Biological Molecules, Enzymes And Metabolic Pathways Flashcards
Classes of nutrients (8)
- carbohydrates
- lipids
- water
- minerals
- protein
- vitamins
- DEBATED: alcohol or finer
Examples of complex chemical structures
- vitamins
- carbohydrates
- proteins
- lipids
- alcohol/fiber
Examples of simple chemical structures
- water
- minerals
Vitamin B12 structure, role in the body
- has a corrin ring, with Cobolt in the Center
- cobolt is bound to 4 nitrogens, meaning wealth of electrons and ability to be bioactive
- cofactor for isomerases (breaking c-c bond) and methyltransferases
- spirulina contains different structure and is referred to as pseudo vitamin b12. Does not behave as a cofactor
Stereoisomers: what are they in the context of amino acids?
- mirror images
- D enantiomer: the right configuration
- L: left configuration, generally preferred by the body
- amino acids can form enantiomers around the chiral carbon (except glycine)
Non- Polar amino acids
Glycine, alanine, cysteine, valine, proline, leucine, isoleucine, methionine, tryptophan, phenylalanine
Polar amino acids
Serine, threonine, tyrosine, asparagine, glutamine
Positively charged (basic) amino acids
Lysine, arginine, histidine
Negatively charged amino acids
Aspartic acid, glutamic acid
Protein secondary structure
- alpha helix: non- polar amino acid R groups in Center (hydrophobic)
- beta pleated sheet: hydrogen bonds form across plane
Largely determined by R group
Protein tertiary structure
3D structure determined by VDWF, hydrogen bonds, disulphide bridges
Example: collagen, lots of proline introduces kinks in chain, tightly wound structure
Definition of an isotope
Electrons and protons are the same, differing number of neutrons, which give a different atomic mass
There are intrinsically stable isotopes (safe for use in humans, such as C13), and radioactive isotopes
Mass spectrometer steps
1) vaporised substance is ionised (charged) at the inlet
2) voltage pushes down the tube
3) electromagnet deflects the particle
4) particle detected at detector
Strength of electromagnet determines deflection and can be used in deciphering peaks (M+ peak as reference)
Quadrupole mass spectrometer
- can be coupled with gas chromatogram
1) ions added into source
2) voltage pushes through
3) the 4 quadrupole rods determine polarity; frequency of polarity changed
4) some ions will reach resonance at particular polarity switching frequency and will fly down tube like a corkscrew
5) detected
Principle of isotope tracer (decay and infusion experiments)
- bath example
- if you know how much isotope you are putting in, and how much is coming out you can work out the rate of reaction (protein turnover)
- the size of the pool
Definition of half life
T 1/2: Time taken for half of a molecule to be replaced
Usually expressed in days
Ornithine decarboxylase is a fast example- ~20 mins in response to skin burning. For polyamine synthesis (molecular grease)
Conversion between half life and fractional rate:
T1/2: log2 (0.693)/fractional rate
Definition of fractional rate
Ks or Kd = The fractional amount replaced per unit time (expressed as d-1)
Example:
0.1 d-1 is 10% replaced per day
Ks or Kd: log2 (0.693)/t1/2
Amino acid supply and ribosome turnover
Example from Clifford (1972)
Cells have constant amino acid demand
Shown in experiment that when in amino acid starved medium, ribosomes and mRNA were broken down to give back to the amino acid pool
Essential amino acids
Protein with essential amino acids is referred to as having a ‘high biological value’; those lacking in one or more are said to have a ‘low biological value’
Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine
Non- essential amino acids
Have wealth in body and can create own
Alanine, aspartate, glutamate, cysteine, tyrosine
Conditionally essential amino acids
