Biochemistry Flashcards
Outline the structure of RNA
Ribonucleic acid - RNA
- Single stranded (usually)
- Ribose (contains oxygen on C2)
- Contains uracil (U) instead of Tyrosine (T)
Describe mRNA
Single strands of RNA composed of codons for protein translation
- Capping at 5’-end (brings mRNA to ribosome)
- Poly(A)-tail at 3’ end (stabilizes mRNA)
- Splicing removes introns from mRNA
Describe rRNA
RNA used in ribosomes
- 80S ribosome made of 60S and 40S subunits
Describe tRNA
Brings AA to the ribosomes during translation
- Some parts are double-stranded
- Have anticodons to bind to codon on mRNA
Describe Translation
Initiation:
- AUG start codon (Methionine) found on mRNA strand
- Signals for assembly of ribosomal subunits
Elongation
- tRNA bring AA to A site
- AA is passed to growing peptide at P site
- tRNA leaves at E site
Termination
- Stop codon causes the ribosomal subunits to disband
Outline the composition and the process of production of ribosomes
Eukaryote ribosomes are 80S
- Large subunit (60S)
- Small subunit (40S)
- rRNA
Outline the process of reverse transcription
Reverse transcription: converting viral ssRNA into DNA in host cell
- DNA nucleotides are matches with ssRNA to make DNA-RNA hybrid
- RNA is removed to make ssDNA
- Complementary strand of DNA is synthesized to make dsDNA
Outline the process of PCR
- Rapid amplification of selected DNA sequences using temperature cycles
- 3 stages:
1) denaturation - heat to around 95 degrees celsius to break hydrogen bonds between purines and pyrimidines
2) annealing - temperature is lowered to around 60 degrees celsius to allow primers to be bound to DNA
3) synthesis - heat to 72 degrees celsius, temperature where polymerase is still functional
Define ‘ribozyme’
Ribozyme - RNA with enzymatic function, active sites that can cause catalytic activity
Describe the structure and function of RNA viruses
RNA viruses are composed of capsid proteins and have ssRNA/dsRNA with positive or negative sense strands. They are sometimes supplemented with reverse transcriptase enzyme
Describe the hierarchy of protein structures
Primary structure - the sequence of amino acids in a polypeptide chain
Secondary structure - alpha-helices and beta-sheets formed by H-bonds between polypeptide backbone. Relatively local structures
Tertiary Structure - 3D structure of entire protein. Covalent and ionic bonding between AA residues and hydrophobic forces
Quaternary structures - spatial arrangement of polypeptide chains in proteins with multiple subunits.
Outline the major secondary structure motifs in proteins
Secondary structure
- Peptide bond holds the six atoms involved in one plane (amide plane)
- Amide plane can be described with two angles (phi and psi)
- Secondary structures are common angles for phi and si.
Alpha-helix
- Tight packed helix (no hole in centre)
- H-bonding between AAs that are four residues apart
- 3.6 AA per turn
- Side-chains point outwards
Beta-sheets
- pleated sheets (fan-like)
- chains can be parallel or anti-parallel
Describe how protein structure and collagen diseases
Collagen - fibrous protein for structural integrity
- Precursor protein = tropocollagen:
1) every 3rd AA is glycine
2) Two unusual AA (hydroxyproline and hydroxylysine) - Three tropocollagen wind together to make collagen
- Only glycine is small enough to fit in centre
Scurvy (diseases of collagen)
- Vitamin C is co-enzyme to make HyP and HyL
- No vitamin C means HyP and HyL can’t be synthesized
- Collagen is unstable
List the features of amyloid and amyloid deposition diseases
Amyloid deposition:
- misfolded proteins are deposited in ECM
- Tissue and organs fail
- Proteins aren’t degraded
List the features of prions and prion disease
- Infectious agent composed of protein material only
- Prions are proteins which catalyze protein unfolding
- Prions will unfold properly folded proteins, which will then go to unfold more
Define the term ‘enzyme’
- Protein (except ribozymes)
- Catalyze biochemistry reactions by lowering the activation energy
- do NOT change equilibrium point of reaction
- do NOT change reaction spontaneity
- May need co-factors:
1) apoenzyme = incomplete enzyme
2) holoenzyme = complete enzyme (apoenzyme + cofactors) - Vmax = maximum rate which product is formed (enzymes are saturated)
- Km = concentration at 1/2 Vmax
- Usually [substrate] «_space;[enzyme]
Describe the modes of enzyme inhibition: competitive,
Competitive inhibitors: inhibitor binds and blocks enzyme’s active site
- Km increases
- Vmax unchanged
- Increasing [S] can overcome inhibition
- Physically blocks substrate from binding
Describe the modes of enzyme inhibition: non-competitive inhibitors
Inhibitor binds to distinct site from active site
- Km unchanged
- Vmax decrease
- Increasing [S] can NOT overcome inhibition
- Locks the enzyme in an inactive formation (can still bind substrate)
Describe the modes of enzyme inhibition: uncompetitive inhibitor
Preferably binds to enzyme-substrate complex and prevents product formation
Trascriptional mode of regulation of enzymes
Regulation of mRNA production
Translational mode of regulation of enzymes
Regulation of ribosomal processing of mRNA
Co-enzymatic regulation of enzymes
Vitamins and protein partners - can be removed
Covalent modification of enzymes
Phosphorylation, glycosylation, addition of fatty acids etc.
