- cystic acne ( TERATOGENIC –> cleft palate and cardiac abnormalities. pt needs a negative pregnancy test and two forms of contraception)
trans retinoic acid to tx acute promyelocytic leukemia (APL)

104
Q

Vitamin B1

A

thiamine

In thiamine pyrophosphate (TPP) - cofactor

ATP mnemonic -
A- alpha ketoglutarate dehydrogenase (TCA cycle)
T- Transketolase (HMP shunt)
P- pyruvate dehydrogenase (links glycolysis to TCA)

Deficiency causes impaired glucose breakdown and ATP depletion. Worsened by glucose infusion

Wernicke-karsakoff syndrome- Classic triad of confusion, ophthalmoplegia, ataxia

Dry Beriberi - polyneuropathy and symmetrical mm wasting

Wet Beriberi - high output cardiac failure (dilated cardiomyopathy) and edema

mnemonic : Ber1Ber1

dx: increased RBC transketolase following B1 administration

105
Q

Vitamin B2

A

riboflavin

component of FAD and FMN (redox rxns)

mnemonic: fiboFlavin (Fad and Fmn)
B2= 2 ATP

deficiency: 2 Cs of B2 ( Cheilosis and Corneal vascularization)

106
Q

Vitamin B3

A

niacin derived from tryptophan. requires B2 and B6 (6/2=3)

starts with N therefore NAD+ and NADP+(redox rxns)

B3= 3 ATP

Can be used to tx dyslipidemia by lowering levels of VLDL and raising levels of HDL

Deficiency? Pellagra (3 Ds: Diarrhea, Dementia, Dermatitis (broad collar rash). Also consider Hartnup disease

Excess? Podagra (gout of the foot)

107
Q

Hartnup disease

A

AR

deficiency of neutral AA like tryptophan transporters on proximal renal tubular cells and enterocytes (cant make vitamin B3 –> pellagra like symptoms)

108
Q

Vitamin B5

A

pantothenic acid

Coenzyme A (CoA) component. CoA is a cofactor for acyl transferase and FA synthase

109
Q

Vitamin B6

A

pyridoxine

converted to pyridoxal phosphate (PLP) which is important for transamination, decarboxylation, and glycogen phosphorylase

110
Q

Vitamin B7

A

biotin

cofactor for carboxylation enzymes

1) pyruvate carboxylase: pyruvate (3C)–> oxaloacetate (4C)
2) Acetyl-CoA carboxylase: acetyl-CoA (2C) –> malonyl-CoA (3C)
3) propionyl-CoA carboxylase: propionyl-CoA (3C) –> methylmalonyl-CoA (4C)

AVIDin in egg whites avidly binds biotin -> causes deficiency

111
Q

Vitamin B9

A

folate –> tetrahydrofolic acid (THF)

folate from foliage

important for the synthesis of nitrogenous bases in DNA and RNA

give Vitamin B9 for the 9 months of pregnancy (atleast 1 month prior)

112
Q

Vitamin B12

A

cobalamin

cofactor for methionine synthase (transfers CH3 goups as methylcobalamin) and methylmalonyl-coA mutase. important for DNA synthesis

refer to picture pathway

VERY large reserve in the liver. Deficiency usually cuased by malabsorption, lack of intrinsic factor, absence of terminal ileum, insufficient intake

antiintrinsic factor antibodies are diagnositc for pernicious anemia

(B9) Folate supplementation can mask the hematologic symptoms of B12 deficiency ( macrocytic, megaloblastic anemia etc) but not the neurologic symptoms. Prolonged deficiency causes irreversible nerve damage

113
Q

Vitamin C

A

ascorbic acid

reduced iron to the Fe2+ state for absorption (can increase risk of iron toxicity when in excess)

necessary for hydroxylation of proline and lysine in collagen synthesis

necessary for dopamine Beta-hydroxylase (dopamine –> NE)

deficiency causes scurvy due to collagen synthesis defect

114
Q

Vitamin D

A 
D3= cholecalciferol (from sun)
D2 = ergocalciferol (from plants etc

D3 and D2 –> 24-OH D3 (storage form) in the liver

1,25-(OH)2D3 = calcitriol is the active form in the kidney

increases intestinal absorption of Ca and PO4, increase bone mineralization at low levels, increase bone resorption at higher levels

if increase in parathyroid hormone ( increase ca reabsorption and decrease phosphate reabsorption), drop in calcium and phosphate –> increase calcitriol production.

calcitriol will feedback inhibit its own production

Deficiency causes rickets and osteomalacia in adults

115
Q

Vitamin E

A

tocopherol and tocotrienol

antioxidant that protects RBCs and membranes from free radical damage

high doses can alter vitamin K metabolism –> enhanced anticoagulant effects of warfarin

can present like B12 deficiency but without megaloblastic anemia, hypersegmented neutrophils, or increase serum methylmalonic acid levels

116
Q

Vitamin K

A

phytomenadione, phylloquinone, phytonadione, menaquinone

synthesized by intestinal flora

activated by epoxide reductase to the reduced form. Which is a cofactor for gamma carboxylation of flutamic acid residues on various proteins required for blood clotting.

