Topic 1

Question 1

Covid 19

How is it different to our cells and how does it work?

Answer 1

Has an RNA genome as opposed to storing the genetic information as DNA.
The spike protein recognises an enzyme on the outside of our cells called the ACE 2 receptor and that’s how it makes its way into our cells. Once inside the cell it replicates many times before it exits the cell. It has a lipid membrane on the spike protein. A layer of fatty acids - a barrier on the outside.

Question 2

Why should we always wash our hands with COVID?

Answer 2

Soap breaks apart lipids on the outside of the cell therefore destroying covid.

Question 3

What is biology?

Answer 3

Biology is the study of life and living organisms.

Question 4

What defines living things?

Answer 4

MRS GREN

Question 5

What are living organisms?

Answer 5

Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain homeostasis.

Have response mechanisms to the environment.

Question 6

Transformation of energy

Answer 6

We will take in fuel and react it with oxygen and burn it to create energy and carbon dioxide. Fuel is brought in as food to create energy. Fuel is food.

Question 7

Open systems

Answer 7

Means that we exchange things. Open systems - constantly exchanging.

Question 8

Maintaining homeostasis by decreasing local entropy

Answer 8

Require energy to decrease local entropy to maintain homeostasis.

need to create order which requires energy. Creating order like making proteins (creating order) needs energy. We require information - for us its DNA. homeostasis - keeping the same

Question 9

Biologists study things in different spatial and time scales

Answer 9

There are different levels of biology - plant level, molecular level etc.

All levels have processes which link to one another.

We can look at things on a molecular time scale or a global time scale.

Question 10

Molecular time scale

Answer 10

Happens in a matter of seconds or nanoseconds.

Question 11

Global time scale

Answer 11

Happens in a matter of years or millions of years.

Question 12

The physiological level of biology

Answer 12

There is a correlation between structure and function. The particular shape a structure has is often perfectly suited for the job it does.

Wings to take flight.
Weightless bones with less structure.
Particular cell structure and connections to allow for interactions.

Question 13

What is the purpose of science?

Answer 13

Science seeks to develop an accurate description through observation and experimentation

Question 14

Discovery vs. Hypothesis based science

Answer 14

Discovery based science often describes nature while hypothesis based science often proposes an explanation

Question 15

Research…

Answer 15

Research can be applied or basic

Question 16

Reductionism

Answer 16

Reductionism breaks larger systems down into their component parts.

an approach to understanding the nature of complex things by reducing them to the interactions of their parts, or to simpler or more fundamental things

Reducing interactions to their simplest parts. Then add levels of complexity. How a cell behaves in a test tube will be different to how they act in the cell.

Question 17

The scientific method

Answer 17

Observation, question, hypothesis, prediction, experiment, result.

Controls are needed and only one variable should be changed.

Consider the ethics of the experiment.

Question 18

Emergence

Answer 18

The way complex systems and patterns arise out of a number of relatively simple interactions

Question 19

How do we make a drug?

Answer 19

Need to make a compound that has high affinity, selectivity, stability, and bioavailability.

Question 20

Drug - Digoxin

Answer 20

‘Dropsy’ (congestive heart failure) causes shortness of breath, leg swelling and fatigue due to the inability of the heart to pump enough blood around. Used for treating heart disease.

In the 1780’s a physician noticed that a patient with dropsy quickly recovered after taking a herbal remedy from the foxglove (Digitalis). Boiling foxglove.

There are lots of compounds in the tea but they were able to isolate the chemical structure responsible for treating heart disease.

Currently used to treat several heart conditions.

Binds to a Na+/K+ pump in the membrane of heart cells.

Question 21

Drug making

Answer 21

In 2014 it was a trillion dollar industry.

Can take 10-15 years to make a new drug.

Question 22

Taxol

Answer 22

A drug primarily used to treat ovarian cancer.

Discovery science with large amounts of science: gathered many different samples from many organisms and watched to see whether they killed the cancer cells or not.

Had to do many trials to make sure they didn’t kill our cells as well as the cancer cells.

They found is you took extract from the bark of a pacific yew tree (growing in America) it was cytotoxic and would kill the cancer cells.

Took 3 years to seperate the compound from the bark. Then methods had to be developed to harvest the compound - there aren’t enough trees and the compound is hard to synthesise.

