First Aid - Biochem

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What are the 4 types of collagen and what do they make?

Type 1-4
1: bone, skin, tendon, cornea
2: cartilage
3: skin, blood vessels, granulation tissue, uterus, RETICULIN
4: basement membrane

What does type 1 collagen make?

Bone, skin, tendons, cornea

What does type 2 collagen make?

Cartilage

What does type 3 collagen make?

Blood vessels, skin, granulation tissue, uterus
Aka reticulin

What does type 4 collagen make?

Basement membrane of kidneys, ears and eyes

How is vitamin C related to collagen?

Hydroxylates proline and lysine

Where does hydroxylation of collagen take place?

ER - needs vitamin C

What step of collagen formation is inhibited in scurvy and why?

Hydroxylation (of proline and lysine residues of preprocollagen)

What step of collagen formation in inhibited in osteogenesis imperfecta?

Glycosylation (of alpha chains into procollagen/triple helix)

What step of collagen formation is inhibited in Ehlers-Danlos?

Cross-linking of collagen fibrils (tropocollagen)

What is Ehlers-Danlos syndrome?

Faulty collagen synthesis (TYPE 3 and 1) causing:
1. hyperextensible skin
2. easy bruising (tendency to bleed)
3. hypermobile joints

What is osteogenesis imperfecta?

Genetic bone disorder (brittle bone disease)
Most common in autosomal dominant (so will have family history)
Abnormal TYPE 1 collagen causing:
1. multiple fractures with minimal trauma (may look like child abuse)
2. blue sclerae due to translucency of tissue over veins
3. hearing loss (abnormal middle ear bones)
4. dental imperfections due to lack of dentin

What is Alport's syndrome?

Abnormal TYPE 4 collagen (basement membrane)
X-linked recessive
Progressive hereditary nephritis and deafness; may have ocular disturbances

What is elastin?

Stretchy protein within lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (vertebrae)
Rich in proline and lysine (nonglycosylated)
Broken down by elastase (normally inhibited by alpha-1-antitrypsin

What usually breaks down elastin? What inhibits that enzyme?

Broken down by elastase
Elastase inhibited by alpha-1-antitrypsin

What 2 diseases are associated with defects in elastin/its pathway to be broken down?

Marfan's and emphysema

Marfan's syndrome is caused by a defect in what?

Fibrillin

Emphysema caused by alpha-1-antitrypsin deficiency results in what? What type of emphysema?

Results in excess elastase activity
Panacinar emphysema (all over acini, not just centralized)

A kid comes in with nephritis and deafness with a positive fam history of the same symptoms mostly in males. What disease?

Alport's sydrome (abnormal type 4 collagen)

What are fat soluble vitamins? What are they important for?

ADEK

A - eye and skin
D - bones (calcium)
E - antioxidant
K - clotting factors

What vitamins are water soluble? What are they important for?

Bs, C, folate, B12

Bs - metabolic
C - collagen synthesis, antioxidant
folate - blood, neural development
B12 - blood, CNS

Where are fat soluble vitamins absorbed? What diseases can cause a fat soluble vitamin deficiency?

Absorbed in the ileum (so dependent on gut and pancreas to digest fats)
Malabsorption syndromes with steatorrhea (CF, celiac) can cause deficiencies

Deficiency of which vitamin is associated with pellagra?

B3 (niacin)

Niacin is essential for which cofactor?

NAD+

Riboflavin is essential for which cofactor?

FAD

Vitamin A (retinol) is necessary for what? What is it found in?

Normal differentiation of epithelial cells into specialized tissue
Constituent of visual pigments
Antioxidant
Found in liver and leafy veggies

How does vitamin A deficiency manifest?

Night blindness, dry skin

What can vitamin A be used to treat? What must you do before prescribing it?

Used topically for wrinkles and acne; for APL
TERATOGENIC so pregnancy test must be done before giving it for skin probs

What is vitamin B1?

Thiamine

What is thiamine needed for in the body?

Cofactor for many enzymes (pyruvate dehydrogenase in glycolysis, alpha-ketoglutarate dehydrogenase in TCA cycle, transketolase in HMP shunt, branched-chain AA dehydrogenase)

A deficiency in thiamine can lead to what? What is it associated with?

Impaired glucose breakdown -> ATP depletion (worsens with glucose infusion), highly aerobic structures like brain and heart are affected first
Associated with malnutrition and alcoholism

A deficiency in thiamine can lead to what diseases?

Wernicke-Korsakoff (confusion, opthalmoplegia, ataxia, confabulation) -> damage to medial dorsal nucleus of thalamus and mamillary bodies

What brain structures are damaged in thiamine deficiency?

