Biochemistry. Just kill me now. Flashcards
mRNA start codon:
AUG
AUG AUGments protein synthesis
What does AUG code for in prokaryotes?
Eukaryotes?
Prokaryotes = formylmethionine Eukaryotes = methionine
mRNA stop codons (3):
UGA
UAA
UAG
U Go Away, U Are Away, U Are Gone
What is an operon (3 components)?
Structural genes to be transcribed
Regulatory regions
Promoter region
Four common structural features shared by proteins that interact with DNA:
helix-loop-helix
helix-turn-helix
Zn fingers
leucine zippers
What are the three types of RNA?
rRNA
mRNA
tRNA
Rampant, massive, and tiny.
T/F: Enhancers and repressors control whether a gene is transcribed.
F. Response elements control the RATE of transcription, not whether it happens.
Features of promoter sequences (3):
Upstream
Rich in AT
TATA or CAAT box
What is an operator region?
It is where inducers and repressors bind, usually located between the promoter region and start.
Briefly review the function of the lac operon.
- Transcription factor
- Repressor
- Conditions
lac = codes for b-galactosidase (lactose -> glucose + galactose).
Tx factor CAP is bound when there is no glucose.
Repressor lac is bound when there is no lactose.
Make product only when the repressor is gone (there is lactose) and when CAP is unbound (there is glucose).
What are the three eukaryotic RNA polymerases and what do they do?
RNA pol I makes rRNA
RNA pol II makes mRNA
RNA pol III makes tRNA
This substance inhibits eukaryotic RNA polymerase II:
Main manifestation of its toxicity?
a-amanitin.
Hepatotoxic.
The two ways in which transcription can be terminated in prokaryotes:
rho-dependent ATPase
rho-indepedent (GC-rich hairpin turn followed by a weak point rich in UUUUUUfall right off)
T/F: Prokaryotes have more than one polymerase:
F. They just have the one, it makes all three kinds of RNA.
Drug that inhibits prokaryotic RNA polymerase and turns your pee red:
Rifampin
Where is rRNA made?
mRNA?
tRNA?
rRNA is made in the nucleolus.
mRNA and tRNA are made in the nucleoplasm.
Before RNA leaves the nucleus it needs to be processed to become mRNA and gain the ability to leave. Three major processing events:
- 5’ cap addition (SAM needed)
- Poly-A tail
- Introns spliced out (by spliceosome)
What is the co-factor required for adding a 5’ cap to hnRNA?
SAM
Poly-A polymerase recognizes this polyadenylation signal:
AAUAAA
Patients with lupus make antibodies against this piece of pre-mRNA processing machinery:
Spliceosomal snRNPs.
These are part of the spliceosome used to remove introns.
Which part of a transcript gets to leave the nucleus: Intron or exon?
EXon is EXpressed and EXits the nucleus
Does tRNA synthetase work at the 5’ or 3’ end of tRNA? What special marker is at this end?
tRNA synthetase works at the 3’ end.
This end always has CCA.
T/F: Amino acids destined for transfer are bound hydrostatically to the 5’ end of tRNA.
F. The bond is covalent, and it is found at the 3’ end.
The ribosome in prokaryotes is a __S ribosome composed of these two subunits:
30S + 50S -> 70S
PrOkaryotic = Odd numbers
The ribosome in eukaryotes is a __S ribosome composed of these two subunits:
40S + 60S -> 80S
Eukaryotic = Even numbers
Where is the prokaryotic ribozme?
It is a 23S rRNA Inside the 50S subunit.
tRNA bound with ATP is in what state?
tRNA bound with GTP is in what state?
ATP bound tRNA is “charged” with its amino acid.
GTP bound tRNA is in the process of translocation.
Initiation of protein synthesis is activated by this hydrolytic reaction:
GTP hydrolysis
This enzyme catalyzes peptide bond formation during protein synthesis. It has two names:
Ribozyme = peptidyltransferase
Where are ribosomes made?
In the nucleus.
