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Genetics And Biochem Flashcards

1
Q

ECM components

A 
1. Fibers
  A. Loose CT
  B. Dense regular elastic CT
  C. Dense regular collagenous CT
2. Ground substance
  A. Adhesion proteins
    1. Fibronectin
    2. Laminin
3. Cells: mostly fibroblasts
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2
Q

Collagen

A
  1. Most abundant protein in human body
  2. Very long lived
  3. 25< types
    A. 30 different genes
  4. Ubiquitously present in different organs and systems
  5. Grouped by structure
    A. Fibrous protein
    B. 3 alpha-chains
    1. Each polypeptide ~1000 aa
    2. Different chains encoded by different genes -> different combos -> many collagen types
      C. Intrachain H-bonds
      D. Rich in glycine (30%) and proline (20%)
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3
Q

Modified aa in collagen

A 
1. Hydroxylated aa
  A. Hydroxyproline
  B. Hydroxylysine: can be further modified to glycosylation
2. Enzyme = prolyl hydroxylase
3. Requires
  A. O2
  B. Fe2+
  C. Ascorbate (vitamin C)
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4
Q

Collagen cross-linking

A 
Enzyme: lysyl oxidase
1. Copper-containing
2. Extracellular
3. Oxidatively deaminates lysine and hydroxylasine residues -> reactive aldehydes (allysine and hydroxyallysine)
  A. Form covalent cross links
4. Copper homeostasis diseases
  A. Menkes syndrome
  B. Wilson’s disease
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5
Q

Elastic fibers

A 
1. Composition
  A. Elastin
    1. Extensively interconnected 
    2. Rubbery
    3. Stretch/bend any direction
    4. Lysyl oxidase- modifies lysyl side chains in tropoelastin -> desmosine cross-linking
    5. Insoluble protein polymer synthesis from precursor tropoelastin
  B. Fibrillins
    1. Family of large glycoproteins
    2. Fibrillin-1 = major one
    3. Scaffold for elastin
2. Genetic defects
  A. Marfan syndrome
  B. Williams -Beuren syndrome
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6
Q

Laminin

A

Adhesion protein
1. Structure
A. Large cross-shaped glycoproteins
1. Heterotrimer encoded by different genes
2. 15 < different laminins
2. Fxn:
A. Hold together basement membrane components
B. Adhesion w/ overlying cells
C. Trigger physiological responses, growth, movement
3. LAMA 2-related muscular dystrophy

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7
Q

Fibronectins

A

Adhesion proteins
1. Structure
A. Most abundant multi-adhesive protein in CT
B. Large protein
1. 2 similar polypeptide chains linked by disulfide bonds
2. Fxns:
A. Glues cells to fibrous mesh work of ECM
B. Embryogenesis- cell movement
C. Cancer- metastasis

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8
Q

Proteoglycans

A 
Complexes of heteropolysaccharides (95% carbs, 5% proteins)
1. Fxns:
  A. Gel-like matrix forming basis of ground substance
  B. Flexible support for ECM
  C. Movement of material thru ECM
  D. Contribute to viscous, lubricating properties of mucous
2. Aggregate structure 
  A. Proteoglycans monomers
    1. Glycosaminoglycans (GAGs)
    2. Core proteins
  B. Hyaluronic acid (type of GAG)
  C. Link protein
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9
Q

Glycosaminoglycans (GAGs)

A
  1. Large complex (-) heteropolysaccharide chains
  2. Branched
  3. Repeating disaccharide units
    A. [acidic sugar-amino sugar]n
    1. Amino sugar
      A. Acetylated (eliminates (+))
      B. Can be sulfated (enhance (-))
  4. (-) charge important for hydrophilicity
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10
Q

GAG classification

A 
1. Based on
  A. Monomeric composition
  B. Type of glycosidic linkages
  C. Degree and location of sulfate units
2. Classes
  A. Chondroitin 4-and 6-sulfates
  B. Keratan sulfates (KS) I and II
  C. Hyaluronic acid
  D. Dermatan sulfate
  E. Heparin
  F. Heparan sulfate
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11
Q

Keratan sulfates (KS) I and II

A
  1. Most heterogenous GAG bc contains additional monosaccharides
  2. KS I: corneas
  3. KS II: loose CT proteoglycan aggregates w/ chondroitin sulfates
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12
Q

Chondroitin 4- and 6-sulfates

A
  1. Most abundant GAG in body
  2. Locations: cartilage (bind collagen), tendons, ligaments
  3. Form proteoglycan aggregates thru monovalent association w/ hyaluronic acid
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13
Q

Hyaluronic acid

A 
1. Different from other GAGs
    A. Not sulfated
    B. Not covalently bound to proteins
    C. Also in bacteria
2. Fxn: lubricant and shock absorber
3. Location: synovial fluid, vitreous humor, umbilical cord, loose CT, cartilage
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14
Q

