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Block 1 > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Outline the structure of RNA

A

Ribonucleic acid - RNA

  • Single stranded (usually)
  • Ribose (contains oxygen on C2)
  • Contains uracil (U) instead of Tyrosine (T)
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2
Q

Describe mRNA

A

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
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3
Q

Describe rRNA

A

RNA used in ribosomes

- 80S ribosome made of 60S and 40S subunits

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4
Q

Describe tRNA

A

Brings AA to the ribosomes during translation

  • Some parts are double-stranded
  • Have anticodons to bind to codon on mRNA
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5
Q

Describe Translation

A

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

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6
Q

Outline the composition and the process of production of ribosomes

A

Eukaryote ribosomes are 80S

  • Large subunit (60S)
  • Small subunit (40S)
  • rRNA
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7
Q

Outline the process of reverse transcription

A

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
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8
Q

Outline the process of PCR

A
  • 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
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9
Q

Define ‘ribozyme’

A

Ribozyme - RNA with enzymatic function, active sites that can cause catalytic activity

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10
Q

Describe the structure and function of RNA viruses

A

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

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11
Q

Describe the hierarchy of protein structures

A

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.

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12
Q

Outline the major secondary structure motifs in proteins

A

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
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13
Q

Describe how protein structure and collagen diseases

A

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
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14
Q

List the features of amyloid and amyloid deposition diseases

A

Amyloid deposition:

  • misfolded proteins are deposited in ECM
  • Tissue and organs fail
  • Proteins aren’t degraded
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15
Q

List the features of prions and prion disease

A
  • 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
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16
Q

Define the term ‘enzyme’

A
  • 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] &laquo_space;[enzyme]
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17
Q

Describe the modes of enzyme inhibition: competitive,

A

Competitive inhibitors: inhibitor binds and blocks enzyme’s active site

  • Km increases
  • Vmax unchanged
  • Increasing [S] can overcome inhibition
  • Physically blocks substrate from binding
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18
Q

Describe the modes of enzyme inhibition: non-competitive inhibitors

A

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)
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19
Q

Describe the modes of enzyme inhibition: uncompetitive inhibitor

A

Preferably binds to enzyme-substrate complex and prevents product formation

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20
Q

Trascriptional mode of regulation of enzymes

A

Regulation of mRNA production

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21
Q

Translational mode of regulation of enzymes

A

Regulation of ribosomal processing of mRNA

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22
Q

Co-enzymatic regulation of enzymes

A

Vitamins and protein partners - can be removed

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23
Q

Covalent modification of enzymes

A

Phosphorylation, glycosylation, addition of fatty acids etc.

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24
Q

Inhibitor mode of regulation of enzymes

A

Molecules to limit activity

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25
Q

Allosteric modulators of regulation of enzymes

A

Products or reactants of metabolic pathways

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26
Q

Proteolysis regulation of enzymes

A

Cleavage of proteins can activate proteins/inactivate proteins

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27
Q

Describe basic characteristics of protein

A

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
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28
Q

Describe the basic characteristics of carbohydrates

A

Monomers, dimers, oligomers and polymers of saccharides

  • Polysaccharides: amylose, amylopectin, glycogen
  • Disaccharides: maltose, lactose, sucrose
  • Monosaccharides: glucose, galactose, lactose, fructose
29
Q

Describe the basic characteristics of fat

A

Esters of carboxylic acids

  • Triglyceride = glycerol backbone with ester linkages to three fatty acids
  • Fatty acid = carboxylic acid with carbon chain
30
Q

Outline the fate of proteins

A

Protein digestion

  • Broken down to short peptide and free amino acids in stomach and small intestine
  • AA are absorbed via small intestine
31
Q

Outline the fate of carbohydrates

A

Carbohydrate digestion

  • Broken down in mouth to dissacharides and in small intestine to monosaccharides
  • Monosaccharides absorbed in small intestine
32
Q

Outline the fate of fats

A

Fat digestion

  • Solubilized via bile salts from gall bladder
  • Broken down to FA and absorbed in small intestine
33
Q

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)

A

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
34
Q

Outline the process whereby the body detects or senses nutrients

A

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

35
Q

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

A

Nutrient sensing is important for:

  • Food selection
  • Hormonal response coordination to food
  • Digestion coordination
  • Growth and storage regulation
  • Appetite control
36
Q

Describe the mechanism of glucose sensing

A

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)
37
Q

Outline the nature and role of Class C G-protein coupled receptors as an example of a nutrient-sensing receptor

