Double Biochem Exam

Question 1

Cells need to do work to live;

Answer 1

Movement, transport, chemical synthesis

Question 2

Metabolism is the collection of…

Answer 2

chemical reactions that transform matter in a cell and enable work. Metabolic pathways can be catabolic or anabolic, and these may be coupled. Metabolic pathways are controlled to meet the needs of the cell. Control occurs through the regulation of enzymes.

Question 3

“Living organisms are composed of…

Answer 3

lifeless molecules.”

Question 4

Are our cells just bags of chemicals?

Answer 4

No. A bag of chemicals is just a bag of chemicals - a cell is living.

Question 5

What is life and how do we define it?

Answer 5

Living cells/organisms can do all sorts of cool stuff - that’s how we try to define life.
Underlying all these properties/processes are 3 things that we collectively refer to as work.
(Movement/mechanical work, membrane transport and chemical synthesis).

Question 6

Movement/mechanical work:

Answer 6

Cells need to move organelles (a specialised subunit in a cell that performs a function) around.
All cells will have a mechanism inside them to move stuff around inside the cell.

Question 7

Vesicles are used to…

Answer 7

move things to specific locations in the cell (e.g. proteins, membrane). Sometimes these are moved from the nucleus to other organelles, different parts of the cell or even the outside of the cell. Sometimes from the outside of the cell to the nucleus. These (things like proteins) are moved to where they need to be in the cell, it’s a process called vesicular trafficking.
Vesicular trafficking - these movements are not random; they are very precisely regulated.

Question 8

An endocrine cell might for example traffic a hormone in this way that is then released and moves around the body. That hormone might be involved in…

Answer 8

reproduction (estrogen), response to the environment (epinephrine), and energy processing (insulin). Sometimes big cells need to mix things around (organelles, nutrients, biomolecules).

Question 9

Cytoplasmic streaming:

Answer 9

a form of mechanical movement you see in large cells. Plant cells are typically larger than animal cells, so this is seen mostly in those with chloroplasts. Plant cells have this large central vacuole (filled with irons, water), the largest organelle you’ll find in a plant cell. Vacuoles are found in fungal cells and also in some protists as well as larger animal cells (eggs/oocytes and embryos). More of a stirring up mechanism, a way to get organelles’ nutrients/biomolecules of equal concentrations throughout the cells (like stirring tea to have it equally concentrated).

Question 10

These intracellular movements are powered by motor proteins. The three main families of motor proteins are:

Answer 10

kinesin, dynein and myosin. These families move along tracks inside the cell; the tracks/scaffolding are formed by microtubules and microfilaments (cytoskeleton). These motor proteins walk along or hop along these tracks.

Question 11

Entire cells also need to move, called cell…

Answer 11

motility or cell migration. Neutrophils, for example, will chase bacteria. Cell motility is also a normal part of development. Cells migrate to their correct location in an embryo to where they need to be to grow the embryo.

Question 12

How do cells move?

Answer 12

Their actin cytoskeleton ‘pushes’ the front end (the membrane, which causes protrusions) of the cell forward and also ‘pulls’ the back end of the cell forward. This pushing of the membrane causes a protrusive area to form, the ‘head’ of the cell. At the back, there are microfilaments pulling the back end forward. Other cells use cilia or flagella to swim. Cilia can also be used to move water past cells (like in our airways, using these cells to push mucus out).

Question 13

Cells like sperm cells have…

Answer 13

flagella to swim through. The microtubules in the cytoskeleton allow the flagella or cilia to bend, so the cytoskeleton is very important in movement.
On a bigger scale, multicellular animals move due to muscle contraction.

Question 14

Membrane transport:

Answer 14

Movement of molecules or ions across membranes. Important to maintain osmotic balance with the solution outside the cell. If not, cells can burst or shrivel up. Proteins involved likely arose very early in evolution. Important for nutrient uptake, excretion of waste, nerve signalling and muscle contraction.

Question 15

How do cells move?

