BioChemistry Flashcards
Define Metabolism
is the sum of all chemical reactions that occur inside a cell
Where do humans get most of their energy from?
Carbs, proteins and fats
Does oxidation or reduction of digested food produce energy?
oxidation
Wich organ stores the most glycogen in terms of concentration?
liver
What stores the most glycogen in terms of amount?
skeletal muscle
dietary fuel that exceeds the body’s immediate energy needs is stored mainly as
glycogen and fat.
Explain how life evolved initially on Earth
Life may also have evolved without the Sun’s energy but harnessed the Earth’s heat and inorganic reduced compounds, metabolic intermediates form under conditions of such as those of deep sea vents
What are the two laws of biochemistry?
1) Energy is conserved (neither lost or made, just transformed) 2) The Universe is becoming more disordered
What does amphibolic mean?
Means both anabolic and catabolic occurs in an organism e.g. plants who use photosynthesis to produce energy and catabolic process of cellular respiration breaks it down. Humans are also amphibolic, as we make proteins and DNA
Explain brown fat
Brown fat is full of mitochondria, and these are very inefficient, but generate heat Brown fat increases in cold challenged adult mammals…if lean (less insulation)
Rank food sources that gives the most amount of energy? in kJ/g
• Carbohydrate • Protein • Alcohol • Fat
At any one time, the average human body holds x grams of ATP, holding
At any one time, the average human body holds 250 grams of ATP, holding
Useful energy is captured from ____ bonds (e.g.____) and transferred to ATP following ______
Useful energy is captured from reduced bonds (C-C and C-H) and transferred to ATP following oxidation
What are the main daily energetic expenditures in the body?
Basal Metabolic Rate, Activity (exercise) and then Feeding (specific dynamic action)
How to measure energy in an energy source?
calorimeter
Rank the caloric content of common food sources in terms of kcal/g:
Carbs, Protein, Alcohol then fat (has the most calories per gram)
Rank in terms of weight where most of the humans’ sources of energy stores are:
Liver Glycogen, Muscle glycogen, protein and fat
What are the Three Stages of Catabolism?
Hydrolysis of complex molecules to their building blocks Conversion of building blocks to Acetyl CoA Oxidation of acetyl CoA – oxidative phosphorylation
Why is ATP the universal energy currency?
Adenosine has a shape (motif) that has been harnessed by many enzymes and proccess over billions of years
Are Phosphoanhydride bonds in ATP relatively stable in water?
Yes
Explain what happens when ATP is hyrdolyzed twice:
ATP can be hydrolyzed twice to ADP and AMP, with two hydrolysis events per “fuel” molecule.
When Other anhydride bonds are possible and may yield more energy per mole, why is it not used and why is ATP used?
they are not as stable in water as ATP is
What are other energy sources besides ATP used by organisms?
cells use GTP, TTP, UTP and also creatine phosphate (CrP), but ATP is the most abundant.
Where is creatine phosphate found?
brain, and voluntary muscles
How does ATP work in terms of the ‘molecular spring’?
The negative charges repel each other, making ATP unstable It generates a “molecular spring” that can force other reactions, or cause shape and charge changes in other molecules, e.g. myosin in muscles, membrane channels….
The ____ (∆fG0) of ATP is greater than the sum of the “_______” of ADP + Pi
The free energy of formation (∆fG0) of ATP is greater than the sum of the “products of formation” of ADP + Pi
What are the Laws of thermodynamics and life?
1) Energy can not be created or destroyed, it just changes form 2) The Universe is becoming increasingly disordered
Explain the first law ‘Energy can not be created or destroyed, it just changes form’, in terms of an equation
ΔH = q + w The change in enthalpy = heat + work done
Explain the second law ‘2) The Universe is becoming increasingly disordered’
The second law of thermodynamics states that systems will progress towards increased entropy (It also predicts that time can not be reversed – well not in this Universe)
Write the equation of gibbs free energy:
ΔH- TΔS= ΔG
What does Gibbs free energy show us?