A

Class C GPCR bind to different nutrient molecules to sense for nutrients

  • Bind AAs and glutamate
  • Binding causes signalling cascades that causes intracellular changes
38
Q

Describe the concept and function of ATP

A

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

39
Q

Summarize the processes of cellular uptake of glucose

A
  • 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
40
Q

Summarize processes of cellular uptake of amino acids

A
  • Deamination

- converted to pyruvate or acetyl CoA

41
Q

Summarize processes of cellular uptake of fatty acids

A
  • Beta-oxidation

- Converts fatty acid into two carbon pieces to form Acetyl CoA

42
Q

Summarize processes of cellular uptake of triacylglycerols (TAG)

A
  • Fatty acids undergo Beta-oxidation

- Glycerol back bone is converted to DHAP and enters glycolysis

43
Q

Summarize processes of cellular uptake of cholesterol

A

Cholesterol can be synthesized from acetyl CoA

44
Q

Summarize process of aerobic metabolism of glucose and elaborate on lactate acidosis

A

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)
45
Q

Summarize the process of anaerobic metabolism and elaborate on lactate acidosis

A

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
46
Q

Outline Kreb’s citric acid cycle with reference to its place in the metabolism of major nutrients

A

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
47
Q

Outline the process of amino acid deamination

A
  • Occurs mainly in liver
  • Removes and converts amine group to ammonia (toxic) then urea/uric acid
  • Converts rest of AA into pyruvate for CAC
48
Q

Outline the role of thiamine in metabolism

A

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.

49
Q

Outline the process of the cellular uptake of oxygen and nutrients

A

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
50
Q

Outline the role of mitochondria in energy production

A

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
51
Q

Describe electrons come from NADH and FADH2 (from matrix) produced by Citric Acid cycle

A
  • 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
52
Q

Describe in general, the complexes are large and contain multiple subunits

A
  • 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

53
Q

Describe uncoupling protein (UCP)

A

Allows H+ to flow through membrane via alternate route. ATP synthesis fails. Used to produce heat in body.

54
Q

Outline the role of oxygen binding proteins

A

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

55
Q

Elaborate on the blockage of electron transport chain (role of poisons)

A

1) Rotenone - blocks Complex 1
2) antimycin A - blocks Complex 3
3) cyanide - blocks Complex 4

56
Q

Outline the relationship between oxygen reduction and ATP synthesis

A

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.

57
Q

Describe how major nutrients (carbohydrates, protein and fat) are stored

A

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.

58
Q

Summarize the processes of synthesis of glycogen and the hormones involved

A

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)
59
Q

Summarize the processes of glycogen breakdown and the hormones involved

A
  • Catalyzed by glycogen phosphorylase
  • Hormones:
    1) glucagon (pancreas): glucagon activates phosphorylase kinase which activates glycogen phosphorylase
    2) adrenalin (adrenal medulla)
60
Q

Outline the processes of synthesis and breakdown of proteins in skeletal muscle and liver

A

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
61
Q

Outline the process of gluconeogenesis

A
  • 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
62
Q

Outline the process of triglyceride synthesis of fatty acids and the different fates of fatty acids

A
  • Promoted by insulin
  • Steps:
    1) glucose -> pyruvate -> Acetyl CoA
    2) multiple Acetyl CoA -> Fatty acids
  • Hormone signal: leptin
63
Q

Outline the process of triglyceride breakdown to fatty acids and the different fates of fatty acids

A
  • 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)
64
Q

List the major types of ketone bodies

A

Ketone bodies - mobile form of Acetyl CoA to be moved between tissues

  • Acetoacetate
  • Beta-hydroxybutyrate
  • Acetone
65
Q

Outline the actions of glucose in brain

A

The brain absolutely requires glucose

  • In low glucose, glucose obtained via:
    1) glycogen breakdown
    2) gluconeogenesis from amino acids
66
Q

Outline the actions of insulin

A
  • 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
67
Q

Outline the actions of glucagon:

A
  • From alpha cells in pancreatic islets
  • Released during low plasma glucose
  • Actions:
    1) Glycogen breakdown
    2) glucose synthesis from AA or lactate (gluconeogenesis)
68
Q

Outline the actions of cortisol

A
  • From adrenal cortex
  • Actions:
    1) proteolysis in muscles
    2) conversion of AA to glucose
    3) induce insulin resistance (increase blood glucose levels)

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