These are amino acids which may become essential under certain conditions
Arginine (essential in pre-term infant), asparagine, glutamine (trauma and cancer), glycine, proline, serine
Carbohydrates
Stimulate insulin secretion
In a fed state, will oxidise glucose for energy
In a faster state, without carbohydrate, will oxidise fat for energy
Types of starch (polymer of D-glucose)
Rapidly digestible (RDS): readily available for pancreatic amylase, digested quickly in small intestine (eg. Freshly cooked starch foods)
Slowly digestible (SDS): slow and complete digestion in small intestine (eg raw cereals)
Resistant starch (RS):
- physically inaccessible eg. Partly milled grains/seeds
- resistant granules eg. Raw potato, green banana
- retrograded amylose eg. Starch that has been cooked and cooled
Glycemic Index (GI)
GI= (area under test food glycemic curve/ area under reference glycemic curve eg. Glucose) x 100
Low GI <40
Medium GI 41-70
High GI >70
(Can later GI by eaten foods which have cooled; reterograded amylose; less available for digestion in small intestine)
Glycemic load
The amount of starch eaten, total
Lipid definition
Groups of compounds that do not readily dissolve in water
Includes: fatty acids, triglyceride, phospholipids
Definitions of saturated/ monounsaturated and polyunsaturated fats
Saturated: no double bond (C18:0) eg. Stearic acid
Monounsaturated: one double bond eg. Oleic acid, 75% constituent of olive oil (C18: 1)
Polyunsaturated: more than one double bond eg. Linoleic or alpha-linoleic acid 18:2n-6 (omega 6), 18:2n-3
Naming system describes number of C on chain: number of c=c(n) - position of double bond on chain (eg. On carbon 3)
Mechanism of fat storage
- Insulin secreted when blood glucose is high
- this stimulates uptake of lipoprotein particles from the liver (VLDL) into adipose tissue; glucose is also being taken in via GLUT4 and engages in lipogenesis
- lipoprotein lipase (LPL) then breaks down into fatty acids which are esterified to triglycerides
Mechanism of fat mobilisation
- during fasting/starvation, hormone-sensitive lipase (HSL) breaks down triglycerides in adipocytes
- this mechanism is stimulated by adrenaline, noradrenaline and possibly glucagon (insulin antagonises this step)
- fatty acids and glycerol leave adipocytes and fatty acids (palmitate) are bound to albumin and transported to periphery (liver) where enter beta-oxidation cycle-> acetyl CoA -> Krebs cycle -> CO2
Metabolism of polyunsaturated fats (omega 6 example)
1) desaturated (via desaturase). delta 6 desaturase: 18:2n-6 -> 18:3n-6
2) elongated (via elongase): 18:3n-6 -> 20:3n-6
3) desaturated again (via desaturase). Delta 6 desaturase: 20:3n-6 -> 20:4n-6 = arachidonic acid
Conversion of omega 3 (18:2n-3) to EPA in humans
- experiment using isotopic labelling (C13), where participants were fed labelled omega 3, and CO2 in breath (palmitate-> beta oxidation -> acetyl coa-> Krebs cycle-> CO2) was measured as a sign of fatty acid oxidation (along with periodic blood tests)
- found that women were more effective than men at converting to EPA (~15% converted vs 2-3%)
- explains why we have gender differences in recommendations
Eicosanoids
- produced from oxidation of PUFA and oxidation or arachidonic acid (from metabolism of omega 6)
- has a role in inflammation, immunity, blood pressure and clotting
Ways of producing ATP
- glycolysis
- creatinine phosphate
- TCA cycle
- amino acid oxidation
- Acetyl CoA (first substrate of the TCA cycle)
- amino acid oxidation
- ketone oxidation
- glycolysis
- beta- oxidation of fatty acids
Definition of redox reactions (NAD+ example)
Reduction, oxidation reaction
(Loss of electrons= oxidation, gain electrons= rescued)
NAD+ is a high energy intermediate (coenzyme) which aids in redox reactions
Types of enzyme and what they do (oxidoreductase, transferases, hydrolases, lyases, isomerases, ligases)
