Biochemistry Flashcards
RNA polymerase I
restricted to nucleolus as it synthesizes majority of rRNA
produces 18S, 5.8S, & 28S
forms essential ribosomal components
mRNA
Produced by RNA pol II
translated by ribosomes to form specific proteins
small nuclear RNA
Produced by RNA pol II
involved in mRNA splicing & transcription regulation
micro RNA
Produced by RNA pol II
cause gene silencing via translation arrest or mRNA degradation
RNA pol III
produces tRNA and 5S ribosomal RNA (essential component of 60S ribosomal subunit)
vitamin A deficiency
sx = night blindness, complete blindness, xerophthalmia, Bitot’s spots (abnromal squamous cell proliferation and keratinization of conjunctiva), corneal perforation, keratomalacia, derm abnl, damage to phagocytes and TC lymphocytes, death
common in Asia, Africa, South America
associated with malnourishment and fat malabsorption (eg CF, cholestatic liver disease)
Give to all children with measles from area with vit A def or with measles mortality >1%
Transformation
Direct uptake of naked DNA from the environment by bacT that are naturally able
- strep pneumo
- Haemophilus influenza
- Neisseria gonorrhoeae & meningitidis
*this is how non-virulent non-capsule-forming strains of s. pneumo can obtain genes that code for capsule and gain virulence
Conjugation
one-way transfer of DNA between bacT cells through direct physical contact
donor cells contain an extra segment of DNA = F factors coding for sex pilus and other prot necessary for transfer to F- recipients
Transduction
transfer of DNA via bacteriophage
during lytic infection when random bacT genes accidentally packaged into viral capsid
lyosgenic infection when selected bacT genes near viral insertion site are excised and packaged into virion
Dry beriberri
think ber1 ber1 –> B1 deficiency
polyneuritis, symmetrical muscle wasting
Wet beriberi
high-output cardiac failure (dilated cardiomyopathy), edema
B1 deficiency
impaired glucose breakdown –> ATP depletion worsened by glucose infusion with highly aerobic tissues affected first (brain, heart)
Thiamine
found in thiamine pyrophosphate (TPP) = cofactor for:
- pyruvate dehydrogenase (links glycolysis to TCA)
- alpha-ketoflutarate dehydrogenase = TCA cycle
- Transketolase (HMP shunt responsible for NADPH production)
vitamin B2
riboflavin
cofactor in oxiation and reduction (eg FADH2)
Mneumonics:
-Fad and Fmn derived from riboFlavin (B2 = 2ATP)
B2 deficiency
Cheilosis
Crneal vascularization
“2 C’s of B2”
B3
niacin
constituent of NAD+, NADP+ (using redox reactions).
Derived from tryptophan – need B6
“NAD derived from Niacin (B3 = 3 ATP)
Niacin deficiency
glossitis
severe = pellagra = diarrhea, dementia, dermatitis
c/b Hartnup dz (dec tryptophan absorption), malignant carcinoid syndrome (inc tryptophan metabolism), INH (dec B6)
niacin excess
flushing - seen at doses used to tx HLD
B5 function and deficiency presentation
pantothenate
essential part of CoA and fatty acid synthase
deficiency = dermatitis, enteritis, alopecia, adrenal insufficiency
B6
pyridoxine
converted to pyridoxal phosphate = cofactor used in transamination (ALT, AST), decarboxylation reactions, glycogen phosphorylase
Needed to make:
- cystathionine
- heme
- niacin
- histamine
- NTs = 5HT, E, NE, GABA
B6 deficiency
convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemia due to impaired Hb synthesis and iron excess
B7 (biotic)
cofactor for carboxylation enzymes (add 1-carbon group):
- pyruvate carboyxlase: pyruvate (3C) –> oxaloacetate (4C)
- acetyl-CoA carboxylase: acetyl-CoA (2C) –> malonyl-CoA (3C)
- Propionyl-CoA carboxylase: propionyl-CoA (3C) –> methylmalonyl-CoA (4C)
deficiency is rare but causes dermatitis, alopecia, enteritis. Occurs if consume too many raw eggs (Avidin binds biotin) or abx.
B9
converted to tetrahydrofolate (THF) = coenzyme for 1-C transfer/methylation rxns
needed to make nitrogenous bases in DNA and RNA
found in green leafy vegetables (“folate in foliage”)
small reserve pool in liver
drugs that cause folate deficiency
MTX, phenytoin, sulfonamides
*remember no neuro sx like in B12 deficiency
B12
cofactor for homocysteine methyltransferase (transfers methyl group as methylcobalamin) and methylmalonyl-CoA mutase
large reserve in liver that lasts years
B12 deficiency
malabsorption (sprue, enteritis, diphyllobothrium latum), lack intrinsic factor, absent terminal ileum
dx with Schilling test
findings = macrocytic, megaloblastic anemia, hypersegmented PMNs, neuro sx (paresthesias) due to abnomral myelin, if prolonged get irreversible nervous system damage
Kwashiorkor
protein deficient MEAL-
Malnutrition
Edema
Anemia
Liver (fatty due to dec apolipoprotein synthesis)
Marasmus
Muscle wasting
loss of SQ fat
variable edema
c/b energy malnutrition
what 3 things are metabolized in both the cytosol and mito.?
