Biochemistry MSK Flashcards
What are the different subsets of collagen?
Fibril-forming
Network-forming
Fibril-associated
Explain the structure of the fibrous protein of collagen.
3 a-chains forming a triple stranded rope.
Each chain has 1000 AA
The chain is stabilized by intracranial H-bonds
Each third amino acid is Glycine.
What is the genetic difference of collagen type 1 and 2
Type one is 2 stands coded by a1 genes and 1 strand of a2.
Type two is 3 strands of a1 genes.
Which modified amino acid allows for hydrogen bonding between alpha chains?
Hydroxyproline
Has the OH group.
What things do post-translational hydroxylation require, and what is one disease that can be acquired without one of these things?
O2, Fe2+, Ascorbate (Vitamin C)
Scurvy: less tensile strength of collagen due to lack of H-bond formation.
Which enzyme aids in cross linking of collagen fibers, and what ion does it contain?
Explain that process, and which disorder goes along with genetic problems of crosslinking.
Lysol oxidase, and it has copper to aid in extracellular crosslinking.
Assembly of the triple helix in ER
N and C end proteinases that helped the helix structure are cut off.
Lysol oxidase cavalently links collagen fibrils outside of the cell.
X-linked recessive gene: Menkes Syndrome (kinky hair). Mutations that lead to lack of Cu2+.
Name and describe 2 collagenopathies
Osteogenesis Imperfecta (brittle bone syndrome). Mutations in collagen 1 by replacement of Gly.
Symptoms: blue sclerae, brittle bones
Ehlers-Danlos Syndrome: Defective collagens or processing enzymes. Involve collagen 5 in classic form and 3 in vascular form.
Symptoms: hyperextensible skin, abnormal tissue fragility. Most severe is potentially lethal vascular problems due to defective collagen in the arteries.
Explain the make up of Elastic Fibers.
Lysyl oxidase modifies lysyl side chain to form desmosine.
Fibrillin acts as the scaffold for elastin
Desmosine and Fibrillin
Explain 2 elastic fiber Genetic Disorders
Marian Syndrome
Mutations in Fibrillin 1 protein
Autosomal dominant: pleiotropic
Symtpoms: Arachnodactyly (long fingers, positive wrist sign), ectopic lensis, weak large arteries.
Williams-(Beuren) syndrome
Chromosomal #7 deletion of 27 genes including elastin.
Random event during formation of reproductive cells. Inherited in small % of cases.
Presentation: developmental disorder, unique personality, distinctive facial features, cardiovascular problem.
Explain the 2 kinds of Adhesion Proteins. And one related disorder
Laminin: large cross-shaped quartnary protein. Holds component of basement membrane
Fibronectin: Most abundant multi-adhesive protein.
Function: Gives cells the fibrous mesh work of the ECM. Quartnary
LAMA2-related muscular dystrophy
Mutation in the LAMA2 gene, messes with laminin 2 and 4 production.
Autosomal recessive.
Presentation: Muscle weakness. Can be early onset or milder late onset.
Explain the difference between Proteoglycans vs Glycoproteins
Proteoglycans: Carbs w/ little protein
Glycoproteins: Protein w/ little carbs.
Explain the 3 structures of the Aggregate
Proteoglycans monomer: - Glycosaminoglycans (GAG) - Core Protein Hyaluronic acid (type of GAG) Link Protein
What are GAGs charge?
Negative
Acidic sugar is negative, amino sugar is +, but it is eliminated and changed to -.
What are the names of the 6 kinds of GAGs, explain them.
Chondroitin 4- and 6-Sulfates:
Most abundant, found in cartilage, tendons, ligaments, and aorta. Form Proteoglycans aggregates
Keratin Sulfates (KS) 1 and 2: Most heterogeneous GAG. Found in corneas, loose connective tissue Proteoglycans aggregates
Hyaluronic Acid:
Not sulfates or covalently attached to protein like other GAG. Also found in bacteria.
Serves as lubricant and shock absorber in synovial fluid, vitreous humor, loose CT, and cartilage
Dermatan Sulfate:
Found in skin, blood vessels, and heart valves
Heparin:
A-linkage joins the sugars, intracellular (only GAG) component of mast cells that line arteries in liver, lungs, and skin. Anticoagulant.