Dermatan sulfate

A 
GAG
1. Locations: 
  A. Skin
  B. Blood vessels
  C. Heart valves
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15
Q

Heparin

A 
GAG
1. Only intracellular one
  A. Mast cells
    1. Arteries in liver, lung, and skin
2. Fxn: anticoagulant
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16
Q

Heparan sulfate

A

GAG
1. Locations:
A. Basement membrane
B. Ubiquitous component of cell surfaces

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17
Q

GAG metabolism

A 
1. Synthesis
  A. Core protein- endoplasmic reticulum
  B. Carb chains- Golgi
  C. Sulfation- ECM
2. Degradation
  A. Endocytosis 
  B. Lysosomes: specific acid hydrolases
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18
Q

Glucose transporters

A 
1. Mechanism
  A. GLUT proteins span membrane
  B. Facilitated diffusion
  C. Glucose binds -> conformational change
2. Isoforms: GLUT 1-5
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19
Q

GLUT 1

A
  1. Erythrocytes
  2. BBB
  3. Blood-placental barrier
  4. Blood-testes barrier
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20
Q

GLUT 2

A
  1. Liver
  2. Kidney
  3. Pancreatic beta-cells
  4. Serosal surface of intestinal mucosa
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21
Q

GLUT 3

A
  1. Brain
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22
Q

GLUT 4

A
  1. Adipose tissue
  2. Skeletal muscle
  3. Heart muscle
  4. Intracellular
    A. Insulin -> move to plasma membrane
23
Q

GLUT 5

A
  1. Intestinal epithelium
  2. Spermatozoa
  3. Fructose transporter
24
Q

Glucose activation

A

Hexokinase: glucose -> G-6-P

  1. 3 isoforms: I, II, and III
  2. Most tissues
  3. Inhibited by end product
  4. High affinity for glucose => low Km
  5. Low Vmax
25
Q

Glycolysis regulation

A 
Phosphofructokinase-1 (PKF-1)
1. Irreversible
2. Rate-limiting and committed step
3. Inhibitors
  A. ATP
  B. Citrate
4. Activators
  A. Muscles: AMP (inc AMP/ATP ratio)
  B. Liver: F-2,6-BisP
26
Q

Anaerobic glycolysis in muscle

A 
Lactate
1. Normal
  A. Exceeding skeletal muscle 
  B. Lactate build-up -> dec. pH and cramping
  C. Lactate outcomes
    1. Plasma
    2. Liver
    3. Cori cycle -> pyruvate
2. Abnormal
  A. Hypoxia
  B. Lactic acidosis: dec pH blood
    1. Normal lactate (<2 mmol/L)
    2. Hyperlactermia (2-5 mmol/L) w/o metabolic acidosis
    3. Lactic acidosis (4-5 mmol/L)
27
Q

Pyruvate dehydrogenase complex (PDH)

A
  1. Structure
    A. 3 separate enzymes (E1, E2, E3)
    B. 5 different coenzymes
    1. Thiamine pyrophosphate, TPP: from thiamine (Vit B1)
    2. Lipoamine (synthesized by cells)
    3. Coenzyme-A (CoA): from pantothenic acid (vit B5)
    4. FAD: from riboflavin (Vit B2)
    5. NAD+: from nicotinamide (Vit B3)
  2. Pyruvate -> acetyl-CoA
  3. Vitamin deficiency
  4. Genetic defects in PDH
  5. Arsenic poisoning
  6. Regulation
    A. Substrate activation
    B. Product inhibition
    C. Covalent modification
    1. Kinase -> phosphorylation -> deactivate
    2. Phosphatase-> dephosphorylation -> activate
      D. Kinase and phosphatase allosterically regulated
28
Q

Fatty acid degradation

A
  1. Muscles use long chain FA
  2. Steps
    A. FA-albumin in blood
    B. Acyl CoA synthetase: activation
    C. Carnitine (CPT I): into mitochondria
    D. (CPT II): Fatty acyl CoA into mito matrix
    E. Beta-oxidation -> acetyl CoA -> TCA
  3. Regulation
    A. MCoADC: inhibits malonyl CoA from blocking carnitine
    1. AMP -> AMPK -> MCoADC
      B. ACC-2: stimulates CPT I
    2. AMPK inhibits ACC-2
      C. Myokinase: 2 ADP -> ATP + AMP
  4. CPT-II deficiency
29
Q