HUGs take 2
Heme
Urea cycle
Gluconeogenesis
What 5 cofactors are needed for the pyruvate dehydrogenase complex?
- Pyrophosphate (B1, thiamine, TPP)
- FAD (riboflavin, B2)
- NAD (niacin, B3)
- CoA (pantothenate, B5)
- Lipoic acid
Goal = pyruvate + NAD+ + CoA –> acetyl-CoA + CO2 + NADH
preparing for TCA cycle
Regulation by Fructose-2,6-bisphosphate in the fasting state
inc glucagon –> inc cAMP –> inc protein kinase A –> inc fructose bisphosphatase-2, dec PFK-2, less glycolysis
Remember:
- fasting means you’re low on E –> get back the phosphate to produce glucose/energy
- going from F2,6BP to F6P
Regulation by Fructose-2,6-bisphosphate in the fed state
inc insulin –> dec cAMP –> dec protein kinase A –> dec FBPase-2, inc phosphofructokinase-2, more glycolysis
Remember:
- you’re fed, have to energy to spare, add phosphates to things
- “energy to burn, don’t give a fructo” – phosphoFRUCTOkinase-2
what are the 2 purely ketogenic amino acids
Lysine and Leucine
mutation in pyruvate dehydrogenase complex deficiency
x-linked gene for E1-alpha subunit
sx = neuro deficits tx = ketogenic diet
4 possible targets of pyruvate metabolism and effector enzyme:
- ALT (with B6): alanine carries amino groups to liver from muscle
- pyruvate carboxylase (with B7): oxaloacetate replenishes TCA cycle or used in gluconeogenesis
- pyruvate dehydrogenase (B1, B2, B3, B5, lipoid acid): transition from glycolysis to the TCA cycle
- Lactic acid dehydrogenase (B3): end of anaerobic glycolysis (RBCs, leukocytes, kidney medulla, lens, testes, cornea)
alpha-ketoglutarate dehydrogenase complex
same cofactors as pyruvate dehydrogenase complex
Citric acid cycle major players in order mneumonic
“Citrate Is Kreb’s Starting Substrate For Making Oxaloacetate”
Citrate 6C Isocitrate 6C alpha-ketoglutarate 5C Succinyl-CoA 4C Succinate 4C Fumarate 4C Malate 4C Oxaloacetate 4C
Products of TCA cycle
3 NADH
1 FADH2
2 CO2 –> from the C decreases, i.e. 6C -> 5C -> 4C
1 GTP per acetyl-coA
Total: 10 ATP/acetyl-CoA (multiply by 2 for each glucose since it produces 2 acetyl-CoA)
Electron transport inhibitors
inhibit Complexes of transport chain dec proton gradient and blocking ATP synthesis
Rotenone –| Complex I
Antimycin A –| Complex III
Cyanide and CO –| Complex IV
ATP synthase inhibitors
directly inhibit mito ATPsynthase causing inc proton gradient. No ATP produced bc electron transport stop
Oligomycin –| Complex V
Uncoupling agent of e- transport chain
inc permeability of membrane –> dec proton gradient and inc O2 consumption –> ATP synthesis stops but e- transport produces heat
2,4-DNP, aspirin (fever recurs after overdose), thermogenin in brown fat
Which tissue can’t do gluconeogensis and why?
muscle bc it lacks G6P enzyme
Which fatty acid chains can produce glucose?
Odd chains becaues they yield 1 propionyl-CoA which can enter the TCA cycle as succinyl-CoA
Even chains can’t bc only make acetyl-CoA equivalents
“Odd FAtty’s have Energy thanks to their PROPortionality”
What is the end product of the HMP shunt (pentose phosphate pathway)?
ribose for nucleotide synthesis and glycolytic intermediates
No ATP is used or produced
Sites: lactating mammary glands, liver, adrenal cortex (sites of FA and steroid synthesis), RBCs
What is the end product of oxidative (irreversible) HMP shunt?
CO2, 2 NADPH, Ribulose-5-Pi
What is the end product of nonoxidative (reversible) HMP shunt?
Ribose-5-Pi, G3P, F6P
What is the action of NADPH oxidase and where is it located?
rapid release of reactive oxygen intermediates and found in neutrophils and monocytes
NADPH plays a role in the creation of ROIs and their neutralization –> important for immune response