Heparin Sulfate:
Extracellular GAG found in basement membrane and as a ubiquitous component of cell surfaces.k
What are the two problems that can go wrong with GAG and what are their associated diseases?
Synthesis and Degradation
Synthesis: Chondrodystrophies: defect in the Sulfate one of the growing GAG chain.
Autosomal recessive: Dwarfism
Degradation: Mucopolysaccharidoses: deficiency of any one of the lysosomal hydrolases involved in the degradation of heparin sulfate and/or dermatan sulfate Autosomal Recessive (except Hunter syndrome, X linked) Progressive disorders that appear normal at birth. GAG accumulate in lysosomes, urine, and various tissues, skeletal and ECM deformities with mental retardation
Types:
Hurler Syndrome: Most severe
Sanfilippo Syndrome: Severe nervous system disorders. 4 enzymatic steps for N-Sulfate residues.
Hunter Syndrome: X-linked: enzyme replacement therapy, degradation of dermatan sulfate and heparin sulfate affected.
SLY syndrome: B-Glucuronidase deficiency. Short stature, corneal clouding, developmental disability.
Which GLUT transporter is insulin dependent and in muscles?
GLUT 4
Facilitated Diffusion: ATP Independent
When insulin is in blood more GLUT 4 is transferred in vessicles to PM to bring glucose in.
Type 2 diabetes and Insulin resistance
What enzyme activates glucose inside muscle cells?
Hexokinase
3 isoforms
Inhibited by it own end product G6P.
High affinity for glucose (low Km) with low Vmax
Explain the first rate-limiting step of glycolysis
Phosphofructokinase-1 (PFK-1)
Irreversible, and first rate-limiting and committed step.
Inhibited by: ATP and citrate
Activated in muscle by: AMP
Activated in liver by: F-2,6-bisP
What are the tissues for each GLUT transporter?
GLUT 1: human erythrocytes, blood-brain, blood-testis, blood-placental barriers.
GLUT 2: Liver, Kidney, B-cell on pancreas, Secrosal surface of intestinal mucosa.
GLUT 3: Brain neurons
GLUT 4: Adipose, skeletal muscle, Heart muscle
GLUT 5: Spermatozoa, Intestinal epithelium
What is normal and abnormal Anaerobic Glycolysis in Muscle?
Normal:
Exercising skeletal muscle
Lactate build up results in lower pH and cramping
Lactate can be released and metabolized back to pyruvate in the liver.
Abnormal: Hypoxia: causing cell damage, necrosis Lactic acidosis: lowers pH of blood -normal less than 2 mmol/L -Hyperlactemia: 2-5 mmol/L without metabolic acidosis -Lactic acidosis: 4-5 mmol/L
Explain the Pyruvate dehydrogenase complex (PDH)
Three separate enzymes:
E1 (pyruvate Carboxylase or dehydrogenase)
E2 (dihyrolipayl transacetylase)
E3 (dihydrolipayl dehydrogenase)
5 coenzymes Thiamine TPP (vitamin B1) Lipoamide Coenzyme-A (vitamin B5) FAD (riboflavin Vitamin B2) NAD+ (nicotinamide, vitamin B3/niacin)
What are problems that can come from the PDH in vitamins, genetics or poisoning?
Vitamin Deficiencies of niacin and thiamine cause CNS problems
Ex: Wernicke-Korsakoff syndrome (thiamine)- seen in alcoholics.
Genetic defects
Ex: Leigh Syndrome: caused by mutation in either PDH, ETC protein or ATP-synthase
-Rare progressive neurodegenerative disorder.
2nd: Chronic lactic acidosis: X-linked dominant deficiency in the activity of a-subunit of PDH.
Arsenic Poisoning: makes stable thrill with the SH group in lipoid acid to ruin coenzyme.
What regulates and activates PDH complex?
Activates phosphatase doing dephosphorylation,
- **Feed forward F 1,6 bisP
- pyruvate,
- NAD+
- ADP
- Ca (muscle)
- CoA
Deactivated by kinase phosphorylation
- Acetyl CoA
- NADH
- ATP
PDH kinase (+ by NADH and Acetyl CoA, - by pyruvate and ADP)**and phosphatase (by Ca)can be allosterically regulated.