Medial dorsal nucleus of the thalamus (memory, organization) and mamillary bodies (memory)

Vitamin B2 is aka?

Riboflavin

What is the function of riboflavin?

Cofactor in oxidation and reducation

What 2 things are derived from riboflavin?

FAD and FMN
B2 = 2 ATP

What diseases are caused by riboflavin deficiency?

Cheilosis (inflammation of lips, scaling and fissures at corners of mouth)
Corneal vascularization
THE 2 C's -> cheilosis and corneal vascularization

What is vitamin B3 aka?

Niacin

What is the function of niacin?

Constituent of NAD, NADP (used in redox reactions)
B3 = 3 ATP

Niacin is derived from what?

Tryptophan

Deficiency of niacin is associated with what diseases?

1. Pellagra (dermatitis, diarrhea, dementia)
2. Hartnup - decreased tryptophan absorption
3. Malignant carcinoid syndrome - increased tryptophan metabolism due to increased 5-HT release
4. Isoniazid therapy (since decreases B6 and B6 is needed to make B3)

What is the function of B5/pantothenate?

Essential component of CoA (cofactor for acyl transfers) and fatty acid synthase

What is the function of B6/pyroxidine?

Cofactor used in transamination (ALT, AST), glycogen phosphorylase, heme synthesis
Required for synthesis of niacin from tryptophan

What symptoms are associated with B6 deficiency?

Convulsions, hyperirritability, peripheral neuropathies, sideroblastic anemia
Deficiency inducible by Isoniazid and birth control pills

What is the function of B12?

Cofactor for homocysteine methyltransferase (transfers methyl groups to methionine) and methylmalonyl-CoA mutase

What symptoms are associated with B12 deficiency?

Macrocytic, Megaloblastic anemia, hypersegmented PMNs, NEUROLOGIC SYMPTOMS due to abnormal myelin
Prolonged deficiency can lead to irreversible nervous system damage

What is the most common causes of B12 deficiency?

Malabsorption (celiac, enteritis, bacteria)
Pernicious anemia (lack of IF)
Lack of a terminal ileum (Crohn's, celiac)

What test do you use to discover the etiology of B12 deficiency?

Schilling test

What is the function of folic acid?

Coverted to THF, a coenzyme for 1-carbon transfer/methylation reactions
Important for synthesis of nitrogenous bases in DNA and RNA

What drugs can cause a folate deficiency?

Methotrexate, sulfonamides, phenytoin (inhibits intestinal absorption of folate)

What symptoms are associated with folic acid deficiency?

Macrocytic, megaloblastic anemia, hypersegmented neuts, NO NEUROLOGICAL DEFECTS

What is the most common vitamin deficiency in the US?

Folate
Seen in alcoholism and pregnancy

What substrate regenerates methionine (takes a methyl off to make homocysteine so it can be turned into methionine again)?

S-adenyl-methionine (SAM) - donates a methyl group

What substrate is required for the conversion of NE to epi?

SAM (S-adenosul-methionine) - transfers a methyl from methionine to generate it (makes homocysteine from methionine so homocysteine can get another methyl from B12 to make methionine)

What is the function of biotin?

Cofactor for carboxylation enzymes (which add a 1-carbon group)

What causes biotin deficiency? What are symptoms of a deficiency?

Antibiotic use
Excessive ingestion of raw eggs (binds biotin)
Symptoms = dermatitis, alopecia, enteritis (deficiency is relatively rare)

What is the function of vitamin C?

Antioxidant
Facilitates iron absorption by keeping iron in Fe2+ reduced state (more absorbable)
Necessary for hydroxylation of proline and lysine in collagen synthesis
Necessary to convert DA to NE

What does a deficiency in vitamin C present as?

SCURVY! - swollen gum, bruising, hemarthroses, anemia, poor wound healing; weakened immune response

What is the function of vitamin d?

Increase intenstinal absorption of Ca and P
Increase bone resorption

What type of vitamin D is ingested from plants? What kind is found in milk? What kind is formed in sun-exposed skin?

Plants - D2
Milk - D3
Sun - D3

What diseases does vitamin D deficiency result in?

Children - rickets
Adults - osteomalacia
Both - hypocalcemic tetany (decreased threshold)

What disease commonly has an increase in vitamin D and consequently Ca?

Sarcoid (granulomatous tissue has 1-alpha hydroxylase, which forms active vitamin D)

What is the function of vitamin E?

Antioxidant (protects erythrocytes and membranes from free-radical damage)

What does a deficiency in vitamin E look like?

Increased fragility of RBCs => hemolytic anemia

What is the function of vitamin K?