In order to accomplish translocation during protein synthesis, this protein is required in eukaryotes. What is its prokaryotic analogue?
Eukaryotic: EF-2
Prokaryotic: EF-G
In eukaryotes, which ribosomal subunit docks with mRNA first?
This subunit needs help, what proteins help it dock?
40S binds first with the help of initiation factors
Describe the orientation of the entrance and exit sites for peptide bond formation on the 60S subunit:
A site is near the 3’ end, for Aminoacyl-tRNA.
P site is in the middle, for the growing Peptide.
E site is at the end, it holds Empty tRNA Exiting.
These antibiotics inhibit initiation complex formation and cause mRNA mis-reading:
Aminoglycosides
These antibiotics bind the 30S subunit of prokaryotic ribosomes and keep tRNA out of the A site:
Tetracyclines
prevent tRNA from binding
Two antibiotics that work at the 30S subunit:
Aminoglycosides
Tetracyclines
buy AT 30
CCELL at 50
These 6 antibiotics work at the 50S subunit of the ribosome:
Chloramphenicol Clindamycin Erythromycin (& other macrolides) Linezolid Lincomycin Streptogramin
These antibiotic binds the 50S su and inhibit peptidyltransferase (2).
This antibiotic binds the 30S su and inhibits tRNA docking.
Chloramphenicol & streptogramins
Tetracyclines
Mechanism of action for macrolides, linezolid, and clindamycin:
Bind 50S and prevent the spent tRNA from leaving once it has donated its amino acid.
Mechanism of action of tetracyclines:
Bind 30S and block tRNA from entering the A.
Tetracyclines are not good for babies.
How do aminoglycosides work?
They bind the 30S subunit and inhibit initiation complex formation.
T/F: Cyclin-dependent kinases are constitutively inactive.
T. They need cyclins to activate them.
Two important tumor suppressors at the G0 to S transition in the cell cycle:
p53
Rb
What kind of cells are exemplified by bone marrow, skin, and other germ cells?
Labile cells
Hepatocytes and lymphocytes are capable of entering G1 when prompted, these cells are known as:
Stable or quiescent cells
These cells remain in G0. Regeneration happens from stem cells:
Examples (3)?
Permanent cells.
Ex neurons, skeletal / cardiac muscle, RBCs
rER in neurons is aka:
You would not see this substance in what portion of the neuron?
Nissl substance.
Nissl bodies are absent from axons
What happens in rER (2 big things)?
- Synthesis of exported proteins
2. Addition of N-linked oligosaccharides
What happens in smooth ER?
- Steroid synthesis
2. Detoxification of drugs and poisons
This cellular organelle will be enormous in people sniffing a lot of glue:
Smooth ER
The golgi has 5 main jobs:
- Distribution center
- Modifies N-linked oligosaccharides
- Adds O-oligosaccharides
- Adds M-6-P
- Forms proteoglycans / sulfates sugars
N-linked oligosaccharides are modified on which amino acid? in which organelle does this happen? In what organelle were they added to a protein in the first place?
Asparagine
Golgi
rER
O-linked oligosaccharides are modified by the golgi on two amino acids:
Serine
Threonine
What happens if mannose-6-phosphate is not added to certain proteins in the golgi?
I-cell disease = inclusion cell disease. M-6-P targets proteins to the lysosome. No M-6-P = proteins leave the cell instead of going to the lysosome.
What is the enzyme that adds M-6-P to lysosome proteins in the golgi?
Phosphotransferase.
Three features of I cell disease:
Coarse facies
Clouded corneas
Restricted joint movement…
2/2 high levels of lysosomal enzymes
This organelle catabolizes very long chain fatty acids and amino acids:
Peroxisome
Three modes of protein degradation:
- Ubiquitin-dependent (in a proteasome)
- Lysosomal
- Calcium-dependent cytosolic enzymes
What is the cause of I cell disease?
Deficiency in M-6-P leading to defective trafficking of lysosomal-bound proteins and excretion.