Explain CPT-ll Deficiency
Disease with Fatty Acids Carinitine palmitoyl transferase ll. FA made to FA CoA, then shuttled into the outer membrane bu CPT-l. Carnitine is added to then move into the matrix by CPT-ll
More than 70 mutations affecting the activity
Affects cardiac and skeletal muscle
Autosomal recessive (rare)
3 forms: lethal neonatal, severe infantile, and mild myopathic.
How is FA degradation Regulated?
Acetyl Coenzyme A Carboxylase-2 (ACC-2)
Changes Acetyl CoA in the cytoplasm (from citrate transport) to Malonyl CoA to inhibit CPT-l and FAs entering mitochondria to be broken down. This is when there is high ATP and high Acetyl CoA.
AMP in the cell activates the Malonyl-CoA Decarboxylase to change Malonyl-CoA back to Acetyl-CoA
The AMP comes from two ADPs to make ATP and AMP using Myokinase.
What are the Irreversible steps of the Krebs Cycle?
- Citrate synthase
- Product is inhibition, substrate is activation. - Isocitrate dehydrogenase
- Rate limiting step.
- Ihibitors: ATP and NADH
- Activators: ADP and Ca2+ - A-ketoglutarate dehydrogenase complex
- Similar to PDH complex
- Inhibitors: It’s products
- Activators: Ca2+ in muscle
What are the Oxidation-reduction components of ETC?
Flavin mononucleotide (FMN)
Fe-S centers
Fe in Cyt b, c1, c, a, and a3
Copper in Cyt a and a3
What phospholipid is exclusive to the inner mitochondrial membrane?
Cardiolipin
2 molecules esterified through their phosphate groups. 2 phosphatidylglycerol.
Maintains the structure and function of ETC
What are uncoupling proteins and where are they?
They are H+ flow back through the membrane without generation of ATP.
UCP (natural) makes heat and are natural in adipose tissue UCP1 and other tissues UCP 2,3,4,5.
Synthetic Uncouplers are chemicals that increase the permeability of the inner mitochondrial membrane to H+
Like Aspirin***
What are 6 inhibitors of ETC?
Rotenone, Amytal
Antimycin C
CO: block transfer of electrons from complex lV to O2
Cyanide: Block electrons through complex lV
Atractyloside
Oligomycin
Why are branches important in Glycogen?
They increase solubility of glycogen molecules
They increase the number of non reducing ends for faster synthesis and degradation.
(In muscle, glucose-6P is sent right into glycolysis no made back into glucose)
What is the rate limiting step of Glycogenesis?
Explain Gycogenin
What is the rate limiting step of Glycogenolysis?
Glycogen synthase taking UDP-glucose and adding it to the glycogen core.
Glycogenin: serves as a primer for glycogenesis
Tyr is an attachment point for UDP-glucose
Glycogenin has catalytic activity.
Glycogen phosphorylase breaking a bond from the glycogen core using phosphate to make G1P.
(Phosphoglucomutase makes G1P to G6P)
What regulates glycogen metabolism allosterically and hormonally?
For Glycogen phosphorylase and Glycogen Synthase
Allosterically Regulation
Glycogen phosphorylase:
-activated: AMP, Ca2+
-Inhibited: G6P, ATP
Glycogen synthase:
-Activated: G6P (inhibited when you run out)
Hormonal Regulation
Glycogen Phosphorylase
-Activated: Epinephrine
-Inhibited: Insulin
Glycogen Synthase
- Activated: Insulin
- Inhibited: Epinephrine
Generally explain Epinephrine cascade on glycogen in muscle cells.
Epinephrine binds to adenylate cyclase. The enzyme uses ATP to make cAMP.
CAMP activates protein kinase A. PKA inactiveates Glycogen synthase and activates glycogen phosphorylase b to its a version. It uses ATP or Ca to change b to a.
The glycogen phosphorylase then degrades glycogen to G1P.
Generally explain Insulin’s role with glycogen in skeletal muscle
Insulin binds and through a cascade makes Akt. This inhibits glycogen degradation and activates glycogen synthesis.