Inhibitor mode of regulation of enzymes
Molecules to limit activity
Allosteric modulators of regulation of enzymes
Products or reactants of metabolic pathways
Proteolysis regulation of enzymes
Cleavage of proteins can activate proteins/inactivate proteins
Describe basic characteristics of protein
Polymers of amino acids:
- Amino acid:
1) alpha carbon attached with hydrogen, amide grouop, carboxylic acid group, and R
2) 20 Common AA
3) linked together via peptide bonds - Peptides - 2-100 amino acids
- Proteins - >100 amino acids
Describe the basic characteristics of carbohydrates
Monomers, dimers, oligomers and polymers of saccharides
- Polysaccharides: amylose, amylopectin, glycogen
- Disaccharides: maltose, lactose, sucrose
- Monosaccharides: glucose, galactose, lactose, fructose
Describe the basic characteristics of fat
Esters of carboxylic acids
- Triglyceride = glycerol backbone with ester linkages to three fatty acids
- Fatty acid = carboxylic acid with carbon chain
Outline the fate of proteins
Protein digestion
- Broken down to short peptide and free amino acids in stomach and small intestine
- AA are absorbed via small intestine
Outline the fate of carbohydrates
Carbohydrate digestion
- Broken down in mouth to dissacharides and in small intestine to monosaccharides
- Monosaccharides absorbed in small intestine
Outline the fate of fats
Fat digestion
- Solubilized via bile salts from gall bladder
- Broken down to FA and absorbed in small intestine
Outline the biochemical and pathological consequences of disordered amino acid metabolism (taking phenylketonuria as an example) and disordered carbohydrate absorption (taking lactase deficiency as an example)
Phenylketonuria (PKU)
- Deficient in phenylalanine hydroxylase
- Can’t convert phenylalanine to tyrosine
- consequence -> mental retardation; accumulation of phenylketones (demyelinated axons)
- Treatment -> restrict phenylalanine in diet; increase tyrosine in diet
Lactase deficiency
- Can’t break down lactose to galactose and glucose
- accumulation of lactose in lumen of the intestine (strong osmotic gradient)
- Water is pulled into intestine -> diarrhea, weight loss, inadequate nutrition
Outline the process whereby the body detects or senses nutrients
Taste
- sweet: sugars
- umami: amino acids
- bitter/salt: ions
- sour: low pH
Stomach and intestines -> AAs, monosaccharides, FA
Internal sensing -> endocrine system and tissue stretch receptors
Outline the significance of nutrient sensing with reference to appetite, food selection, satiety, coordination of hormonal and digestive responses, control of growth and nutrient storage
Nutrient sensing is important for:
- Food selection
- Hormonal response coordination to food
- Digestion coordination
- Growth and storage regulation
- Appetite control
Describe the mechanism of glucose sensing
Glucose sensed by pancreatic islet beta-cells
- Glucose enters cells via GLUT2
- ATP produced
- ATP-sensitive K+ channel opens; depolarization
- Ca2+ channel opens
- Insulin is released (and causes uptake in other cells)
Outline the nature and role of Class C G-protein coupled receptors as an example of a nutrient-sensing receptor
Class C GPCR bind to different nutrient molecules to sense for nutrients
- Bind AAs and glutamate
- Binding causes signalling cascades that causes intracellular changes
Describe the concept and function of ATP
ATP = Adenosine triphosphate
- Mobile source of energy
- Used as energy source for cellular functions
- High energy bond between 2nd and 3rd phosphate:
ATP + H2O -> ADP + Pi + H+ + Energy
- Ribose + Adenine (base) + phosphates
Summarize the processes of cellular uptake of glucose
- Glycolysis, Krebs Cycle and ETC/ATP Synthase
- Cytoplasm: Glucose -> 2 pyruvate
- Mitochondria outer membrane: pyruvate -> Acetyl CoA
- Matrix: acetyl CoA into Krebs Cycle (NADH and FADH2 production)
- Mitochondria inner membrane: electron transport chain and ATP synthase
Summarize processes of cellular uptake of amino acids
- Deamination
- converted to pyruvate or acetyl CoA
Summarize processes of cellular uptake of fatty acids
- Beta-oxidation
- Converts fatty acid into two carbon pieces to form Acetyl CoA
Summarize processes of cellular uptake of triacylglycerols (TAG)