K is for Koagulation - necessary for maturation of clotting factors II, VII, IX, X and proteins C and S. Inhibited by warfarin

NOT in breast milk. given as injection at birth to prevent hemorrhagic disease of the newborn (with increased PT and aPTT but normal bleeding time). Neonates have sterile intestines and cannot synthesize vitamin K (also risk with prolonged broad spectrum antibiotic use)

117
Q

Zinc

A

important for enzymes and zinc finger formation ( TF motif)

deficiency causes acrodermatitis enteropathica

118
Q

Kwashiorkor

A

protein deficient MEALS

M-malnutrition
E-edema (decreases plasma oncotic pressure)
A-anemia
L-Liver malfunction (fatty change due to decreaed apolipoprotein synthesis)
S-skin lesions (hyperkeratosis, dyspigmentation)

119
Q

Marasmus

A

Muscle wasting

No edema

calorie deficient

120
Q

metabolism site - mitochondria

A 
Beta oxidation (FA)
acetyl CoA production
TCA cycle
Oxidative phosphorylation
Ketogenesis
121
Q

metabolism site - cytoplasm

A

Glycolysis
HMP shunt
Synthesis of steroids, proteins, FA, cholesterol, and nucleotides

122
Q

Metabolism site - both mitochondria and cytoplasm

A

HUGs take two

Heme synthesis
Urea Cycle
Gluconeogenesis

123
Q

Rate determining enzyme: glycolysis

A

Phosphofructokinase-1 (PFK 1)

+ AMP, F-2,6-BP
- ATP, Citrate

124
Q

Rate determining enzyme: gluconeogenesis

A

Fructose-1,6-bisphosphate

+ citrate
- AMP, F-2,6-BP

125
Q

Rate determining enzyme: TCA cycle

A

Isocitrate dehydrogenase

+ ADP
- ATP, NADH

126
Q

Rate determining enzyme: glycogenesis

A

Glycogen Synthase

+G6P, insulin, cortisol
- Epi, glucagon

127
Q

Rate determining enzyme: Glycogenolysis

A

Glycogen phosphorylase

+ epi, glucagon, AMP
- G6P, insulin, ATP

128
Q

Rate determining enzyme: HMP shunt

A

Glucose-6-phosphate dehydrogenase (G6PD)

+ NADP
- NADPH

129
Q

Rate determining enzyme: de novo pyrimidine synthesis

A

Carbamoyl phosphate synthetase II

+ ATP, PRPP
- UTP

130
Q

Rate determining enzyme: de novo purine synthesis

A

Glutamine- phosphoribosylpyrophosphate (PRPP) amidotransferase

  • AMP, inosine monophosphate (IMP), GMP
131
Q

Rate determining enzyme: Urea cycle

A

Carbamoyl phosphate synthetase I

+ N-acetylglutamate

132
Q

Rate determining enzyme: FA synthesis

A

acetyl-CoA carboxylase (ACC)

+ Insulin, citrate
- glucagon, palmitoyl-coA

133
Q

Rate determining enzyme: FA oxidation

A

CArnitine acyltransferase I

  • malonyl-coA
134
Q

Rate determining enzyme: ketogenesis

A

HMG CoA synthase

135
Q

Rate determining enzyme: cholesterol synthesis

A

HMG CoA reductase

+insulin, thyroxine
-glucagon, cholesterol

136
Q

ATP production (aerobic, anaerobic)

A

aerobic - 1 glucose –> 32 ATP (heart and liver, malate-aspartate shuttle) or 30 ATP ( muscles, glycerol-3-phosphate shuttle)

anaerobic- 1 glucose –> 2 net ATP

137
Q

Universal electron acceptors

A

NAD+ - catabolic

NADPH- anabolic (HMP shunt)

138
Q

Hexokinase vs glucokinase

A

Glucokinase: to store glucose in the liver and beta cells of the pancrease. It has low affinity and high capacity. Induced my insulin . Not feedback (-) by G6P

Hexokinase- sequesters glucose in tissues. Most tissues except liver and beta cells of pancrease. High affinity and low capacity. Not induced by insulin and is feedback inhibited by G6P