• This predicts whether a reaction is going to, or can occur spontaneously • It predicts the maximum possible change (the potential) in concentrations between reactants and products
The more negative (- ΔG) the more _____!!!!!
The more negative (- ΔG) the more work can be done!!!!!! (and more spontaneous the reaction)
Does Gibbs free energy predict the rate of reaction?
no
What die a positive gibbs free energy show?
the reaction will not occur spontaneously, energy must be invested to make this process occur
What is Glycolysis?
Splitting of sugar (glyco-lysis): Glucose, - 6 carbon (6C) molecule is trapped using phosphate, rearranged and split into 2 x 3C molecules
Does glycolysis only happen to glucose?
No
How many ATP are produced in glycolysis?
2 ATP are first invested, 4 more added (2 not using ATP) then all harvested so 2 ATP produced in total
In the metabolism of fuels there are 2 reaction types:
• 1) Rearrangement/preparation • 2) Oxidation
The only bonds we get energy from by oxidation are from
C-H bonds
Why is the rearrangement step necessary?
Energy from C-C bonds = that of C-H, but C-Cs are not oxidised directly in biology, so need to be rearranged
What are the three types of oxidation reactions?
1) Conversion of alcohol to ketone 2) alkane to alkene 3) aldehyde to an acid
Which is the only oxidation reaction that happens in glycolysis?
aldehyde to an acid (Also protects the cell from the aldehyde (think formaldehyde!))
Biological Redox reactions are undertaken by what enzymes?
Dehydrogenases
Cellular respiration has three stages:
– Glycolysis – The Citric Acid Cycle – Oxidative phosphorylation
Can Glycolysis anaerobic or aerobic?
anaerobic
What does Hexokinase and Glucokinase do?
Glucose is trapped! They add phosphate (it is negatively charged,) Also changes the glucose’s shape so GLUT can not recognise it
Where is hexokinase found?
most tissues
Where is glucokinase found?
liver and beta cells
Explain hexokinase’s affinity for its substrate
hexokinase has a very high affinity for its substrate
Explain glucokinase’s affinity for its substrate
glucokinase has a very low affinity for its substrate
Which kinase enzyme can be inhibited by glucose-6-phosphate?
hexokinase
Explain hexokinase’s saturation in comparison with glucokinase:
Hexokinase gets saturated much faster but absorbs it faster, while glucokinase takes a longer time to become saturated.
a high KM means a __ affinity
a high KM means a low affinity
Glucokinase has a ____ KM than hexokinase for glucose
Glucokinase has a higher KM than hexokinase for glucose • Therefore it has a lower affinity for glucose!
Explain the trapping and investment step:
Glucose now trapped in the cell Phosphate is charged and glucose is no longer recognised by GLUTs Glucose-6-Phosphate is now tagged for other things
Explain rearrangement step:
Glucose is rearranged to fructose shape
Explain commitment and investment step:
After fructose shape has been made, ATP gets converted to ADP
Explain each stage of the glycolysis reaction:
Explain where each major enzyme is placed in the glycolysis reaction:
PFK is regulated by several things:
Inhibited by high ATP (why make more?)
AMP activates PFK (i.e. not very much ATP, make more!)
Too many protons (decreased pH) inhibits PFK (save fuel, demands too high on metabolism?)
Explain the role of lactate dehydrogenase
NADH is oxidized to NAD+ anaerobically
LDH can go forwards and backwards, explain how lactate is involved in the Cori Cycle.
Is the heart good at using lactate?
Yes
What is the purpose of mitochondrial fusion?
mitochondrial fusion enhances ATP production
WHat is the purpose of mitochondrial fission?
mitochondrial fusion protects mitochondria from degradation
Does NADH or FADH2 have more reeox potential?
NADH
What is the role of NADH oxidase?
It is in the electron transport cycle,
It works as a proton pump
Pumps 4 protons per NADH
What is FMN stand for?