5 drugs that act on microtubules:
Mebendazole / thiabendazole (for BENDy worms) Griseofulvin Vincristine / vinblastine Paclitaxel Colchicine
What does Chediak-Higashi syndrome have to do with microtubules?
LYST = mutated lysosome traffic regulator gene. Needed for microtubule-dependent sorting of endosomal proteins into late endosomes.
This protein is responsible for retrograde movement down the micrtubule.
This one is responsible for anterograde.
Dynein (moves from assembing end to assembling end).
Kinesin
Characteristic arrangement of microtubules in a cilum:
9+2
Defect found in Kartagener’s syndrome:
Immotile cilia
Defect is in the dynein arm.
Connective tissue can be identified by this immunohistochemical stain:
Vimentin
Muscle can be identified by this immunohistochemical stain:
Desmin
Epithelial cells can be identified by this immunohistochemical stain:
Cytokeratin
Neuroglia can be identified by this immunohistochemical stain:
GFAP identifies neuroGlia
This immunohistochemical stain identifies Neurons:
Neurofilament stain
This immunohistochemical stain can be used to identify adrenal neuroblastoma:
Neurofilament
This immunohistochemical stain can be used to identify astrocytomas:
GFAP
Cilia use this organizational feature to coodinate contraction:
Gap junctions
This drug inhibits the Na+/K+ ATPase by binding to the K+ site:
Ouabain
Drug that inhibits the Na+/K+ ATPase directly:
Digoxin / digitoxin
Type of collagen defective in OI:
Type I
Type of collagen most frequently defective in Ehlers-Danlos:
Type III
Type of collagen defective in Alport syndrome:
Type IV
Where would you find Type I collagen?
Bone
Skin
Tendons
Where would you find Type II collagen?
Cartilage
Where would you find Type III collagen?
Reticulin-containing organs: Skin Blood vessels Uterus / fetal tissue Granulation tissue
Where would you find Type IV collagen?
Basement membrane
Collagen synthesis begins with this molecule:
Pre-pro-collagen
Hydroxylation of pre-pro-collagen requires this vitamin:
Vitamin C
Deficiency in vitamin C leads to a defect at which point in the synthesis of collagen?
Hydroxylation of pre-pro-collagen at lysine and proline residues.
What is procollagen made of?
Glycosylated hydroxylysine residues wound in a triple helix.
What structural feature of pro-collagen is distorted in osteogenesis imperfecta?
Triple helix
Problems with cross-linking tropocollagen lead to this inherited connective tissue disease:
Ehlers-Danlos
Mode of inheritence of OI:
Autosomal dominant
Four very common presenting features of OI:
- Multiple fractures, minimal trauma
- Blue sclerae
- Hearing loss
- Dental problems due to lack of dentin
What is the defect in Alport syndrome?
Type IV collagen
Most common mode of inheritence for Alport syndrome:
X-linked recessive
Three common features of Alport syndrome:
- Progressive hereditary nephritis
- Deafness
- Lenticonus = thinning of capsule around lens
“Can’t SEE, can’t PEE, can’t HEAR me.”
Enzyme that breaks down elastin?
Protein that inhibits this enzyme?
Elastase
a1-antitrypsin
Emphysema in a young non-smoker, think:
a1-antitrypsin deficiency
Marfan’s syndrome is caused by a defect in this protein. What is its function?
Fibrillin.
Function is to be the “scaffold” for tropoelastin in elastin formation.
In what tissues is elastin particularly important?
Blood vessels
Alveoli
Larynx
Spine
First step in the metabolism of alcohol is catalyzed by this enzyme:
Drug that inhibits this enzyme?
Alcohol dehydrogenase.
Fomepizole
The enzyme alcohol dehydrogenase is limited by this reagent:
NAD+
Enzyme that catalyzes acetaldehyde -> acetate in alcohol metabolism:
Drug that inhibits this enzyme?
Acetaldehyde dehydrogenase.
Antabuse
Antidote for methanol and ethylene glycol poisoning?