- Fatty acids undergo Beta-oxidation
- Glycerol back bone is converted to DHAP and enters glycolysis
Summarize processes of cellular uptake of cholesterol
Cholesterol can be synthesized from acetyl CoA
Summarize process of aerobic metabolism of glucose and elaborate on lactate acidosis
Glycolysis:
- Glucose + 2 ATP -> 2 Pyruvate + 4 ATP + 2 NADH
- Net of 2 ATP produced (even with no oxygen)
- Require ATP to start the process
- Pyruvate converted to lactate under anaerobic conditions
Pyruvate dehydrogenase
- Pyruvate -> Acetyl CoA + NADH + CO2 (2x per glucose)
- Catalyzed by pyruvate dehydrogenase
- Requires oxygen and thiamin (vitamin B1 = coenzyme for pyruvate dehydrogenase)
Citric Acid Cycle
- Acetyl CoA -> 3 NADH + 1 FADH2 + 2 CO2 + 1 GTP (2x per glucose)
- Step 1: oxaloacetate + acetyl CoA -> citrate
Oxidative phosphorylation Total for one glucose: - 10 NADH - 2 FADH2 - 6 ATP - -2 ATP - -2NADH (transport into mitochondria) - = 36 ATP per glucose (3 per NADH + 2 per FADH2 + 1 per GTP)
Summarize the process of anaerobic metabolism and elaborate on lactate acidosis
Glycolysis:
- With no oxygen, only glycolysis can occur
- 2 ATP per glucose
- Pyruvate is then converted to lactate and then lactic acid
Lactic acidosis:
- Accumulation of lactate within the body
- When ATP breakdown exceed ATP synthesis
- Clinical synthesis:
1) Blood pH lowers
2) High serum lactate levels
3) elevated breathing
4) muscle aches - caused by thiamine deficiency (needed for pyruvate dehydrogenase)
Outline the process of fatty acid oxidation:
- beta-oxidation of fatty acids occurs in mitochondria
- Generates acetyl-CoA which enters the citric acid cycle
- Each cycle consists decreases fatty acid chain by 2 carbons
1) old beta-carbon is the new carboxyl carbon
2) old alpha-carbon and old carboxyl carbon are now Acetyl CoA - Entire cycle takes four steps
Outline Kreb’s citric acid cycle with reference to its place in the metabolism of major nutrients
Kreb’s cycle (citric acid cycle) is the main metabolic mechanism for liberating energy from all major nutrient types
- Carbohydrates and proteins enter as pyruvate
- Fatty acids enter as acetyl CoA
- Produces high energy electrons for electron transport chain and ATP synthase
Outline the process of amino acid deamination
- Occurs mainly in liver
- Removes and converts amine group to ammonia (toxic) then urea/uric acid
- Converts rest of AA into pyruvate for CAC
Outline the role of thiamine in metabolism
Thiamine is a co-enzyme, it is required for binding of pyruvate by thiamine pyrophosphate. Without thiamine, pyruvate can build up leading to conversion into lactic acid and results in acidosis.
Outline the process of the cellular uptake of oxygen and nutrients
Oxygen acts as an electron sink for end of electron transport chain needed for ATP synthesis.
- Gut provides major nutrients for ATP via absorption
- Lungs provide oxygen
- Heart and circulation transport the nutrients and oxygen to tissues
Outline the role of mitochondria in energy production
Mitochondrial reactions:
- Outer membrane: pyruvate to acetyl CoA in
- Matrix: Kreb’s cycle
- Inner membrane: electron transport chain and ATP synthase
- Intermembrane space: H+ reservoir for ATP synthase
Describe electrons come from NADH and FADH2 (from matrix) produced by Citric Acid cycle
- Ubiquinone (Co-enzyme Q) -> electron acceptor/donator molecule; Transports electrons between Complex 1 and Complex 3
- cytochrome C -> reduceable protein; contains heme (oxygen binding molecule): transports electrons between Complex 3 and Complex 4
Describe in general, the complexes are large and contain multiple subunits
- Complex 1 -> accepts NADH to reduce Coenzyme Q
- Complex 2 -> Accepts FADH2 to reduce Coenzyme Q
- Complex 3 -> Accepts Coenzyme Q to reduce Cytochrome C
- Complex 4 -> Accepts cytochrome C to reduce oxygen
- Complex 5 -> Allows H+ to flow through and run ATP synthase (make ATP); breaks down ATP in absence of nutrients
Complex 1, 3 and 4 (not 2) pump H+ across membrane into intermembrane space
Describe uncoupling protein (UCP)
Allows H+ to flow through membrane via alternate route. ATP synthesis fails. Used to produce heat in body.