Flavin mononucleotide
Which has more reducing power? (gaining electrons) FMN or NADH
FMN has a greater reducing power than NADH
Explain the purpose of iron sulfur clusters:
Electrons can effectively flow through these molecules as the Fe atoms can change oxidation state Fe3+ Fe2+ Although they are not in contact with each other, they effectively act as a wire, through …. QUATUM TUNNELING (PPPs)
Explain how a conformational change occurs in complex 1
The ubiquinone comes in to complex 1 and becomes ubiquinol which changes the shape of the complex 1 as orientation of transmembrane helices changes and which opens gates
What is the roel of complex 1?
it pumps 4 protons for 1 NADH And it reduces Q to QH2
WHat is the difference between ubiquinone and ubiquinol?
ubiquinone( has =O groups) is reduced to form ubiquinol (it has OH groups)
What are the three form of ubiquinone in the process of ubiquinone?
Oxidised -Ubiquinone
1⁄2 reduced/oxidised - Semiquinone
Reduced – Ubiquinol
What is another name for complex 2?
Succinate Dehydrogenase
What is the olre of complex 2?
reduces FAD to FADH2
succinate turns into x as it reduced FAH to FADH2
fumarate = x
Explain why FAD is more dangerous than NADH2
FAD can accept e-s one at a time (NADH 2 at a time)
This means dangerous free radicals can form, but they don’t do so in health
Which two complexes use Q10?
complex 1 and 2
Is complex 3 a pump?
Complex III is not a pump, mediated by transfer through chemical reactions
Why is thehe q ycle complex?
The complexity of the Q- cycle is likely because Cytochrome c can only carry 1 e- at a time
How is complex 1 blocked?
Blocked by anaesthetics (amytal, barbituates, halogen gases and rotenone…)
How is complex 3 inhibted?
Mythioxiol, antimycin a,
How is Cytochrome C oxidase (CIV) blocked?
Nitric oxide (NO), H2S, CO and cyanide
What happens in Complex IV, CCO ?
Overall, 2 protons are pumped and two removed from the matrix (net effect is an increase in membrane potential)
The ETS is arranged into
supercomplexes
NADH moves x more hydrogens than
FADH2
NADH moves 4 more hydrogens than
FADH2
Explain the acetyl coA reaction
Pyruvate is decarboxylated then oxidised and then CoA attached
Where does the acetyl coA reaction occur?
in mitochondrial matrix
Explain the role of Pyruvate Dehydrogenase
Complex, actually has 3 enzymes
has decarboxylase activity (removes CO2) and is a dehydrogenase
What role does vitamin b1 play in cell respiration?
It functions primarily as a cofactor to help enzymes perform their molecular reactions, in many parts of the respiartion cycles
Explain the process of citrci acid cycle step by step
1 = Citrate synthase
Acetyl group adds 2C to oxaloacetate
2 = aconitase
H2O removed and re-added rearrangement
3 = isocitrate dehydrogenase
NAD is reduced to NADH and CO2 removed
4 = alpha-ketoglutarate dehydrogenase
Another CO2 removed and another NAD reduction, and CoA-SH added (weak bond)
5 = succinyl CoA synthetase
CoA-SH released & substrate level phosphorylation, GTP formed and converted to ATP at no cost
6 = succinate dehydrogenase
2 H+ transferred to FAD (FADH2) Succinate oxidised
7 = fumarase
Water added to fumarate & rearrangement
8 = malate dehydrogenase
Last oxidation and oxaloacetate reformed
which enzyme is part of the citric acid cycle and the elctron trasnsport chain?
succinate dehydrogenase
alpha-ketoglutarate dehydrogenase is similair to which enzyme?
pyruvate dehydrogenase
Where is SDH located? (succinate dehydrogenase)
SDH is part of the electron transport system and sits in the inner mitochondrial membrane
Which enzyme handles some very dangerous free radicals, but somehow appears to be very robust?
succinate dehydrogenase
What is the REDOX state ?