Catalyzes gamma-carboxylation of glutamic acid residues on various proteins concerned with blood clotting
Synthesized by intestinal flora

What does a deficiency of vitamin K present like in a newborn? Why?

Neonatal hemorrhage with increased PT and PTT but normal bleeding time
Neonates don't have intestinal bacteria so they can't make vitamin K -> get a vitamin K shot after born

What factors need vitamin K to be made?

2, 7, 9, 10
Protein C and S

In vitamin K deficiency, what clotting pathway would be most effected?

Extrinsic (7->10->2->thrombin)

What is the function of zinc?

Essential for activity of 100s of enzymes
Important for formation of zinc fingers (transcription factor motif)

What does a deficiency of zinc look like?

Delayed wound healing, hypogonadism, decrease in adult hair (axillary, facial, pubic), loss of taste and smell (dysgeusia and anosmia)
May predispose to alcoholic cirrhosis

What is the limiting reagent in alcohol metabolism? What is its precursor?

NAD+
Made from niacin

What are the steps in ethanol metabolism?

Ethanol to acetaldehyde by alcohol dehydrogenase
Acetaldehyde to acetate by acetaldehyde dehydrogenase

Where are the steps in ethanol metabolism found in the cell?

1st step in cytosol
2nd step in mitochondria

What is fomepizole and what does it do?

Inhibits alcohol dehydrogenase and is antidote for methanol or ethylene glycol poisoning

What is the antidote for methanol or ethylene glycol poisoning? What does it do?

Fomepizole - inhibits alcohol dehydrogenase

What is disulfiram and what is it used for?

It's Antabuse -> inhibits acetylaldehyde dehydrogenase and gives alcoholics hungover feeling whenever they ingest alcohol

What drug inhibits acetylaldehyde dehydrogenase and why is it useful?

Disulfiram (Anatabuse) -> used for alcoholics since it inhibits the enzyme that takes away acetylaldehyde when alcohol is ingested
Acetylaldehyde is what causes hungover feeling

Alcohol dehydrogenase operates via what kind of kinetics?

Zero-order (operates independent of substrate concentration -> always detoxes 1 drink/hour no matter what)

How does alcohol abuse lead to hypoglycemia?

Ethanol metabolism increases NADH/NAD+ ratio in liver (metabolism uses NAD+ to make NADH), causing:
1. diversion of pyruvate to lactate
2. OAA to malate
Inhibits gluconeogenesis and stimulates fatty acid synthesis (why alcoholics have fatty livers)

What is Kwashiorkor?

PROTEIN deficiency resulting from:
M - malnutrition
E - edema
A - anemia
L - liver (fatty change due to decrease apolipoprotein synthesis)

What is Marasmus?

ENERGY malnutrition resulting in MUSCLE wasting, loss of subQ fat and variable edema

What is the difference between Kwashiorkor and marasmus?

Kwashiorkor - PROTEIN deficiency due to malnutrition, edema, anemia or liver (fatty)
Marasmus - ENERGY deficiency resulting in muscle wasting, loss of subQ fat, edema

What metabolic processes take place in the mitochondria?

Beta oxidation of fatty acids (matrix)
Acetyl CoA production (glycolysis) (matrix)
TCA cycle (matrix)
Oxidative phosphorylation (inner membrane)
Ketogenesis (matrix)

What metabolic processes take place in the cytoplasm?

Glycolysis
Fatty acid synthesis
HMP shunt
Protein synthesis (rER)
Steroid synthesis (sER)

What metabolic processes take place in both in the mitochondria and the cytoplasm?

Heme synthesis
Urea cycle
Gluconeogenesis

Where does beta oxidation take place?

Mitochondrial matrix

Where does acetyl CoA get made?

Mitochondrial matrix

Where does the TCA cycle take place?

Mitochondrial matrix

Where does oxidative phosphorylation take place?

Inner mitochondrial membrane

Where does ketogenesis take place?

Mitochondrial matrix

Where does glycolysis take place?

Cytosol

Where does fatty acid synthesis take place?

Cytosol

Where does the HMP shunt take place?

Cytosol

Where does protein synthesis take place? Which ER?

Cytosol
rER

Where does steroid synthesis take place? Which ER?

Cytosol
sER

Where does heme synthesis take place?

Both the mitochondial matrix and the cytosol

Where does the urea cycle take place?

Both the mitochondrial matrix and the cytosol

Where goes gluconeogenesis take place?

Both the mitochondrial matrix and the cytosol

What does a "kinase" do?

Uses ATP to put a phosphate group onto another substrate
i.e. glucokinase puts a phosphate on glucose

What does a "phosphorylase" do?