Answer 15

Their actin cytoskeleton ‘pushes’ the front end (the membrane, which causes protrusions) of the cell forward and also ‘pulls’ the back end of the cell forward. This pushing of the membrane causes a protrusive area to form, the ‘head’ of the cell. At the back, there are microfilaments pulling the back end forward. Other cells use cilia or flagella to swim. Cilia can also be used to move water past cells (like in our airways, using these cells to push mucus out).

Question 16

~50% of the energy used by the brain/the brain requires is simply used to move…

Answer 16

Na+ and K+ across cell membranes. Important in nerve cells and nerve impulses.

Question 17

Na pump…

Answer 17

(a protein known as the Na+/K+ ATPase), 2 alpha, 2 beta and 2 gamma cell units. This pump moves sodium and potassium across all cell membranes, predominantly in nerve and brain cells. It maintains sodium and potassium at certain concentrations (high potassium, low sodium) across membranes. This is very crucial for the way our cells operate.

Question 18

In your muscle cells, there is calcium…

Answer 18

pump (Ca2+ pump, Ca2+ -ATPase) is very important. It keeps Ca2+ levels in the cells very low (moves Ca2+ out). It keeps calcium levels in the cells very low, it moves calcium out of the muscles, but if the muscle needs to contract, then other membrane transporters move calcium back into the cells. Then the muscle responds to a sudden increase in Ca2+ (which is a signal for the muscle cells)and contracts. The proteins that react with the active microfilaments shift with an increase in calcium, which allows the motor proteins to move along the track and contract the muscle. To relax the muscle, the calcium pump works really hard to move the calcium back outside the cell.

Question 19

Subunit sugar has what macromolecule?

Answer 19

Polysaccharide

Question 20

Subunit amino acid has what macromolecule?

Answer 20

Protein

Question 21

Subunit nucleotide has what macromolecule?

Answer 21

Nucleic acid

Question 22

Chemical synthesis:

Answer 22

Making macromolecules from monomer subunits. Polysaccharides from sugars, proteins from amino acids and nucleic acids from nucleotides.

Question 23

Chemical synthesis:

Answer 23

Making macromolecules from monomer subunits. Polysaccharides from sugars, proteins from amino acids and nucleic acids from nucleotides.

Question 24

Cells can do work because they…

Answer 24

can transform molecules and energy.

Question 25

Molecules are transformed (i.e. slightly modified) via chemical...

Answer 25

reactions that occur within a cell. You typically have a starting molecule (the reactant) that is converted into a product. When we talk about reactions in biology, they are typically categorised by enzymes, and we refer to the starting molecule as the substrate. The substrate is what the enzyme reacts upon. This is a metabolic pathway, a series of sequential reactions.

Question 26

Respiration is the oxidation of...

Answer 26

glucose.

Question 27

Reactions are very tightly controlled. Typically, proteins are called...

Answer 27

enzymes (specificity for the most part, so most enzymes are specific). Catalyse reactions decrease the time taken to come to equilibrium (speed up reactions). This is more complicated in biology than in chemistry.

Question 28

Phosphorylating means the addition...

Answer 28

of a phosphate group.

Question 29

First reaction in glycolysis...

Answer 29

Glucose is converted to glucose-6-phosphate. Catalysed by the enzyme hexokinase. The hexokinase phosphorylates the glucose. So it takes a phosphate from the ATP, and gives it to the glucose which gives us glucose-6-phosphate. If glucose, hexokinase and ATP were isolated in test tube, the reaction would come to an equilibrium. So that means after the glucose is converted to glucose-6-phosphate, the reverse reaction would then start to occur. So you’d eventually reach an equilibrium where there is no net change between the concentrations of glucose and glucose-6-phosphate. This is fine in a test tube, but in a cell, this would cause a huge problem. In a cell, the reaction doesn’t come to equilibrium, it is called metabolic disequilibrium. So the glucose-6-phosphate. Rather than being converted back to glucose, in a cell because it’s not isolated, the glucose-6-phosphate can be catalysed in another reaction. This is done by the enzyme phosphoglucose isomerase, which converts it to fructose-6-phosphate. Glucose-6-phosphate is the substrate for the second reaction in glycolysis. So instead of going in a backwards reaction, glucose-6-phosphate will be used for another reaction going forward- a metabolic pathway. So it’s a metabolic disequilibrium. If all of the cells had their reactions coming to equilibrium, then they’d all be dead because they wouldn’t be able to do their work.