139
Q

Km and Vmax

A

low Km = high affinity

low Vmax= low capacity

140
Q

pyruvate dehydrogenase complex

A

pyruvate + NAD + CoA –> acetyl CoA + CO2 + NADH

3 enzymes that require 5 cofactors

“The Lovely Coenzyme for Nerds”

T- Thiamine pyophosphate (B1)
L- Lipoic acid (This is inhibited by arsenic--> skin changes,vomiting, diarrhea, QT prolongation, garlic breath
C-CoA (B5, pantopenthic acid)
F-FAD (B2, Riboflavin)
N- NAD (B3, niacin)

SAME for alpha-ketoglutarate dehydrogenase complex in TCA cycle

Deficiency causes buildup of pyruvate –> increase in lactate or alanine

141
Q

TCA cyle product

A

3 NADH, 1 FADH2, 2CO2, 1 GTP for eaach acetyl-coA

10 ATP per acetyl coa (x2 everything per glucose)

142
Q

electron transport chain complexes

A 
complex I - NADH
Complex II (succinate dehydrogenase)- FADH2
Complex III
complex IV 
Complex V (ATP synthase)
143
Q

ATP produced by ATP synthase

A

1 NADH –> 2.5 ATP

1 FADH2 –> 1.5 ATP

144
Q

gluconeogenesis

A

primarily in the lvier

mm cannot participate because lacks G6phosphatase

145
Q

HMP shunt

A

NADPH source –> reductive rxns
Also ribose for nucleotide synthesis

Oxidative and non oxidative phases both occur in cytoplasm

No ATP used or produced

146
Q

glucose-6-phosphate dehydrogenase deficiency

A

NADPH is necessary to keep glutathione reduced –> detox

low NADPH –> decreases RBC defenses –> hemolytic anemia

Heinz bodies- denatured globin chains ppt within RBCs due to oxidative stress

Bite cells –> phagocytic removal of heinz bodies by splenic macrophages

147
Q

Essential fructosuria

A

defect in fructokinase

KINASE is KIND - benign fructose in blood and urine

148
Q

Hereditary fructose intolerance

A

deficiency in aldolase B

accumulation of F-1-P –> decrease phosphate –> inhibit glycogenolysis and gluconeogenesis

hypoglycemia, jaundice, cirrhosis

149
Q

Galactokinase deficiency

A

deficiency in galactokinase causes accumulation of galactitol

galactosemia, galactosuria

failure to track objects or to develop a social smile

KINASE IS KIND

150
Q

classic galactosemia

A

absence of galactose-1-phosphate uridyltransferase

toxic substances accumulate in the eye

symptoms develop when infant begins feeding

151
Q

lactose

A

galactose +glucose

152
Q

Sorbitol

A

alternative method of trapping glucose in the cell is to convery it to sorbitol via aldose reductase (Retina, Kidneys, Schwann cells)

Liver, ovary, and seminal vesicles can convert it to fructose via sorbitol dehydrogenase

153
Q

LActase

A

digests lactose into glucose and galactose

154
Q

essential AA

A 
PVT TIM HaLL
P-phenylalanine
V-valine
T-Tyrosine
T-THreonine
I-Isoleucine
M-methionine
H-histidine
L-leucine
L-lysine
155
Q

Glucogenic AA

A

Met His Sweet Valentine

M- methionine
H-Histidine
V-Valine

Sweer- glucogenic

156
Q

Glucogenic AA/Ketogenic

A

TTIP

Threonine
Tyrosine
ISoleucine
Phenylalaine

157
Q

Basic AA

A

His Lys Are Basic

Histidine
Lysine
Arginine

158
Q

Asterixis is a sign of

A

Hyperammonemia/ammonia accumulation

Excess NH3 depletes glutamate (GABA) in CNS and alpha ketoglutarate –> inhibits the TCA cycle

Tx by limiting protein in diet

159
Q

Ornithine transcarbamylase deficiency

A

Urea cycle disorder

cant eliminate ammonia

excess carbamoyl phosphate –> orotic acid (pyrimidine synthesis)

160
Q

2 week old baby with musty body odor

A

phenylketonuria

due to decrease in phenylalanine hydroxylase or tetrahydrobiopterin (BH4) cofactor (mlaignant OKU)

Screen babies 2-3 days after birth because normal at birth due to maternal enzyme during fetal life

phenyl ketons: phenylacetate, phenyllactate, and phenyl pyruvate
disorder of AROMATIC AA metabolism therefore a musty body AROMA

must avoid artificial sweetner aspartame

tx with BH4 and tyrosine.