TCA cycle

A 
1. Irreversible steps
  A. Citrate synthase
    1. Produces 1st intermediate
    2. Regulation
      A. Substrate activation
      B. Product inhibition
  B. Isocitrate dehydrogenase
    1. Rate-limiting step
    2. Regulated allosterically
      A. Inhibitors: ATP and NADH
      B. Activators: ADP and Ca2+
  C. Alpha-ketogluterate dehydrogenase complex
    1. Similar to PDH complex
      A. Mult copies of 3 enzymes
      B. Same coenzymes
    2. Regulation
      A. Inhibitors: products
      B. Activators: Ca2+ in muscle
30
Q

Redox components of ETC

A 
1. Flavin mononucleotide (FMN)
  A. Complex I
2. Fe-S centers
  A. Complex I, II, and III
3. Fe in Cyt b, c1, c, a, and a3
  A. Complex III and IV
4. Cu in Cyt a and a3
  A. Complex IV
31
Q

Mobile components of ETC

A
  1. CoQ
    A. Between II and III
  2. Cyt C
    A. Between III and IV
32
Q

Coupling in Mitochondria

A
  1. ATP synthesis couples to ETC thru H+ gradient
  2. Change in one affects other
  3. Cardiolipin
    A. 2 molecules esterfied thru PO4 groups
    B. Inner mito membrane
    C. Maintain structure and fun of ETC complexes
33
Q

Uncoupling in Mitochondria

A
  1. H+ flow back w/o making ATP
  2. Non shivering thermogenesis
  3. Natural: uncoupling proteins (UCPa) in inner mito membrane
    A. UCP1: brown adipose tissue
    B. UCP2,3,4,5: other tissues
  4. Synthetic: chem inc permeability inner mito mem to H+
    A. Salicylic acid cmpds (aspirin)
34
Q

ETC inhibitors

A
  1. Rotenone, Amytal: e- from complex I -> CoQ
  2. Antimycin C: e- from complex III -> Cyt C
  3. CO: e- from complex IV -> O2
  4. CN: e- from complex IV -> O2
  5. Atractyloside: inhibits adenine nucleotide translocase (ANT)
  6. Oligomycin: inhibits H+ thru F0 of ATP synthase
35
Q

Lactic acidosis

A
  1. Dec NADH and FADH2 [O] in ETC -> pyruvate -> lactate and FA -> triglyceride
  2. Dec/inhibition of TCA enzymes inhibits CoA [O] -> inc pyruvate and lactate
  3. Genetic defects in mtDNA -> dec ETC and ATP -> anaerobic glycolysis -> lactate and ATP
  4. Interrupt ETC inhibits e- flow and ATP -> anaerobic glycolysis -> lactate and ATP
36
Q

Glycogen

A 
1. Structure
  A. Alpha-1,4-glycosidic bonds
  B. Alpha-1,6-glycosidic bonds
  C. Branch every 8-10 residues
    1. Inc solubility
    2. Inc number nonreducing ends -> faster synthesis and degradation
37
Q

Glycogenesis

A
  1. Glycogen synthase
    A. UDP-glucose -> UDP, glucose added to chain
    B. Rate-limiting step
  2. Glycoenin: initiates glycogenesis by attachment
    A. Serves as primer
    B. Try is attachment point for UDP-glucose
    C. Catalytic activity
38
Q

Glycogenolysis

A 
Glycogen phosphorylase
1. Rate-limiting, regulatory
2. Tissue specific isoforms
  A. Muscle
  B. Liver
39
Q

Regulation of Glucose metabolism

A
  1. Synthesis: inc begins at rest
  2. Degradation: ing during rest
  3. Allosteric regulation
    A. Glycogen phophorylase
    1. Activation: AMP, Ca2+
    2. Inhibited: G-6-P, ATP
      B. Glycogen synthase
    3. Activated: G-6-P
  4. Hormonal regulation
    A. Glycogen phosphorylase
    1. Epinephrine= activated
    2. Insulin = inhibited
      B. Glycogen synthase
    3. Insulin = activated
    4. Epinephrine = inhibited
40
Q

Glycogen degradation in lysosome

A
  1. Enzyme: lysosomal alpha(1,4)-glucosidase
    A. From housekeeping gene
    B. Regulation at protein expression level
    C. Optimal pH 4.5
    D. Only 1-3% of glycogen
    E. Pathway not well understood
    F. GSD Type II: Pompe disease
41
Q

Creatine phosphate

A 
1. Fxn
  A. Reservoir of Pi
  B. Energy during exercise
  C. Transports high-energy PO4
2. Synthesis
  A. Kidney -> liver
  B. Phosphorylation step
    1. Creatine (phospho) kinase (CPK or CK)
    2. Reversible
3. Degradation and excretion
  A. Spontaneous cyclization -> creatinine
  B. Excreted in urine
  C. Diagnostic measure of muscle loss and kidney fxn
42
Q