Question 30

All of the metabolic pathways in a cell constitute its...

Answer 30

metabolism. There is also a metabolic map, where all of the major metabolic reactions within a cell can be illustrated. The dots represent the metabolites (the chemicals in the reaction), the lines represent one metabolite being converted to another.

Question 31

Metabolic pathways can be catabolic:

Answer 31

Breaking complex molecules into simpler ones, that are spontaneous or yields energy.

Question 32

Metabolic pathways, anabolic:

Answer 32

Small molecules assemble into larger ones. Energy is required they build (or join smaller molecules into larger ones) complex molecules from simpler ones, are non-spontaneous, and they cost energy.

Question 33

Metabolic pathways, catabolic:

Answer 33

Large molecules break down into small ones. Energy is released.

Question 34

Energy coupling:

Answer 34

Energy derived from catabolic pathways can be used to drive anabolic pathways. So energy that is released from catabolic pathways is converted into useful energy, which can be used to provide for anabolic pathways (energy coupling). These pathways are tightly regulated depending on the energy needs of the cell or organism. They are regulated via the enzymes, which can be switched on and off. This can be done allosterically (bind to enzymes, changing the shape to switch on or off), covalently (by adding a phosphate to turn it on or off) and genetically (you can switch on or off the genes for the enzyme).

Question 35

Energy carriers:

Answer 35

ATP, NADH, NADPH.

Question 36

1st law of thermodynamics means...

Answer 36

that cells can’t create energy to do work, so they transform and transfer energy.

Question 37

1st law of thermodynamics means...

Answer 37

that cells can’t create energy to do work, so they transform and transfer energy.

Question 38

2nd law of thermodynamics means...

Answer 38

that as cells/organisms develop, they become more complex (more order/low entropy) in their reactions, some energy is lost as hea,t and the environment becomes less ordered/higher entropy.

Question 39

Free energy is energy available to do...

Answer 39

work. Reactions occur spontaneously if the free energy of the products is lower than that of the reactants (-∆G). Exergonic reaction. An endergonic reaction has a +∆G value and is nonspontaneous. Work that occurs in cells as reactions does not come to equilibrium.

Question 40

1st Law of Thermodynamics:

Answer 40

Energy in the universe is constant (quantity (amount), not quality(type)), energy can’t be created or destroyed, but it can be transferred or transformed. We have to get the energy from somewhere else, so we take it from something else and convert it. To do work, cells need energy.

Question 41

Cells transform energy from the sun (plants/bacteria), from chemicals (certain bacteria) or from...

Answer 41

food (animals/fungi/protists) to enable work. For example, chemical reactions in an emu will convert the chemical (potential) energy from food (plants) into the kinetic energy of running. The diving example shows potential energy converted into kinetic energy.

Question 42

1st Law of Thermodynamics:

Answer 42

Energy in the universe is constant (quantity (amount), not quality(type)), energy can’t be created or destroyed, but it can be transferred or transformed. We have to get the energy from somewhere else, so we take it from something else and convert it. To do work, cells need energy.

Question 43

Kinetic energy is anything that...

Answer 43

moves. Light, electrical, heat.

Question 44

Potential energy is energy related to the...

Answer 44

structure or location of things.

Question 45

Chemical energy (where electrons are in a molecule) and...

Answer 45

proton gradient across a membrane (concentration).

Question 46

Chemical energy (where electrons are in a molecule) and...

Answer 46

proton gradient across a membrane (concentration).

Question 47

Plant transforms light energy into...

Answer 47

chemical energy (photosynthesis) - they are photoautotrophs.

Question 48

Plant transforms light energy into...

Answer 48

chemical energy (photosynthesis) - they are photoautotrophs.

Question 49

Animals, fungi, and protists convert chemical energy in...

Answer 49

food into chemical energy they can use to power work using ATP (respiration) - they are heterotrophs.

Question 50

What’s gradually gonna be done through a metabolic pathway is the...

