Biochemistry Flashcards
Glycolysis : What is glycolysis, describe the two stages and what does it generate ?
Glycolysis is the splitting of glucose
- generates -2820 Kjmol-1
- 2 net ATP molecules
- 2 pyruvate molecules
- 2 NADH molecules
The process occurs within the cytoplasm of cells
There are two stages
Stage one - Energy investment five steps, 2 ATP consumed and 2 D-Glyceraldehyde-3- phosphates generated
Stage two - energy recovery five steps, 4 ATP generated and 2 pyruvates
gGlycolysis : Name the three regulatory mechanisms of stage one step one
Regulation Glycolysis Stage one, step one
Irreversable step - commits cell to glucose metabolism
Type of glucose transporter
- Glut one , all cells (RBC and brain), back ground rate of transport
- Glut two - liver high capacity but low affinity for glucose
- Glut 4 - muscle adipose can fuse to cell membrane when conc of glucose is high in response to insulin.
Type of enzyme Hexokinase or Glucokinase
- Hexokinase almost always saturated even at low glucose conc, negatively inhibited by G6P
- Glucokinase only active in the liver when glucose is at a high concentration (not inhibited by G6P)
Note - stage one step one tightly regulated as glucose -6- phosphate is an important intermediary for a number of different pathways ( glycogen storage, glycolysis pyruvate, and ribulose-5-phosphate.
Glycolysis : Describe stage one, step three regulation
Glycolysis stage one, step three
This is an irreversable reaction
- kinase activity up-regulated by insulin (energy poor cell)
- phosphorylation of Fructose-6-phosphate to Fructose 1,6-bisphospahte occurs through Phosphofructokinase 1
- Phosphofructonkinase-2 synthesiszes F-2, 6-BP (Fructose 2-6-bisphosphate)
- F-2, 6-BP activates phosphofructokinase 1 by increasing the affinity of the enzyme for Fructose-6-phosphate
- kinase activity may be down regulated by glucagon
Describe the three types of energy currency between all living animals ?
Three types of energy currency
- Universal molecules
- high energy phosphate compounds
- reduced coenzymes
What are the universal molecules ?
The universal molecules
- carbohydrates
- amino acids
- lipids
- nucleic acids
allow heterotrophs to derive energy from other biological sources
Describe high energy phosphate compounds ?
High energy phosphate compounds
- short term storage of energy
- ATP, ADP and AMP with ATP with the highest energy
- intermediate between the higher energy and lower energy phosphate compounds (currency)
- High activation energy so relatively stable (overcome by enzymes kinases)
- reaction is spontaneous due to -ve Gibbs free energy
- ratio of ATP/ADP/AMP indicate energy levels of the cell.
Describe coenzymes, and how they work and what are they derived from?
Coeenzymes NAD+, NADPH and FAD+
- Oxidative, reduction reactions / hydrolysis
- GER ; LEO
- coenzymes are organic molecules used for enzymatic reactions
- versatile functions
- actively involved in catabolic reactions
Coenzymes are derived from Niacin a essential vitamin in many animals.
Humans can make Niacin from tryptophan an essential amino acid
Describe the redox reaction of NADH, and where is this coenzyme regenerated ?
NADH
- NADH is an electron donor
- NAD+ is an electron acceptor (catabolic pathway)
- function carries two electron on an hydride ion
- NADH is regenerated in the ETC (aerobic) or fermentation (anerobic)
- reaction catalysed by dehydrogenase
Describe NADPH, and how is it regenerated ?
NADPH
- NADPH is an electron donor in reductive (biosynthetic pathways), moves electrons from fuel molecules to drive synthesis of biomolecules
- regenerated in the pentose phosphate pathway
- catalysed by NADPH specific dehydrogenase
Describe FAD Flavin adenine dinucleotide, how is it synthesised ?
FAD
- Syntheised by B2 ribflavin
- 3 different oxidative states FAD+, FADH2, FADH
- prosthetic group permantly attched to an enzyme
- reactions catalysed by dehydrogenase
- involved in the TCA cycle
Describe the structure of glycogen and why this is important in biochemistry ?
Glycogen Battery
- Excess glucose is stored as glycogen (liver and skeltal muscles mostly)
- mostly linear (1-4 glycosidic bonds), and branch point (1-6 glycosid bonds).
- branches every 8-12 residues
- glycogen allows the liver to maintain blood glucose concentrations
- A highle branched structure allows for rapid release of energy as it provides multiple sites for degradation simultaneously.
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Describe the two stages of the Pentose Phosphate pathway, where it occurs and what for?
Pentose Phosphate pathway
- Occurs in the cytoplasm of tissues
- fat synthesis (liver, adipose tissue)
- DNA synthesis (rapidly dividing cells)
Oxidative stage
- generates ribulose-5-phosphate (nucleic acid synthesis)
- NADPH (fatty acid synthesis + other uses)
Non-oxidative phase (3 alternatives)
- regeneration of NADPH
- ribose-5-phosphate (nucleotide synthesis)
- able to feed back into glycolysis through a number of intermediates
Describe how the pentose phosphate pathway is regulated ?