Question 23

Taxol Timeline

Answer 23

1964 – it was found that an extract from Pacific Yew bark was cytotoxic.
1967 – the compound was isolated, and named Taxol 1971 – 10g of Taxol was produced from 1,200 kg of bark.
1978 – it was shown to be effective against leukemia in mice
1984 – beginning of human trials, which were shown to have a response rate of 30% of patients with ovarian cancer.
1992 – approved for general treatment
1993 – developed processes to harvest Taxol from cell cultures

Question 24

Tamiflu and Zanamivir

Answer 24

Hypothesis based. Rational drug design - more specific approach rather than testing everything out there.

The two main anti flu drugs.

Influenza will usually attack the sialic acids which naturally occur in our cells. To make a drug targeting a particular enzyme we will make these other enzymes that look like the natural substrate but they have a few other bits and pieces (differences) tacked on there. Slight changes to the structure.

Hypothesizing that adding something on doing something else - may be an inhibitor.

Used the structure of neuraminidase, a viral protein, in complex with an inhibitor Computational modelling was used to improve the binding of the ligand (eg a hydroxyl group near a negatively charged region was changed to an amino group)

Question 25

Penicillin

Answer 25

Alexander Fleming was plating out some dishes - noticed that he had a fungus growing in the corner and started inhibiting the growth of the bacteria growing on the plate. 1939 - WW2 - huge demand for antibiotics. 1940 - animals, 1941 - human trials 1942 mass production Serendipity - not often going out to look for something - dumb luck/random chance. Some of the biggest discoveries are when you’re trying to do something else. Found a mouldy cantaloupe which made 200 times more penicillin than the fungi Fleming found.

Question 26

Good science?

Answer 26

What is the evidence? - fact vs opinion. Where did the research come from? Conflicts of interest? Is it a company that has invested interest that shows that something is really good. Is it reviewed and repeatable? Reviewing usually takes a long time and it is a long process to publish the information that you’ve found - you can't just throw your information out there. With COVID this is different because labs are taking their results and putting them straight into open access databases - this is good because it helps to get the information out sooner - communication of information faster. People may be putting information up that hasn't undergone a peer review process - needs to have quality control. Are appropriate conclusions being drawn? Do the results match what the experiment aimed to do? Correlation vs. causation → random chance that numbers relate to each other.

Question 27

What science can't do:

Answer 27

Science can’t tell right from wrong Science doesn’t make aesthetic judgement Science doesn’t tell you how to use the knowledge Science doesn’t judge on supernatural phenomena We can change genetic sequences of organisms with CRISPR - but should we be doing that? Ethics. Is it ethical? How you use information told by science - comes down to ethics.

Question 28

What compounds are we mostly made up of?

Answer 28

We are mostly made up of C, N, O and H (with some P, S, metals and salts)

Question 29

Covalent bonds are...

Answer 29

very strong

Question 30

What causes molecules to stick together?

Answer 30

Weaker bonds.

Question 31

What is temperature?

Answer 31

the average kinetic energy of molecules

Question 32

Why is water a good solvent?

Answer 32

because lots of biomolecules are polar

Question 33

What is diffusion?

Answer 33

the movement of a substance from a region of high concentration to a region of low concentration

Question 34

The universe...

Answer 34

hates order, and tends to create disorder

Question 35

Transfer of energy...

Answer 35

is not very efficient (tend to get heat as a byproduct)

Question 36

What elements make up human body weight and by how much?

Answer 36

Oxygen, carbon, hydrogen, nitrogen → these elements make up 96% of human body weight

Question 37

Trace elements in the body

Answer 37

Trace elements - molybdenum and selenium - important for enzymes we need a small amount of them to allow our body to function.

Question 38

Covalent bonds

Answer 38

are the sharing of electrons | Things are most stable if they have 2 electrons in the inner shell and 8 electrons in the outside shell.

Question 39

Unequal electron sharing result in..

Answer 39

polarity. Sometimes if there is an oxygen or a nitrogen on one side and a hydrogen on the other side, the oxygen and nitrogen are really electronegative and tend to steal the charge. The electrons like to hand around the electronegative elements rater than the hydrogen which will give the O,N side a slightly negative charge and the hydrogen a slightly positive charge. Sometimes if you have one atom on one side and a hydrogen on the other side the electrons tend to spend more time hanging out near the electronegative atom. As a result it gets a slightly negative charge and the other gets a slightly positive charge.

Question 40

Non polar covalent bonds

Answer 40

The electrons between them - where there is the same element on each side - spend all of their time in the middle and it is even. Sometimes if there are the same amount of electrons on each side the covalent bond is non polar → hydrogen. Electrons are just as likely to be found near one atom, as the other atom.

Question 41

Vaccine trials - COVID.