Answer 50

breakdown of glucose into simpler molecules. Eventually, the glucose will be broken down into carbon dioxide and water. We’ve got a series of reactions where the glucose will gradually be oxidised, so the electrons of the glucose are removed and are passed onto an energy carrier (this carrier is referred to as NAD).

Question 51

Plants also do ________ despite being autotrophs.

Answer 51

respiration

Question 52

The mitochondria are an organelle found in eukaryotic cells, some cells may have 1000s of these. The membrane of the mitochondria is full of...

Answer 52

protein complexes. 90% of the oxygen we breathe in is used as an electron acceptor in an electron transportation chain (yellow arrow). As the electrons move through these complexes, they are losing energy. The energy is then passed onto the large protein complexes.

Question 53

Some prokaryotes use different energy sources. For example, inorganic compounds (e.g...

Answer 53

H2S, NH3, Fe2+), chemical energy. Converts energy in the electrons to chemical energy (ATP) through the electron transport chain or makes sugars by reducing CO2. We’ve got certain prokaryotic organisms, we have chemoautotrophs.

Question 54

The potential energy the electrons have is converted into...

Answer 54

kinetic energy, this kinetic energy enables protons to move across the inner mitochondrial membrane. There is an uneven distribution of protons across the membrane, a form of potential energy. This potential energy in the proton gradient is then transformed back into kinetic energy as the protons move through the protein called ATP synthase. This is a rotational protein, like a merry-go-round; subunits go around it. As they go around, you get changes in some additional parts of the protein, and they will enable the addition of a phosphate group to ADP (generating for us ATP). ATP is a useful form of energy.

Question 55

2nd Law of Thermodynamics:

Answer 55

Every energy transfer or transformation increases the disorder (entropy) of the universe. Less order = higher entropy.

Question 56

In chemical synthesis, energy is released as...

Answer 56

heat, increasing disorder/entropy in the surrounding environment. Thus, cells/organisms can develop order and still obey the second law.

Question 57

Free energy (G) is essentially a measure of something’s...

Answer 57

stability. Unstable systems are rich in free energy, so if something is more unstable, it has more free energy.

Question 58

If something has high free energy, there’s a tendency...

Answer 58

to try and push it to a lower free energy state (a spontaneous change). Due to the 2nd law of thermodynamics, they tend to change more spontaneously to a more stable state.

Question 59

higher free energy =

Answer 59

greater instability = greater order = lower entropy (disorder)

Question 60

lower free energy =

Answer 60

more stability = more order = higher entropy)

Question 61

The free energy changes...

Answer 61

∆G < 0 (i.e. is negative, less than zero).

Question 62

Free energy charges enable...

Answer 62

work in cells. Free energy is the thing that underlies the ability to do work in cells.

Question 63

Glucose has higher free...

Answer 63

energy, carbon dioxide and water have lower free energy.

Question 64

The free energy change for the reaction (∆G (delta G)) can be calculated by subtracting...

Answer 64

G (glucose) from G (carbon dioxide and water). ∆G = G (carbon dioxide and water, the product) - G (Glucose, the reactant) ∆G = 2 - 6 = -4 Negative ∆Gs indicate that a reaction will occur spontaneously. This is an exergonic reaction. Note: arbitrary values were used to simplify things; the actual ∆G or glucose oxidation is -2,870 kj/mol.

Question 66

Exergonic and endogonic relate to changes in...

Answer 66

free energy.

Question 67

Exothermic and endothermic relate to changes in...

Answer 67

heat (enthalpy).

Question 68

What would happen if the reaction went the other way?

Answer 68

With the same calculation (but reversed) it’d be +4, which makes it an endergonic reaction. Remember, arbitrary values were used to simplify things - the actual ∆G for the reduction of carbon dioxide to form glucose is +2,870 kj/mol.

Question 69

Most reactions come to an...

Answer 69

equilibrium. As a product forms a back reaction occurs and it is converted back to the reactant. Thus, the two ∆G values cancel each other out. ∆G = 0

Question 70

Metabolic disequilibrium:

Answer 70

Reactions in cells do not come to equilibrium - metabolic disequilibrium. They are not occurring in isolation. Typically, the product of one reaction becomes the reactant for another reaction i.e. is part of a metabolic pathway. ∆G does not equal zero, and free energy changes can be used to enable work.