Regulation of the pentose phosphate pathway
- allosteric regulation
- high high NADPH indicates eneergy rich cell cepresses PPP
- Low NADPH stimulates PPP
The phate of phosphorylated sugars entering the pentose phosphate pathway depends on the needs of the cell
- not primarily used for energy production
- NADPH (fatty acid synthesis)
- ribsoe-5-phosphate (nucleotide synthesis)
- intermediates may feed back into glycolysis ( F6P and G3P
How does NADPH act to reduce oxidative stress ?
NADPH and oxidative stress
Cells are continually in contact with oxidative species (free radicals) reactive oxygen species ROS
- ROS will cause cell damage if not neutralised
- Glutathione and thioredoxin are important antioxidants
- antioxidants need to continullly be returned to their reduced state
- NADPH is constantly required to reduce oxidised glutathione
- helps maintain haemoglobin in a reduced state
What happens to the pentose phosphate pathway in an animal affected with cancer ?
Pentose phosphate pathway
- alter regulation for increased rapid proliferation of cells
- require large amount of pentose-5-phosphate
- increased funneling of glucose through the PPP pathway
Glycolysis stage two, step ten and regulation, inhibition and stimulation ?
Stage 2 step 10
Phosphoenolpyruvate (2 molecules) + 2ADP - Pyruvate (2 molecules) +2ATP
- enzyme pyruvate kinase
- irreversable key control point three
- This step is stimulated under pyruvate kinase from the liver
- Insulin and glucagon from the pancrease regulate pyruvate kinase release
- insulin stimulated by high blood glucose increases activity
- glucagon stimulated by low blood glucose decreases activity
Inhibition
- ATP
- Acetyl CoA
- Alanine
- cAMP
Stimulation
- AMP
- Fructose-1-6-bisphosphate
Describe the pathway for energy production under aneraobic conditions ?
Anearobic Lactate dehydrogenase
- under anearobic conditions pyruvate is converted to lactate
- majority located in the liver and muscles
- recycles NAD+ and produces a small amount of ATOP (2 ATP)
- lactate will thyen be transported to the liver for gluconeogenesis (production of glucose)
What is the cori cycle and why is it important, and how is it regulated ?
The cori cycle is a mechanism to recycle lactate
- lactate formed anearobically in muscles
- recycled back to glucose in the liver
- glucose is then transported back to the muscles
Pyruvate ⇔ Lactate
The direction of reaction is regulated by the ratio of NAD+ / NADH
- high NAD+ drives pyruvate production in liver
- low NAD+ drives lacate production in muscle
Describe the glycogeneis ?
Glycogenesis - adding glucose to the glycogen chain
- Glycogen synthesis for storage
- Hexokinase/ Glucokinase break glucose down into glucose-6-phosphate
- Phosphoglucomutase converts G6P to G1P
- this process requires energy
- a different enzyme glycogen synthase than adds the glucose to the glycogen primer
G1P is then activated by ATP and UDP to join on to the glycogen molecule
Describe the general process of glycogenolysis ?
Glycogenolysis
The breakdown of glycogen into glucose
- glycogen phosphorylase converts glycogen into G1P
- Phosphoglucomutase converts G1P to G6P
- Glucose-6-phosphate is a key intermediate which can then be made into glucose (gluconeogenesis), pyruvate (glycolysis) and ribose and NADH (pentose phosphate pathway)
What dose glycogen phosphorylase, and debranching enzyme do ?
Glycogen phosphorylase
- glycogenolysis the break down of glycogen (catabolism)
- only works on the non reducing end of glycogen (branches)
- 4+ residues away from the branching point
requires a debranching enzyme to break down the branches otherwise glycogen phosphorylase can not continue - Glycogen debranching enzyme
Glycogen debranching enzyme
- transfers terminal triglyceride from one branch point to another adjacent chain
- removes the last glucose by breaking the glycosidic bond
What is glycogenolysis (catabolism) inhibited and stimulated by ?
Glycogen metabolism
- Glycogenolysis ( producing glucose) catabolism
- tightly regulated as producing glycogen requires eneergy
Stimulation
- low energy cell
- high AMP
Inhibition
- high energy cell
- high glucose
- high ATP
- high glucose-6-phosphate
Describe the four ways in which Glycogen catabolism is regulated ?
Glycogen catabolism regulation
- Competitive inhibitor = glucose
- Allosteric modifications = AMP, ATP
- Covalent modifications = phosphorylation of glycogen synthase
- Hormonal control = glucagon and epinephrine
Describe the allosteric inhibition of glycogen phosphorylase ?
Glycogen phosphorylase
Glycogen phosphorylase breaks glycogen down into glucose (catabolism) .
When the cell has high energy = high ATP increases Km = poorer subtrate affinity
When the cell has low energy = high AMP decreases Km = higher substrate affinity