Outline the role of oxygen binding proteins
1) haemoglobin - binds Oxygen and carries it to tissues with high metabolic demands
2) myoglobin - binds oxygen within the muscles for storage of oxygen when high metabolic demands occur
Elaborate on the blockage of electron transport chain (role of poisons)
1) Rotenone - blocks Complex 1
2) antimycin A - blocks Complex 3
3) cyanide - blocks Complex 4
Outline the relationship between oxygen reduction and ATP synthesis
Oxygen is the final electron transport acceptor in the electron transport chain. Without oxygen, the ETC cannot continue and the H+ gradient required to cannot be established. Without the H+ gradient, the ATP synthase stops and no ATP is created.
Describe how major nutrients (carbohydrates, protein and fat) are stored
carbohydrates - stored as glycogen in the liver (also in muscles) -> releases glucose
Protein - stored in muscle and liver -> releases amino acids
Fat - stored as triglycerides in adipose tissue and liver (packaged as lipoproteins) -> releases fatty acids.
Summarize the processes of synthesis of glycogen and the hormones involved
Steps:
- Glucose activation: UTP + glucose -> UDP-glucose
- Addition to glycogen via glycogen synthase
Hormones:
- Insulin (pancreas): insulin inhibits glycogen synthase kinase (GSK) which usual inhibits glycogen synthase
- Cortisol (adrenal cortex)
Summarize the processes of glycogen breakdown and the hormones involved
- Catalyzed by glycogen phosphorylase
- Hormones:
1) glucagon (pancreas): glucagon activates phosphorylase kinase which activates glycogen phosphorylase
2) adrenalin (adrenal medulla)
Outline the processes of synthesis and breakdown of proteins in skeletal muscle and liver
Muscle protein synthesis:
- Promoted by amino acids, growth factors and exercise
- Regulator molecules:
1) AMP kinase: - Reads ratio of AMP to ATP (“Fuel” gauge)
- Activates when AMP is high and ATP is low (low energy state)
- Promotes ATP synthesis
2) mTOR (mammalian target of rapamycin) - promotes muscle growth
- Inactivated by low nutrients or reduced growth hormones
Outline the process of gluconeogenesis
- Production of glucose
- Only in liver and kidneys
- Oxaloacetate-> pyruvate -> glucose
- Uses amino acids (converted to CAC intermediates) and lactate as substrates
- Emergency supply of glucose
Outline the process of triglyceride synthesis of fatty acids and the different fates of fatty acids
- Promoted by insulin
- Steps:
1) glucose -> pyruvate -> Acetyl CoA
2) multiple Acetyl CoA -> Fatty acids - Hormone signal: leptin
Outline the process of triglyceride breakdown to fatty acids and the different fates of fatty acids
- Promoted:
1) low energy
2) low plasma glucose
3) low insulin
4) high glucagon - Breakdown into 3 Fatty acids, catalyzed by hormone-sensitive lipase
- Fatty acids are released into blood
1) Muscles -> energy source
2) liver -> fatty acid oxidation to Acetyl CoA then ketone bodies (for export)
List the major types of ketone bodies
Ketone bodies - mobile form of Acetyl CoA to be moved between tissues
- Acetoacetate
- Beta-hydroxybutyrate
- Acetone
Outline the actions of glucose in brain
The brain absolutely requires glucose
- In low glucose, glucose obtained via:
1) glycogen breakdown
2) gluconeogenesis from amino acids
Outline the actions of insulin
- From beta cells in pancreatic islets
- Released during elevated nutrients (glucose, AA, peptides, or FA) in plasma
- Actions:
1) glucose uptake into adipose or muscle cells
2) glycogen synthesis in liver
3) enhanced protein mass in muscles
Outline the actions of glucagon:
- From alpha cells in pancreatic islets
- Released during low plasma glucose
- Actions:
1) Glycogen breakdown
2) glucose synthesis from AA or lactate (gluconeogenesis)
Outline the actions of cortisol
- From adrenal cortex
- Actions:
1) proteolysis in muscles
2) conversion of AA to glucose
3) induce insulin resistance (increase blood glucose levels)