Can also have maternal PKU- due to lack of proper dietary therapy –> microcephaly, intellecual disability etc in baby

161
Q

Urine smells like burnt sugar

A

Maple syrup urine disease

Blocked degradation of branched AA (Isoleucine, leucine, and Valine) due to decrease in branches chain alpha-ketoacid dehydrogenase (B1)

Causes increase in ketoacids ESPECIALLY leucine

tx with restriction of branched AA in diet and give thiamine (B1) supplementation

“I Love Vermont maple syrup from B1-ranches of the tree”

162
Q

bluish black CT, sclera, and black urine after prolonged exposure to air

A

Alkaptonuria

deficiency of homogentisate oxidase in the degradative pathway of tyrsosine for fumarate –> homogentisic acid accumulates in tissues (black pigment)

also homogentisic acid is toxic to cartilage –> arthralgia

163
Q

Homocystinuria

A

excess homocysteine

HOMOCYstinuria

Homocystein in urine
Osteoperosis
Marfanoid habitus
Ocular changes (down and in VS up and fan out in Marfan)
CV effects --> stroke or MI
kYphosis
164
Q

Cystinuria

A

Cystine, Ornithine, Lysine and Arginine (COLA)

recurrent hexagonal cystine stones (cystine is two cysteines connected by a disulfide bond)

tx by alkanization of urine and chelating agents

165
Q

Glycogen

A

branches have alpha- (1,6) bonds

Linkages have alpha-(1,4) bonds

166
Q

Steps to glycogenolysis

A

In skeletal mm : –> G1P–> G6P –> metabolized in excercise

in hepatocytes: glycogen is stored and is used to maintain blood sugar at appropriate levels

branched glycogen (some degraded in lysosome only)

–> glycogen phosphorylase frees up G1P residues off branches glycogen until only 4 units remain (limit dextrin)

–>4-alpha-D-glucanotransferase is the debranching enzyme and removed 3 of the 4 G1P

–> alpha-1,6-glucosidase is a debranching enzyme that cleaves the last G1P

–> GLUCOSEEE

167
Q

Glycogen storage diseases

A

Very Poor Carb Metabolism

V-von gierke disease (type 1)
P-Pompe disease (type 2)
C- Cori disease (type 3)
M - McArdle disease (type 4)

168
Q

Von Gierke Disease

A

Type I glycogen storage disease

deficient in glucose-6-phosphatase and therefore cannot break down glycogen

increase in glycogen in liver and kidneys
Increase in uric acid –> gout

169
Q

Pompe disease

A

Type II glycogen storage disease

deficient in lysosomal acid alpha-1,4-glucosidase with alpha-1,6-glucosidase activity (Acid maltase)

Heart defects
Liver (hepatomegaly)
Muscle myopathy

170
Q

Cori disease

A

Type III glycogen storage disease

milder form of type I

deficient in debranching enzyme alpha-1,6-glucosidase

171
Q

McArdle disease

A

think M=Muscle (glycogen build up) –> cramps and myoglobinuria (Red urine with exercise)

deficient in skeletal mm glycogen phosphorylase (Myophosphorylase)

hallmark sign: flat venous lactate curve with normal rise in ammonia levels during exercise

172
Q

Sphingolipidoses

A

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

Tay-sachs disease

Fabry Disease

Metachromatic leukodystrophy

Krabbe disease

Gaucher disease

Niemann-Pick disease

173
Q

Tay Sachs disease

A

tAy-saX lacks heXosaminidase A

build up GM2 ganglioside

neurodegeneration
“cherry red” spot on the macula
NO hepatosplenomegaly
Onion skin lysosomes

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

174
Q

Fabry disease

A

alpha-galactosidase A deficient

build up ceramide trihexoside

triad: episodic peripheraly neuropathy, angiokeratomas, hypohidrosis

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

175
Q

Metachromic leukodystrophy

A

Lack arylsulfatase A

build up of cerebroside sulfate

central and peripheral demyelination –> dementia and ataxia

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

176
Q

Krabbe disease

A

Deficient in galactocerebrosidase

build up of galactocerebroside and psychosine

peripheral neuropathy and progressive damage to nervous system

Globoid cells

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

177
Q

Gaucher disease

A

Most common

deficient in glucocerebrosidase

build up of glucocerebroside

Gaucher cells - lipid laden macrophages resembling crumpled tissue paper

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

178
Q

Niemann-Pick disease

A

“no man picks his nose with his spinger”

deficient in sphingomyelinase

build up of sphingomyelin

Neurodegenration
Cherry red spot on macula
Foam cells (lipid laden macrophages)
HAS hepatosplenomegaly (compared to tay sachs)

lysosomal storage disease - lipid storage disorders relating to sphingolipid metabolism