The NADH/NAD ratio is often referred to as the REDOX state
If there is too much Succinyl-CoA or Acetyl- CoA, what happens to the CAC?
CoA becomes limiting and the CAC slows
What is Isocitrate dehydrogenase and how does this affect cac cycle?
ADP/ATP ratio
10/2 goes faster
2/10 goes slower
What is an example of another proton drive biological machine other than in the mitochondria?
Mitchell contended that H+ powered bacterial flagella
Indeed, they do and there are striking similarities to the ATP synthase H+ powered rotation of flagella and the ATP synthase
What two gradients constitute the proton motive force?
There is a concentration gradient ( pH) and an electric charge in mV
Where are ATP synthases often found on the cristae?
on the tips of the crista on the curved parts
The matrix is 50% or more preotein true or flase?
true
As ATP synthase is a dimer what does this do to the plasma membrane?
bends it
Explain the bend in the cristae membrane and how this helps pH of the matrix
The charge density is greatest at the inside surface of tips of the cristae, attracting positively charged hydrogen (protons)
Protons then concentrate in the cristae ridges, this lowers the pH locally and now can drive the ATP synthase
Explain how ATP synthase works
1 H+ ions flowing down their gradient enter a half channel in a stator, which is anchored in the membrane.
2 H+ ions enter binding sites within a rotor, changing the shape of each subunit so that the rotor spins within the membrane.
3 Each H+ ion makes one complete turn before leaving the rotor and passing through a second half channel in the stator into the mitochondrial matrix.
4 Spinning of the rotor causes an internal rod to spin as well. This rod extends like a stalk into the knob below it, which is held stationary by part of the stator.
5 Turning of the rod activates catalytic sites in the knob that produce ATP from ADP and Pi.
Explain the proof that ATP synthase rotor spins
If ATP is added the rotor spins
i.e. the rotor works in reverse and the ATP synthase becomes a proton pump
Explain how the rotor of the ATP synthase works:
The internal rod moves around within the catalytic knob, this exerts pressure on the alpha and beta subunits and changes their conformations
For each rotation of the internal rod 3 ATP are made (as an aside, if there is no proton gradient the ATP synthase will consume ATP!, this occurs in anoxia (no oxygen)
For each rotation of the internal rod
3 ATP are made
The bigger the C‐ring,
the less ATP is made per H+
Mutation in the C‐ring of the ATP synthase
- Results in proton slippage
- i.e. less ATP made per H+
- Results in encephalopathy
There are 2 routes of cytosolic NADH!
1) Malate aspartate shuttle
2) G3PDH shuttle
Which out of
1) Malate aspartate shuttle
2) G3PDH shuttle
is more efficient?
1) Malate aspartate shuttle
Explain the role of The G3PDH shuttle
The G3PDH shuttle makes less ATP as like Complex II it uses FADH2
Why is it not exact? Why 26‐32 ATP
1) Membranes can be leaky when hot, in the early days experiments were done at 25oC (we are 37oC)
2) Membranes leak, generate heat
3) NADH from glycolysis has two fates!
a) the malate aspartate shuttle gives ~2.5 ATP/NADH,
b) the glycero‐3‐phosphate dehydrogenase shuttle gives ~ 1.5 ATP/NADH.
Which complex out of all three is most likely to be damaged under stressful conditions?
Under stressful conditions Complex I is very prone to damage (e.g. oxidative stress, heart attack…), Complex II appears to be robust
Where is glycogen stored in the cell?
Storage in the cytosol, in many tissues
Is glycogen water soluble?
no it is not soluble
How does glycogen Protect osmotic pressure of the cell
(small glucose molecule attracts water, large polymers do not).
Which are the ony two tissues in the human body which releases glucose?
Only liver & some kidney glycogen is accessible to other tissues (only these tissues release glucose)
In the middle of glycogen what is found?
A protein called glycogenin
What role does glycogenin play in the formation of glycogen?
Glycogenin atttches to the reducing end of the glucose molecules, meaning glucose ttatches to eachother only on the non reducing ends.