Fomepizole
Mechanism of action of antabuse:
Blocks acetaldehyde dehydrogenase, allows acetaldehyde to build up. Instant hang-over.
Explain the mechanism behind ethanol-induced hypoglycemia (5 steps):
- NADH/NAD+ ratio is increased (need NAD+ to metabolize alcohol)
- Detoxifying = more important than gluconeogenesis, so pyruvate -> lactate and OAA -> malate to generate NAD+ for detox.
- TCA cycle shuts down, depletion of OAA.
- Acetyl CoA -> ketone production, not gluconeo.
- Malate -> NADPH -> FA synthesis.
Severe protein malnutrition is aka:
Four big signs:
Kwashiorkor
Malnutrition (skin lesions, hypopigmentation)
Edema (protein holds water in place)
Anemia
Liver is fatty (can’t make apoB100, fats can’t leave liver)
Energy malnutrition is aka:
Marasmus
Rate-limiting enzyme for glycolysis:
Phosphofructokinase-1
= PFK-1
Rate-limiting enzyme for gluconeogenesis:
Fructose-1,6-bisphosphatase
Rate-limiting enzyme for glycogen synthesis:
Glycogen synthase
Rate-limiting enzyme for glycogenolysis:
Glycogen phosphorylase
This enzyme is responsible for trapping glucose in the cell:
Version in the liver and glucose-regulating cells? Version in skeletal muscle and adipose?
Glucokinase
LIver cells have glucokinase
Adipose / skeletal muscle cells have hexokinase
Enzyme responsible for glucose-6-phosphate release from the cell as glucose:
Glucose-6-phosphatase
Enzyme responsible for generating pyruvate:
Pyruvate kinase
Enzyme responsible for converting pyruvate to oxaloacetate:
Pyruvate carboxylase
Enzyme that sends pyruvate into the TCA cycle:
5 co-factors required to do this:
Pyruvate dehydrogenase Makes Acetyl-CoA from pyruvate Thiamine (B1) Lipoic acid CoA (B5) FAD (B2) NAD (B3 = niacin)
Main presenting feature of glycolytic enzyme disease:
RBC cannot maintain their Na/K-ATPase -> hemolytic anemia.
Most common glycolytic enzyme deficiency:
Pyruvate kinase deficiency
Pyruvate has four major fates. What are they, and what is the rate-limiting enzyme that takes it down that path?
- Alanine cycle (ALT)
- Cori cycle (make lactate, LDH)
- TCA cycle (PDH, make acetylCoA)
- Oxaloacetate (Gluconeogenesis, P.carboxylase)
Three main features of arsenic poisoning:
Garlic breath
Vomiting
Rice water stool
Pyruvate dehydrogenase deficiency can come about in three ways:
Congenital (X-linked)
Acquired (arsenic poisoning, vitamin deficiency)
Pyruvate dehydrogenase deficiency results in this major metabolic disturbance. Why?
Lactic acidosis, this is because pyruvate can’t enter the TCA cycle, so it builds and gets shunted down the Cori cycle.
Treatment of pyruvate dehydrogenase deficiency:
High fat diet
Lysine and Leucine onLy pureLy ketogenic amino acids
Vitamin deficiencies that can lead to pyruvate dehydrogenase deficiency:
Thiamine (B1) Lipoic acid (remember arsenic messes this one up) CoA (B5) FAD (B2) NAD (B3, niacin)
Enzyme that starts the Kreb cycle:
Citrate synthetase
Substances that inhibit Complex I of the ETC (3):
Amytal (barbiturate)
Rotenone (fish poison)
MPP (from MPTP, of home opiate lab fame)
This substance inhibits Complex III of the ETC:
Antimycin A
These substances inhibit Complex IV of the ETC (4):
CN
CO
H2S
N3 (sodium azide)
This substance inhibits Complex IV of the ETC, aka the ATP synthase:
Oligomycin
Name as many substances that are wrenches in the ETC as you can:
Rotenone Amytal MPP Antimycin A CN CO N3- H2S
What is the goal, overall, in simplistic terms, of the ETC?