- oxidoreductases: transfer of electrons
- transferases: group transfer reaction
- hydrolases: hydrolysis reaction (transfer of functional groups to water)
- lyases: addition of groups to double bonds or formation of double bonds by removal of groups
- isomerases: transfer of groups within molecules to yield isomeric forms
- ligases: formation of c-c, c-s, c-o and c-n bonds via condensation reactions coupled to atp cleavage
How enzymes overcome energy barriers for reactions
- enzymes reduce the activation energy (free energy, G0) needed for a chemical reaction
- forms a transition state with substrate, and a series of intermediates formed with lower energy requirements, so the deltaG is lower
Mineral cofactor examples
- Fe2 or 3+: cytochrome oxidase, catalase, peroxidase. Ferrous and ferric forms allow for series of redox reactions to occur
- FeMo: denitrogenase, donates a series of electrons to progressively reduce nitrogen until protons donated
Coenzyme examples and dietary sources
- biocytin : transfers CO2, found in biotin
- coenzyme b12: transfers H and alkyl groups, found in b12
- NAD: transfers hydrides, found in niacin
The difference between coenzymes and cofactors
- coenzyme: organic, bind loosely to the active side and aid in substrate recruitment
- cofactor: helper molecules, can be inorganic or organic
POGSM abbreviation for enzymes
P: proximity O: orientation G: geometry S: strain M: microenvironment
Michealis-Menton enzyme kinetics
Vm: the maximum velocity of enzyme reaction
Km: concentration of substrate at which enzyme working at max velocity
Hexakinase example: different isomerases of hexakinase have different Km
Competitive inhibition (folic acid example)
Competitive inhibition can be reversed with increase in substrate
Folic acid: methotrexate has a similar structure and competitively inhibits folic acid reactions. Such as the production of purines/pyrimidines (needed for DNA/RNA synthesis)
Allosteric enzymes
- kinetic characteristics are modulated (sped up/slowed down) by small molecules
- small molecules could be produced within the pathway or result of hormonal signals
- these are rate-limiting enzymes
Allosteric enzyme example: glycogen breakdown in phosphorylation cascade
- hormone- triggered activation by adrenalin
- cAMP dimerises protein kinase (inactive form)
- 2 further catalytic subunits join once phosphorylated by ATP (active form)
- this is now a phosphorylase kinase and is active and will go on to phosphorylase
Allosteric enzyme example: (phosphorylation) hexakinase and phosphofructokinase in regulation of glycolysis
- hexakinase and phosphofructokinase phosphorylate sugars in the first few steps of glycolysis
- pacemakers of glycolysis flux
- dimers of PFK are relatively inactive, form tetramers with full activity (this can be done in muscle with calcium and release of calmodulin) when sense low ATP
Action of glutamine synthetase
- using ATP and ammonia, makes glutamine
- removes ammonia which is vital for reducing toxicity
- provides fuel for gut and immune cells
- transfers nitrogen between amino acids
- provides precursors for DNA/RNA synthesis
Regulation of glutamine synthetase (5)
1) feedback mechanism by end-products (purines)
2) allosteric modification by divalent cations
3) covalent modification (adenylation) inactivates (causes by cyclic cascade)
4) formation modified by phosphorylation of RNA factor that governs transcription activities
5) degradation after site-specific metal-ion catalysed oxidation (now target for proteolysis)
cAMP kinase- insulin pathway
1) Insulin bonds to insulin receptor
2) insulin in cells
3) glucose enters cell through GLUT4 (insulin stimulates influx)
4) glycogen synthesis
5) glycolysis, increased pyruvate
6) lipogenesis, increased fatty acid production
Macro minerals
Calcium
Phosphorus
Magnesium
Functions of calcium in the body