How is a ball of glycogen made (explain via glycosidic bonding)
A ball of glucose is made by having both alpha 1-6 or alpha 1-4 glycosidic linkages to form branches
Explain Glycogenesis
Glucose enters a hepatocyte through a glucose transporter,
Hexokinase or glucokinase (liver, kidney only) forms glucose-6-phosphate.
Phosphoglucomutase then rearranges this gliucose-6-phosphate into a glucose-1-phosphate
Pyrophosphorylase adds UTP to this glucose-1-phosphate turns it into UDGP
Then glycogen synthase occurs and glucose is added to the non-reducing ends.(alpha1-6 glycosidic linkage causes branches)
What is the role of Amylo (1,4)(1,6)-transglycosylase?
It is a branching enzyme which permits dense construction of glycogen.
Branches are created by the transfer of ~7 glycosyl residues
Each branch must grow to ~11 residues before transfer
New branches are exactly 4 residues away, & move in towards the core, this keeps the overall granule dense!!
What 3 (or 4) enzymes are involved in glycogenolysis?
1) Glycogen Phosphorylase
2) Glycogen de-branching enzyme (actually 2 enzymes)
3) Phosphoglucomutase
From which ends does glycogenolysis occur in the glycogen molecule?
From the non-reducing ends
Explain Glycogenolysis
Glucose 1 phosphate (G1P) is released Glycogen phosphorylase only works till the 5th glycosyl residues, leaving 4 Glycogen phosphorylase is inhibited by
ATP, glucose, and G6P (i.e. products of glycogenolysis and catabolism)
Debranching enzyme acts as a transferase that transfers 3 glycosyl units and then hydrolyses the α-1,6 link
Phosphoglucomutase turns G1P to G6P
Glucose 6-phosphatase (which is only found in the liver and kidney returns G6P into glucose)
What are the sources of building blocks for
gluconeogenesis ?
- Lactatepyruvate/alanine (Cori Cycle)
- Amino acids (except leucine and lysine)
- Glycerol (remainder of fats cannot be used in animals to make glucose)
- CAC intermediates (conversion to citrate/oxaloacetate/malate)
Is glycolysis reversible?
Parts of glycolysis are reversible Some are not!
What is Bypass 1 to make glucose in the glycolysis process?
phosphoenolpyruvatecarboxykinase and pyruvatecarboxylase
What is Bypass 2 to make glucose in the glycolysis process?
fructose1-6biphosphate
What is Bypass 3 to make glucose in the glycolysis process?
glucose-6-phosphotase
Draw a diagram of all the enzymes involved in glycolysis and Gluconeogenesis
What is a group of endocrine cells that secrete glucagon and insulin in the liver?
islets of langerhans
α-cells produce glucagon in response to ___ BGL
α-cells produce glucagon in response to LOW BGL
__-cells produce insulin in response to ____ BGL
β-cells produce insulin in response to HIGH BGL
How does insluin lower BGL? and what are insluin’s other effects?
Insulin LOWERS blood glucose levels by:
- Stimulating all body cells (except brain cells) to take up glucose
Has numerous other effects such as:
- Stimulating glycogen synthesis
- Promoting storage of fuel e.g. glycogen and fat
How does glucagon raise BGL?
RAISES blood glucose levels by: - stimulating glycogen break down
- signalling the liver cells to break down glycogen polymers into glucose, this can go into the blood
Glucagon is a __aa polypeptide
Glucagon is a 29aa polypeptide
Insulin is a __aa polypeptide
Insulin is a 51aa polypeptide
Roles of insulin
Insulin also promotes fat deposition, glycogen storage, growth
Insulin is part of a broad hormone family that are generally anabolic
How does insulin cause an uptake of glucose?
Insulin regulates glucose uptake into these cells by recruiting membrane vesicles containing the GLUT4 glucose transporters from the interior of cells to the cell surface, where it allows glucose to enter cells by facultative diffusion.
Once in the cytoplasm, the glucose is phosphorylated and thereby trapped inside cells.