Why is calcium special in glycogen degradation?
The release of Ca from SR is able to activate Glycogen Phosphorylase without phosphorylation (ATP) to cause glycogen degradation
What is the only none cytosolic enzyme that can breakdown glycogen?
What is the glycogen storage disease connected with this deficiency.
Lysosomal a(1,4)-glucosidase
Product of a housekeeping gene (in all cells). Works best at pH 4.5
With deficiency you get Type ll: Pompe Disease Generalized effects (mostly in heart, liver, muscle).
Only GSD that is a lysosomal storage disease
Get massive cardiomegaly, hypotonia and muscle weakness.
You get normal glycogen and normal blood sugar levels.
What are the 6 glycogen storage diseases (GSD)
- Von Gierke: Affects G6Pase
- features: severe fasting hypoglycemia, hepatomegaly, hyperlipidemia, hyperurecemia, short stature
Glycogen structure: Normal
- Pompe: Affects Lysosomal alpha (1,4)-glucosidase
- feature: cardiomegaly, muscle weakness, death by 2.
Glycogen structure: glycogen-like material in lysosomes
- Cori: Affects Debranching enzymes
- Features: Mild hypoglycemia, liver enlargement
Glycogen: short outer branches residue
- Anderson: Branching enzyme
- features:Infantile hypotonia, cirrhosis, death by 2 years
Glycogen: very few branches especially towards periphery
- McArdle: Muscle glycogen phosphorylase
- features: muscle cramps, weakness in exercise, myoglobinuria
Glycogen: normal
- Hers: Hepatic glycogen phosphorylase
- features: mild fasting hypoglycemia, hepatomegaly, cirrhosis
Glycogen: Normal
What is the function of creatine Kinase?
Reservoir of Pi
Plays important role during exercise
Transporter of high-energy phosphate
Explain the synthesis of creatine phosphate
Begins in kidney and sent to liver.
Phosphorylation in respective tissue (brain, heart, skeletal muscle) by Creatine kinase (CPK creatine phophokinase or CK)
It is a reversible step
Explain the degradation of creatine phosphate
Spontaneous cycle action to creatinine. Excreted in the urine and is diagnostic measure of muscle loss.
Describe Creatine kinase’s structure and diagnostic role
Dimer of B and M subunits
Has three combos
CK1 only in BB, only in brain
CK2 MB, only in heart
CK3 MM, in skeletal muscle and heart.
Diagnostic for MI. CK2 isoenzyme in the plasma is specific for MI. Appears 4-8 hours after MI and peaks at 24 hours
Explain Myoglobin
Soluble globular protein with 1 chain and 1 heme
Found in skeletal and heart muscle cells
Bins O2 from hemoglobin and transports it to the ETC donating it to cytochrome oxidase.
Gives red color to Type 1 and Type llA muscles
What does resting skeletal muscle do to AA and Glucose in absorptive state?
Fasting State?
AA: Increase synthesis of protein, uptake of AA, and degradation of excess AA in other pathways.
Glucose: Increase GLUT 4 mediated transport, glucose phosphorylation, glycogen synthesis, glycolysis, TCA cycle as needed
-decrease: glycogen degradation.
Fasting
Glucose-decrease GLUT 4 mediated transport (no insulin)
- decrease glycogen synthesis and glycolysis (after glycogen is used)
- increase glycogen degradation
FA: Increase flux of FA from adipose, and FA oxidation. Primary fuel source during first 2 weeks and exclusively used during starvation.
Ketone bodies: increase from liver for first 2 weeks.
AA: Increase degradation of protein for first few day, and increase release of AA to provide liver with Gluconeogenesis substrate.
-Decreased degradation after several weeks.
What is Cachexia?
Wasting syndrome in cancer patients. A combo of:
Protein wasting, malabsorption, immune days Regulation, increased glucose turnover, and mostly due to tumor-induced increases in energy expenditure.
What are cardiac muscle metabolic preferences?
Can’t store energy as glycogen or lipids.
ALWAYS aerobic
Rich in myoglobin
Uses: 60% FA, 35% Glucose, 5% KB
What are metabolic preference of Smooth muscle?
Contains very few mitochondria so glycolysis is primary source of energy