- mineralisation of bone: calcium and phosphate and collagen make up hydroxyapatite (if low Ca osteoclasts will be stimulated to form sealed zone and breakdown bone for Ca, if enough, osteoblasts will be stimulated to build bone back up)
- blood clotting
- muscle and nerve stimulation
- prevention of osteoporosis
- hormones
- growth and metabolism
Active transport system for calcium
- Ca crosses the brush border membrane of the duodenum through TRPV6
- binds to Calbindin D (it’s production is stimulated by calcitrol hormone) which carries across the cytosol of the enterocyte
- Ca-ATPase pumps Ca across basolateral membrane into the blood
Peak bone mass
- occurs usually by age 30 and then declines
- higher in males and Afro-Caribbean’s
- for women, loss of bone mass accelerated by menopause
- reduces Ca intake may affect due to lack of mineralisation of bone
Metabolism of calcium in low calcium conditions
1) Parathyroid gland detects low blood Ca and stimulates release of PTH
2) PTH binds to bone receptors promoting osteoclast activity to release Ca
3) PTH acts on kidneys to produce active form of vitamin D (calcitrol)
4) PTH and vitamin D promote reabsorption of Ca from kidneys into blood
5) Vitamin D travels to intestine promoting Ca reabsorption on the brush border membrane
Metabolism of Ca in high Ca conditions
- counteracts PTH
- major effect: inhibits osteoclast activity in bones
- minor effect: inhibits renal tubular cell reabsorption of Ca and phosphate (allows you be excreted in urine)
Dietary sources of Ca
- milk (~40% of Ca)
- cereal (~30% Ca)
- fish
- soya beans
- green veg
- dried fruit
- nuts
- pulses
Consequences of Ca deficiency
- tetany (muscle spasm, numb hands/feet)
- cardiac arrhythmia
- Hypertension?
- some links to osetoporosis, but supplementing with more Ca has been shown not to significantly improve fracture risk
Dietary sources of phosphorous (macromineral)
- cheese
- yoghurt
- lentils
- black beans
- milk
- chicken
- beef
- soy
- peanut butter
Function of phosphorous
- present in ATP, DNA, RNA, phospholipids
- forms part of the hydroxyapatite in bone (mineralisation)
- phosphoproteins
- activation/deactivation of enzymes eg. Hexakinase, PFK
Metabolism/ homeostasis of phosphorus
- kidneys, bones, intestines all regulate
- ensure equal loss in urine as absorbed
- vitamin D needed for absorption
- FGF23 releases from bone cells in high phosphate conditions, causing renal phosphate excretion and decreases intestinal absorption through decreased vitamin D production
Phosphate deficiency: hypophosphatemia
- rare and almost never due to dietary intake
- causes: anorexia, proximal muscle weakness, skeletal effects, increased infection risk
- preterm neonates at risk as 2/3 of bone mineral content occurs in 3rd trimester
Magnesium (macromineral) dietary sources
- almonds
- spinach
- cashews
- peanuts
- wheat cereal
- soya
- black beans
Magnesium role/ functions
- cofactor for >600 enzymes, regulates ATP binding
- cell growth and proliferation: DNA polymerase have 2 Mg binding sites needed for conformational stability
- DNA stability
- neuromuscular activity Eg. Cardiac muscle contraction
- cellular second messenger: activated enzymes for carbohydrate and protein metabolism, transportation of sodium and potassium across cell membranes
Magnesium homeostasis
- cellular homeostasis regulated by combined action of transporters: TRPM7, SLC41A1, MagT1, CNNM3
- mitochondrial homeostasis regulated by MRS2 transporters
Micro minerals (trace minerals)
- iron
- zinc
- copper
- iodine
- selenium
- manganese
Dietary sources of iron (micro mineral)
- haem form: red meat, liver
- non-haem form: dark leafy veg, cereals (fortified)
Functions of iron
- carrying o2 in the blood via haemoglobin
- cofactor in many enzymatic redox reactions
- Fe-S proteins in the electron transport chain in the mitochondria for ATP synthesis