Question 71

ATP is a cell’s...

Answer 71

energy shuttle. ATP hydrolysis is exergonic; in cells is coupled to endergonic reactions/processes. Coupling occurs by loss/transfer of a phosphate; we get things called phosphorylated intermediates, which are more reactive Catabolic pathways enable the production of ATP from ADP and Pi (inorganic phosphate).

Question 72

ATP is a...

Answer 72

nucleotide. Reaction of ATP and water (hydrolysis) yields ADP (adenosine diphosphate), inorganic phosphate and also releases energy. ∆G = approx -29 kj mol-1 Why negative ∆G? ADP + Pi more stable than ATP Think of the 2nd law of thermodynamics - hence it’s a spontaneous reaction. ATP4-, ADP3- Electronegative repulsion of the negative charges on the phosphates is greater in ATP (as there are 4 compared to 3 in ADP) If we carry out this reaction in a test tube, how is energy released? Heat energy. Can cells utilise this type of energy to do work? No, cells cannot utilise heat energy to do work Phosphate is joined to another molecule or protein and is not released into a solution. Increases the molecule/protein’s free energy: More unstable, more reactive, enables conformation change. This enables work

Question 73

Work depends on energy (ATP). Movement/mechanical work, motor proteins like...

Answer 73

kinesin have sites where ATP binds and becomes hydrolysed. Also multiple phosphorylation sites. ATP hydrolysis powers conformational change.

Question 74

Na+ pump present in animal cells...

Answer 74

Nucleotide binding domains and phosphorylation site on the pump. Conformational change in the pump when phosphorylated enabled Na+ and K+ to move across the membrane.

Question 75

Sodium pump belongs to a family of membrane transport proteins called

Answer 75

P-type ATPases (e.g. Ca2+ pump, H+ pump) - all have conserved aspartate which is phosphorylated. This is an example of chemical synthesis through ATP hydrolysis. This is a reaction that is part of metabolism; the formation of glutamine. Glutamic acid is made more reactive when it is phosphorylated by ATP. Will join with ammonia to give glutamine. An endergonic reaction, it will not occur just in a test tube, as it needs energy. This is coupled with the hydrolysis of ATP

Question 76

Why can’t cells use heat energy to do work?

Answer 76

Heat will simply increase the random motion of molecules/proteins (the vibrational energy of proteins). For work, you need specific conformational changes (needs to be the exact shape) in proteins; it needs to be exact. Binding of ATP, its hydrolysis and the formation of phosphorylated intermediates will allow specific conformational changes and thus reactions/work to occur.

Question 77

Where does ATP come from?

Answer 77

To ATP a Pi is added to ADP. Pi = inorganic phosphate. So to make ATP, we add an inorganic phosphate. Endergonic reaction as ATP has greater free energy than ADP and Pi. ∆G = approx. +30 kj mol-1

Question 78

ATP cycle:

Answer 78

Catabolic reactions/pathways release energy. This catabolic energy is used to make ATP, which provides the energy for cellular work.

Question 79

The active site of an enzyme is where a...

Answer 79

substrate binds. Enzymes can change shape when a substrate enters the active site - induced fit. The various ways in which an enzyme lowers EA. Enzymes have an optimal pH and temperature. What irreversible, reversible, competitive and non-competitive inhibitors are. The types of regulation - genetic, allosteric, and covalent.

Question 80

Enzymes:

Answer 80

Biological catalysts. They make reactions go faster. Substrate specific (they typically will only catalyse a specific reaction). They are highly regulated (this enables metabolic control). Even for exergonic reactions (spontaneous), there is an energy barrier that has to be overcome (activation energy) for the reaction to occur. Enzymes lower this activation energy (EA) for both exergonic and endergonic reactions. This makes the reaction go faster. Enzymes lower the EA in the active site. Start by looking at the active site and the catalytic cycle. REactact (substrate) enters the active site. Chemical and physical interactions happen here to lower the EA. Typically a close shape match between the active site and the substrate (lock and key match) specificity. But shape and active site change when the substrate enters the active site - induced fit.