179
Q

ashkenazi jews

A

tay sachs
niemann pick
gaucher

180
Q

Mucopolysaccharidoses

A

disorder that results in the buildup of glycosaminoglycans (formerly known as mucopolysaccharides)

type 1: Hurler syndrome - deficient in alpha-L-iduronidase. Corneal clouding

type 2: Hunter syndrome - deficient in iduronate-2-sulfatase
“hunters see clearly and aim for the X” –> x linked recessive and no corneal clouding. Mild hurler + aggressive behavior

both accumulate herparan sulfate and dermatan sulfate

181
Q

FA synthesis and break down

A

synthesis: citrate (“ SYtrate=Synthesis”)
Degradation: Carnitine (“CARnitine=CARnage”)

Hypoketotic hypoglycemia

systemic primary carnitine deficieny - cant transport LCFAs into mitochondria –> toxic accumulation

Medium chain acyl coA dehydrogenase deficieny- cant break down FA into acetyl coA –> accumulation of fatty acyl carnitine

182
Q

Ketone bodies

A

acetone, acetoacetate, beta hydroxybutyrate

In the liver:

FA and AA –> acetoacetate and beta hydroxybutryrate –> to use in mm and brain

in starvation and diabetic ketoacidosis: oxaloacetate is depleted for gluconeogenesis

Alcoholism: excess NADH shunts oxaloacetate to malate

BOTH cause buildup of acetly coA –> shunts towards production of ketone bodies

HMG coA lyase is used to ketone production

183
Q

Calories in carb, alcohol, fatty acid

A

carb = 4
alcohol= 7
Fatty acid=9

184
Q

starvation

A

day 1: glycogen reserves depleted
RBC lack mitochondria and cannot use ketons

after day 3: adipose stores and used until depleted then protein degradation accelerates

185
Q

Lipid transport

A

1) chylomicron enter lymphatics
2) HDL transfers APO CII and ApoE to he chylomicron
3) the APO CII can activate Lipoprotein lipase
4) FFA enters adipocytes and chylomicron remnant to hepatocytes

____

1) Liver releases VLDL(APO B100)
2) HDL transfers APO CII and APO E to VLDL
3) APO CII activates lipoprotein lipase
4) FFA enter adipocyte and IDL remains
5) IDL delivers to liver via APOE

___

1) LDL released from hepatocyte
2) endocytosis of LDL by peripheral cells

186
Q

Hepatic lipase

A

degrades TGs –> IDL

187
Q

Hormone sensitive lipase

A

degrades TGs stored in adipocytes

188
Q

Lecithin-cholesterol acyltransferase

A

catalyzes esterification of 2/3 of plasma cholesterol

nascent HDL –> mature HDL

APO AI activates

189
Q

Apo E

A

EVERYTHING Except LDL

mediates remnant uptake

190
Q

APO CII

A

chylomicron, VLDL, HDL

catalyzes lipoprotein lipase cleavage

191
Q

B48

A

chylomicron, chylomicron remnant

mediates secretion into lyphatics

192
Q

B100

A

VLDL,IDL, LDL

binds LDL receptor

only liver originating particles

193
Q

VLDL

A

heptic Tgs –> peripheral tissues

194
Q

LDL

A

hepatic cholesterol –> peripheral tissues

formed by hepatic lipase modification of IDL

195
Q

HDL

A

cholesterol from periphery –> liver

196
Q

Abetalipoproteinemia

A

chylomicrons, VLDL, LDL absent

Deficient in APOB48. APO B100

severe fat malabsorption

197
Q

Type I - hyperchylomicronemia

A

LPL or APO CII deficieny

increases chylomicrons, TC, cholesterol in blood

Pancreatitis, hepatosplenomegaly, eruptive/pruritic xanthomas, NO increased risk for atherosclerosis

198
Q

Type II - familial hypercholesterolemia

A

LDL receptors or APO B100 defective

increase LDL, cholesterol levels in IIa
iib also has increases VLDL

accelerated atherosclerosis
Tendon xanthomas (achilles)
199
Q

Type III - Dysbetalipoproteinemia

A

Defective ApoE

chlymocrons and VLDL increase in blood

premature atherosclerosis
tuberoeruptive xanthomas
palmar xanthomas

200
Q

Type IV- hypertriglyceridemia

A

Hepatic overproduction of VLDL

Increases blood levels of VLDL and TG

Hyperriglyceridemia (>1000 mg/dL)

related to insulin resistance

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