Metabolism of iron
- enters enterocytes in the upper duodenum
- via myoglobin/haemoglobin: proteases attack, and gene is bound to hcp1 on brush border. Haem oxygenanase then removes Fe2+ which binds to cytosolic proteins
- via bound non-haem Fe: HCl/proteases attack, produces Fe3+ and Fe2+ (Fe3+ needs to be reduced by reductase at brush border), then enters enterocyte via DMT1
- ferroportin can then transport Fe back out of cell into blood
Iron deficiency (symptoms and high risk groups)
- iron deficiency: fatigue, lack of energy, susceptible to infection
- iron deficiency anaemia (more severe): brittle nails, hair loss, mouth ulcers, heart palpitations
- high risk groups: vegetarians, females in child bearing years (menstruation), pregnant women, adolescents in early growth spurt
Dietary sources of zinc (micromineral)
- seafood
- meat and poultry
- eggs and dairy products
- legumes
- nuts
Role/ function of zinc
- major role in metalloenzymes eg. Carboxypeptidases (Zn found one active site)
- gene expression: bound zinc can form zinc finger motifs (with cysteine and histidine) which are found in transcription factors (stabilises binding to promoter region)
Metabolism/ homeostasis of zinc
- Zinc enters cells via zinc transporters (Zip 1,2,4)
- ZnT4,5 then place Zn into secretory vesicles
- ZnT2,4 then place in endoscopes
- ZnT3: synaptic vesicles
- ZnT5,6,7 place Zn into trans-golgi network
- excess zinc bound and stored by metallothionein which regulates homeostasis (increased synthesis in response to dietary zinc), binds Zn through cysteine residues
Zinc deficiency (causes and symptoms)
- cause: may be genetic, Zip4 mutation, causes dermatitis, dwarfism, poor immune function
- symptoms: delayed puberty (reduces targeted androgens, zinc has a role in steroid hormone receptors), poor wound healing, impairment in smell and taste
Symptoms of excess zinc
- lethargy
- nausea/ vomiting
- elevated risk of prostate cancer
Dietary sources of iodine (micro mineral)
- milk
- shellfish
- seaweed
- fortified foods e.g flour, salt
Function of iodine
- forms part of thyroid hormones (thyroxin, T3) which regulates BMR and cellular metabolism
- needed for nervous system development in fetus (greater requirements in pregnancy)
Symptoms of iodine deficiency
- goitre
- mental retardation
- dwarfism
- squint
- motor spasticity
Direct and indirect causes of iodine deficiency
- direct: low dietary iodine i.e poor soil quality
- indirect causes: high levels of oestrogens, these blood iodine absorption in the thyroid (hence greater requirements during pregnancy)
Dietary sources of selenium (micro mineral)
- Brazil nuts
- fish: cod, mackerel, shrimp
- kidney
- liver
- beef
- turkey
Functions of selenium
- present in selenoproteins I.e glutathione peroxidase, which is important in oxidative stress by converting H2O2 into H2O. Protects immune cells against reactive oxygen species
- sperm capsule selenoproteins which are important for sperm motility
- for normal testosterone metabolism
Metabolism of selenium
- absorption pathway is common with amino acids
- selenide is excreted primarily through the urine
Dietary sources of copper (micro mineral)
- beef liver
- oysters
- shellfish
- nuts/seeds (cashews, sunflower seeds)
- lentils
Function of copper
- cofactor in enzymatic reactions, allows for redox reactions e.g Cu/Zn superoxide dismutase (cytosolic antioxidant defence), cytochrome c oxidase (electron transport chain), Lysyl oxidase (crosslinks in collagen and elastin, which is key in skeletal and vascular structures)
Copper absorption
- absorbed in the stomach and duodenum
- each day copper is absorbed and returned to GI tract through biliary copper excretion
- after absorption returned to liver via albumin and distributed amongst hepatocytes
- > 95% of copper in cytoplasm is bound to ceruloplasmin (transports Cu)