Adds inorganic phosphate onto substrate without using ATP
i.e. glycogen phosphorylase

What does a "phosphatase" do?

Removes phosphate group from substrate

What does a "dehydrogenase" do?

Oxidizes substrate (removes H)

What does a "carboxylase" do?

Adds 1 carbon with the help of biotin

What is the rate determining enzyme of glycolysis?

Phosphofructokinase-1 (PFK-1)

What is the rate determining enzyme of gluconeogenesis?

Fructose-1,6-bisphosphatase

What is the rate determining enzyme of the TCA cycle?

Isocitrate dehydrogenase

What is the rate determining enzyme of glycogen synthesis?

Glycogen synthase

What is the rate determining enzyme of glycogenolysis?

Glycogen phosphorylase

What is the rate determining enzyme of the HMP shunt?

Glucose-6-phosphate dehydrogenase (G6PD)

What is the rate determining enzyme of de novo pyrimidine synthesis?

Carbamoyl phosphate synthetase II

What is the rate determining enzyme of de novo purine synthesis?

Glutamine-PRPP amidotransferase

What is the rate determining enzyme of the urea cycle?

Carbamoyl phosphate synthetase I

What is the rate determining enzyme of fatty acid synthesis?

Acetyl CoA carboxylase (ACC)

What is the rate determining enzyme of fatty acid oxidation?

Carnitine acyltransferase I

What is the rate determining enzyme of ketogenesis?

HMG-CoA synthase

What is the rate determining enzyme of cholesterol synthesis?

HMG-CoA reductase

Phosphofructokinase-1 is the rate determining enzyme for what?

Glycolysis

Fructose-1,6-bisphosphate is the rate determining enzyme for what?

Gluconeogenesis

Isocitrate dehydrogenase is the rate determining enzyme for what?

TCA cycle

Glycogen synthase is the rate determining enzyme for what?

Glycogen synthesis

Glycogen phosphorylase is the rate determining enzyme for what?

Glycogenolysis

Glucose-6-phosphate dehydrogenase is the rate determining enzyme for what?

HMP shunt

Carbamoyl phosphate synthetase II is the rate determining enzyme for what?

De novo pyrimidine synthesis

Glutamine-PRPP amidotransferase is the rate determining enzyme for what?

De novo purine synthesis

Carbamoyl phosphate synthetase I is the rate determining enzyme for what?

Urea cycle

Acetyl-CoA carboxylase is the rate determining enzyme for what?

Fatty acid synthesis

Carnitine acyltransferase I is the rate determining enzyme for what?

Fatty acid oxidation

HMG-CoA synthase is the rate determining enzyme for what?

Ketogenesis

HMG-CoA reductase is the rate determining enzyme for what?

Cholesterol synthesis

In chromatin structure, what is positively and negatively charged?

DNA is negatively charged
Histones are positively charged
Histones form an octomer around which DNA winds

What histones are part of the octomer core that DNA wraps around?

H2a, H2b, H3, H4

Which histone is NOT part of the octomer core?

H1

What is heterochromatin?

Condensed, transcriptionally inactive, sterically inaccessible

What is euchromatin?

Less condensed, transciptionally active, sterically accessible

What type of chromatin is able to be transcribed? What type is not?

Able to be copied = euchromatin
Unable to be copied = heterochromatin

What type of chromatin is condensed? What type isn't? What does that mean for transcription?

Condensed = heterochromatin -> unable to be copied
Not condensed = euchromatin -> able to be copied

What nucleotides are purines? What ones are pyridimines?

Purines = adenine and guanine
Pyridimines = cytosine, uracil, thymine

Which nucleotides have 2 rings? Which ones have only 1 ring?

Purines have 2 rings
Pyridimines have 1 ring

Uracil is found in what? Thymine is found in what?

Uracil - RNA
Thymine - DNA

Which nucleotide bases bond together? How many bonds are between each pair?

cytosine and guanine - triple bond
adenine and thymine/uracil - double bond

How does nucleotide composition affect the melting temp?

More C-G increases melting temp

Deamination of cytosine makes what?

Uracil

Which nucleotide has a ketone?

Guanine

Which nucleotide has a methyl?

Thymine (THYmine has a meTHYl)

What is a nucleoside composed of?

Base + ribose

What is a nucleotide composed of?

Base + ribose + phosphate

What amino acids are necessary for purine synthesis?

Glycine
Aspartate
Glutamine

What bond links nucleotides?

3'-5' phosphodiester bond

What precursor are purines made from? Pyridimines?

Purines - IMP
Pyridimes - orotate

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