CK isoforms in clinical diagnostics

A 
1. Structure
  A. Dimer (B and M subunits)
  B. Combinations
    1. CK1 = BB - brain only
    2. CK2 = MB - heart only
    3. CK3 = MM - skeletal muscle and heart
2. Dx role: 
  A. Myocardial infarction
  B. CK2 in plasma for MI
  C. Timing
    1. Appears 4-8 hr after MI
    2. Peaks ~24hr
    3. Returns to baseline 48-72 hrs
43
Q

Type I muscle fibers

A
  1. Slow-twitch
  2. Slow-oxidative (low glycogen)
  3. High myoglobin (red)
  4. Small diameter
  5. Metabolism
    A. Highly vascularized (more O2)
    B. Aerobic metabolism
    C. Resistant to fatigue
    D. Prolonged aerobic exercise
44
Q

Type IIA muscle fibers

A
  1. Intermediate-twitch
  2. Fast-oxidative glycolytic (intermediate glycogen)
  3. High myoglobin (red)
  4. Intermediate diameter
  5. Metabolism
    A. Inc oxidative capacity w/ training
    B. Intermediate resistance to fatigue
45
Q

Type IIB muscle fibers

A
  1. Fast-twitch
  2. Fast-glycolytic (high glycogen)
  3. Low myoglobin (white)
  4. Large diameter
  5. Metabolism
    A. Limited aerobic (low mito)
    B. Sensitive to fatigue
    C. Least efficient (primarily glycolytic)
    D. Sprinting and resistance tasks
46
Q

Myoglobin

A
  1. Soluble, globular protein
    A. 1 chain and 1 heme
  2. Skeletal and heart muscles
  3. Binds O2 from hemoglobin -> Cyt oxidase in ETC
47
Q

Fed (absorptive) state postprandial

A
  1. Timing: 2-6 hr after meal
  2. Plasma:
    A. Inc glucose
    B. Inc AA
    C. Inc TAGS
  3. Pancreas:
    A. Inc insulin
    B. Inc glucose
  4. Tissues
    A. Inc synthesis of glycogen
    B. Inc TAGs
    C. Inc synthesis proteins
  5. Resting skeletal muscles
    A. Amino acids: inc protein synthesis
    1. inc uptake and metabolism branched AA
    2. Inc degradation xs AA
      B. Glucose
    3. Inc GLUT 4 mediated transport
    4. Inc phosphorylation
    5. Inc glycogen synthesis, dec degradation
    6. Inc glycolysis, TCA cycle
48
Q

Fast (post-absorptive) state

A
  1. Timing: >6-12 hr after eating
  2. Plasma: dec glucose, AA, and TAGs
  3. Pancreas: dec insulin, inc glucagon
  4. Inc degradation glycogen, TAGs, and proteins
  5. Resting skeletal muscle
    A. Fasting
    1. Postabsorptive: 6-12 hrs
    2. Prolonged: several days (3-4)
    3. Starvation: several weeks
      B. Glucose
    4. Dec GLUT 4 transport
    5. Dec glycogen synthesis and inc degradation
    6. Dec glycolysis after glycogen used
      C. Fatty acids
    7. Inc flux from adipose lipolysis
    8. Inc FA oxidation
      A. Primary fuel source 1st 2 weeks
      B. Exclusively used during starvation
      D. Ketone bodies: inc flux from liver 1st 2 weeks
      E. Amino acids
    9. Inc degradation protein
    10. Inc AA release -> GNG substrates to liver
    11. Dec degradation after several weeks
49
Q

Metabolic timing during exercise

A
  1. Creatine phosphate: 5-20 sec
  2. Glycolysis ATP: 20 sec-2 min
  3. Oxidative metabolism ATP: thereafter
50
Q

Cardiac muscle energy preferences

A
  1. Can’t store energy
  2. Always aerobic
  3. Rich in myoglobin
  4. Utilizes
    A. FA (60%)
    B. Glucose (35%)
    C. Ketone bodies (5%)
51
Q

Smooth muscle energy preferences

A
  1. Few mitochondria

2. Glycolysis: primary energy source

52
Q

Aerobic exercise training adaptations

A 
1. Inc aerobic capacity
  A. More mitochondria (in fast fibers)
  B. Higher utilization of FA
2. Inc capillary density
  A. Better blood supply
  B. More oxygen
53
Q

Resistance exercise muscle adaptations

A
  1. Inc muscle hypertrophy and hyperplasia
  2. Mechanisms: not well understood
    A. Stimulator of protein synthesis: mTORC1 (mammalian target of rapamycin complex 1)
    B. Inhibition of protein synthesis: myostatin (hormone-like protein released by muscle tissue and circulated in the blood)

MSK (13 decks)

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