The effect of insulin on GLUT4 distribution is reversible. Within an hour of insulin removal, GLUT4 is removed from the membrane and restored intracellular in vesicles ready to be re-recruited to the surface by insulin.
Explain Type 1 diabetes:
Insulin dependent, common in juveniles,
Sometimes in adults viral infection triggers loss of cells.
Loss of Insulin production.
Explain Type 2 diabetes:
Non – Insulin dependent, common in older people (90%), obesity, stress,
variable insulin levels, start high then drops
Insulin insensitivity no insulin
Explain the causes of inculin sensitivity:
High fat content of the blood may alter signalling, and or glucose metabolism
Too much fuel
Too few mitochondria can cause Free radicals released by mitos
The cell responds and protects the cell by decreasing GLUT transporter
Blood glucose rises
Mitochondrial DNA mutations can also impair glucose uptake
What happens when u go into starvation mode? Specifically talk about the brain:
The brain requires glucose However it can use ketone bodies
Acetoacetateandβ-hydroxybutyrateare acidic, pH of the blood drops, resulting in ketoacidosis.
How does creatine kinase work?
It takes the phosphate off of creatine phosphate and adds this phosphate to an ADP molecule to form ATP
Label the structure of a chloroplast
Chloroplast thylakoid membranes have
chlorophyll a and b
How does light energy get passed on between chlorophylls?
The flow of electrons occurs through quantum tunnelling
Explain photosystem II
Light hits Photosystem II and electron is transferred to a higher energy state.
Water is split into 2 protons and one oxygen to release 2 electrons
Electron gets transferred to plastiquinone to be passed to the cytochrome complex
H+ in Thylakoid space - Adds to proton gradient
Explain photosystem I
Light hits photosystem I, and flows down to NADP reductase to turn NADP+ to NADPH.
Note that NADPH removes 2H+ from the stroma (adds to the charge difference)
Chloroplast ATPase is Very similar across species, but there are 14 c-ring subunits in plants, only 8 subunits in mammals As it turns each subunit binds a proton.
What does this mean for ATP synthesis efficiency (ATP/H)?
Difference between mitochondria and chloroplasts?
Chloroplasts are more reliant on pH (H+ gradient)
As Chloroplast inner membranes are permeable to Cl- and Mg2+ So mitochondria use net charge potential and H+ gradient
Larger pH difference required in chloroplasts as only H+ gradient is used.
What is the purpose of lamellae?
allows cyclic electron flow
The Calvin Cycle is confined to the
Stroma
Why is the The Calvin Cycle is confined to the Stroma?
This partitioning stops intermediates and products (e.g. glyceraldehyde 3 phosphate) being metabolized Some of the intermediates feed directly into glycolysis and plants have mitochondria and glycolytic enzymes!
Draw the Calvin Cycle
There are three phases to the Calvin cycle:
- CO2 fixation
- Reduction
- Regeneration
Explain how rubisco does photorespiration.
RuBisCo is odd. It also binds O2 (photorespiration) and
makes useless products and this wastes water!
Thus when O2 is high (& low CO2) wasteful work occurs as no Carbon fixation!
Why?
Many plants shut down photosynthesis at midday. Not so good for farmers!
Oxidative stress?
WHat is the differnce between c3 and c4 plants?
Some plants (hot climates) concentrate CO2 (called C4 plants sugarcane and corn).
Partitioning of specific cycles among leaf cells, and use of 4-carbon oxaloacetate ( has 4 Cs hence C4) as a “CO2” shuttle.
If C3 plants split water at a high rate, a lot of O2 accumulates. O2 accumulates and results in photorespiration.
This is wasteful use of H2O and carbon.
The C4 pathway means more CO2 is concentrated so less O2 is present for photorespiration through RUBISCO binding O2
But C4 plants uses more ATP!
This extra ATP comes from cyclic electron flow and sunlight is cheap, especially in the tropics.
Ultimately C4 plants can use water more efficiently.