- Send NADH electrons down a chain of molecules.
- Build high H+ concentration in the intermembranous space, use it to drive ATP production in the mitochondrial matrix.
- Final acceptor = water.
What is the mechanism of action of oligomycin?
It directly inhibits ATP synthesis.
What is an uncoupling agent?
Can you name 3?
Something that increases the permeability of the mitochondrial inner membrane. This causes consumption of oxygen and dissipation of heat.
2,4-DNP, aspirin, thermogenin
Why can’t muscle do gluconeogenesis?
It does not have glucose-6-phosphatase, can’t release glucose.
T/F: Even chain fatty acids can serve as a glucose source.
F. They can only make acetyl-CoA. Odd chain FA yield propionyl-CoA, which can go into the TCA cycle.
What are the four irreversible enzymes of gluconeogenesis?
Pathway Produces Fresh Glucose: Pyruvate carboxylase PEP carboxykinase Fructose-1,6-bisphosphatase Glucose-6-phosphatase
What five really huge things do you need NADPH for?
Needed for reductive reactions: 1. Making fatty acids / cholesterol 2. Making O2 free radicals 3. Protecthing RBCs from free radicals 4. In the CYP450 system Also needed for: 5. Ribose (nucleotide synthesis)
Which tissues in the body use the pentose phosphate pathway?
Lactating mammary glands
Liver
Adrenal cortex (… anything making fatty acids / steroids)
RBCs (reducing, protect themselves)
Three important enzymes in respiratory burst and what each makes:
NADPH oxidase (makes O2 free radicals)
SOD (makes H2O2)
Myeloperoxidase (makes HoCl)
NADPH oxidase deficiency results in this immune deficiency disease:
Chronic granulomatous disease
What is the overall purpose of the HMP shunt (aka pentose phosphate pathway)?
Make NADPH from G-6-P.
NADPH = used in reductive reactions.
Think of this as the body’s endogenous anti-oxidant when it is in its reduced form:
Glutathione
Enzyme defect that leads to an inability to keep glutathione reduced:
G-6-P deficiency, these cells have no NADPH to help them.
Mode of inheritence of G-6-P deficiency:
X-linked recessive
Two features of RBCs in someone with G-6-P deficiency:
Heinz bodies = oxidized Hb
Bite cells
Pathogenesis behind G-6-P deficiency:
Low NADPH in RBC -> hemolytic anemia especially in the presence of oxidizing agents
Name 5 things that can precipitate massive hemolysis in someone with G-6-P deficiency:
Infection TB drugs Sulfonamides Fava beans Primaquine
The milder disorder of fructose metabolism:
Essential fructosuria
Deficiency of aldolase B:
What does it cause?
Fructose intolerance. Fructose -> fructose-1-phosphate eats up available phosphate. Glycogenolysis and gluconeogenesis are both inhibited.
Symptoms of fructose intolerance:
Vomiting
Hypoglycemia
Cirrhosis
Jaundice
Symptoms of essential fructosuria:
Mild diuresis on high intake, otherwise none.
Enzyme deficient in essential fructosuria?
In fructose intolerance?
Essential fructosuria = fructokinase
Fructose intolerance = aldolase B (FAB)
Two disorders of sugar metabolism that can cause infantile cataracts:
Which is the more severe?
Galactokinase deficiency
Galactosemia *
Substance that accumulates in galactokinase deficiency:
Glactitol
Enzyme defective in classic galactosemia:
T/F: This enzyme is used earlier in galactose metabolism than galactokinase, resulting in more severe disease.
Galactose-1-P uridyltransferase.
F. This enzyme is actually downstream, both galactose-1-P and galactitol build up -> cataracts, liver problems, mental retardation.
What is the action of insulin on protein kinase A and glycolysis?
INsulin INactivates glycogenolysis.
Epinephrine and glucagon share this action on protein kinase A
They both increase cAMP and activate protein kinase A