Copper distribution
- copper chaperones bind copper with high affinity and deliver to specific target protein
- example: copper chaperone CCS donates a Cu to Cu/Zn superoxide dismutase (SOD1) which is involved in cytosolic antioxidant defence
Copper detoxification and elimination
- metallothioneins have metal binding capacity due to being cysteine rich
- they function as metal scavenger/storage proteins
Copper deficiency (and related genetic disease)
- vitamin C can interfere with absorption
- Menkes syndrome: Cu is absorbed by the gut but cannot be released
- Wilson’s disease: Cu accumulates in the brain and liver
- treatment: reduce intake, Cu chelators, Zn supplements
Example of homeostasis going wrong: myostatin-deficiency
- myostatin is a negative regulator of skeletal muscle growth
- gene deletion/mutation can cause extreme muscular development in animals
Key hormonal systems involved in homeostasis
- thyroid gland: regulates BMR through thyroxin
- pituitary gland: central for growth, GH
- adrenal gland: adrenaline/noradrenaline (medulla), cortisol (cortex)
- gonads: androgens, estrogens
- adipose tissue: leptin, ghrelin
- pancreatic islets: insulin, glucagon
Weight homeostasis: ghrelin
- produced by the stomach
- ligand for growth hormone secretagogue, increases growth hormone
- orexigenic peptide: increases appetite
- rises in between meals, activated through neuropeptideY and agouti- related protein
Weight homeostasis: leptin
- released by adipose tissue, and is anorexigenic peptide (decreases appetite)
- stimulates the hypothalamus to release TRH (thyrotropic hormone) which activates the pituitary gland, which stimulates the thyroid to produce thyroxin
- thyroxin stimulates peripheral tissues to engage in oxidative metabolism for ATP
- leptin can also act directly on periphery for fat oxidation via AMPkinase activation
- high leptin= high energy expenditure, low energy consumption
Thyroid hormones and browning of adipose tissue
- thyroxin is stimulates to release by leptin
- unregulates beta- adrenergic activity
- shift adipocyte phenotype from white-> brown (increases mitochondria)
- increases energy production
Glucose homeostasis: low blood glucose
- glucagon is released from alpha cells in the islets of langerhans
- stimulates hepatic glycogenolysis and gluconeogenesis in hepatocytes and in kidneys (cortisol, adrenaline and noradrenaline can stimulate this mechanism too)
- in hepatocytes, glucagon binds to GPCR on membrane which activate adenylate cyclase, through downstream phosphorylation this activates glycogen phosphorylase, which releases glycogen and glucose-1-P which leaves the cell
Glucose homeostasis: high blood glucose
- insulin is released from beta cells in the islets of langerhans
- this stimulates glucose uptake in periphery, glycogenesis, lipogenesis, protein synthesis (inhibits lipolysis)
- insulin binding to muscle/adipose tissue causes mobilsation of vesicles in cell with GLUT4 channels via PI3kinase insulin signalling pathway
- GLUT4 allows insulin to enter cells
Utilisation of ATP in muscle
- during muscle contraction, Myosin ATPase breaks down ATP for free energy
- adenylate kinase then reverses this step and resynthesises ATP, using AMP as critical gauge in cell
- ATP breakdown can also be stimulated by adrenaline
- as ATP levels fall during muscle contraction, this activates AMP kinase (activates in high AMP concentrations) which switches on pathways to enhance nutrient breakdown and uptake
AMP kinase role
- found in cardiac muscle as this is critical for protecting ATP concentration
- In high AMP concentrations this stimulates the uptake of fatty acids via CD36 to be oxidised (beta- oxidation pathway)
- stimulates entry of glucose via GLUT4 for glycolysis and oxidation (kreb’s cycle)
- inhibits protein synthesis
- all of this increases intracellular ATP