Answer 41

A study was carried out to see if the vaccine works or not - If we have a vaccine and want to know if we can use it we need to make sure it is safe and applicable to the general community - does it actually work? There were 46,000 participants - no forced exposure. Placebo controlled trial → half the participants got injected with a placebo and the other half with the vaccine. Side effects → fatigue and headache. After 14 days - hardly anyone who was given the vaccine got covid. After their second dose only 8 people were infected with covid. People dying during the trial - most of the people are older - over 80s. People will end up dying with such a big trial group - is it due to the vaccine or due to something else?

Question 42

Covalent bonds/sharing electrons

Answer 42

Atoms come together to share electrons → hydrogen, oxygen, nitrogen and carbon don’t have the full complement of electrons in their shells, they want to get electrons so that they have a nice stable arrangement.

Question 43

Bonds on carbon, hydrogen, oxygen and nitrogen:

Answer 43

If it's carbon it will have four bonds to it, hydrogen will have one, oxygen will have two and nitrogen will have three. Carbon is seen in the backbones, if combined with four different partners then there is much more variation of what can be made.

Question 44

Important chemical groups in biology: | Ethanol

Answer 44

Carbon hydrogen bond → non polar, hydrogen and oxygen polar.

Question 45

Important chemical groups in biology: | Acetic acid

Answer 45

Oxygen is so electronegative that it can take all of the electrons to itself and hydrogen loses its electrons and heads off as a proton. Example of a chemical group acting as an acid.

Question 46

Important chemical groups in biology: | Glycine

Answer 46

Chemical group acting as a base. | We can put atoms together in various combinations to get some different chemistries happening.

Question 47

Important chemical groups in biology: | Sulfur groups

Answer 47

Amino acids | Phosphates in nucleotides

Question 48

Difference between ionic bonds and transfer of electrons.

Answer 48

Covalent bonds share electrons, ionic bonds transfer electrons. Opposites attract - positive and negative charges.

Question 49

Weak chemical bonds - Van der Waals interactions

Answer 49

Two atoms like to be close to each other but if they get close they start pushing apart and if they get too far apart they lose their force. When they are just the right amount of closeness, they form a very stable arrangement. Weak interactions can accumulate to make up what we are lacking in strength → not as strong as covalent or ionic bonds. How the gecko can stick to a wall. Van der Waals interactions result from uneven electron distributions

Question 50

How much water are we made of?

Answer 50

70%

Question 51

Water and ammonia.

Answer 51

Polar bond. An electronegative atom (can be oxygen or nitrogen) - tends to hog the electrons tends to spend more time around the nitrogen rather than the hydrogen and we get a slight uneven charge distribution. The uneven charge distribution means that the slightly positive hydrogen likes interacting with the electronegative atom so we start getting bonds forming between them - not as strong as covalent bonds.

Question 52

How do hydrogen bonds occur

Answer 52

Hydrogen bonds occur when hydrogen is attracted to an electronegative atom

Question 53

Hydrogen bonding

Answer 53

Hydrogen bonding gives water unusual properties. If we have lots of water molecules then we can get lots of hydrogen bonds forming. Water molecules in the middle, each of the hydrogens can form some hydrogen bonds and there are some lone electrons. Each water can form hydrogen bonds with four other waters and those can form hydrogen bonds with other waters and so on. Network where molecules are connected together.

Question 54

Different atoms can accept a different number of hydrogen bonds.

Answer 54

Ammonia - 2 hydrogen bonds, can only accept one hydrogen bond - can interact with 2 molecules, ethanol - less than four - there are a whole bunch of non-polar bonds there and only one hydrogen - it can only form a couple of interactions.

Question 55

Water molecules

Answer 55

Water molecules tend to stick together. Surface tension - bugs that can walk across water → force of hydrogen bond molecules holding the water molecules together so that they can walk across the top of it. Droplets - tree pulls water up through the tree the water diffuses out the top and the water molecules get dragged up by hydrogen bonds, as the water leaves the leaves all are attached by tiny chains of hydrogen bonds so that it pulls everything up. Because its a little big sticky you can get droplets. Forms a meniscus because it likes sticking to surfaces.

Question 56

Ice

Answer 56

Ice floats because hydrogen bonds break and reform. Water is one of the only liquids where the solid floats on top. This is because the hydrogen bonds are constantly breaking and reforming. One interacts with water and then breaks and interacts with another water and so on. Once we start getting a solid everything slows down and we get more of a lattice pattern. Each water molecule interacts with other water molecules and starts forming a neat arrangement. They start separating everything apart holding each other at bay but also pushing each other apart. Because they are further apart that makes it less dense so it floats on top. Ice has an insulating effect - insulation layer. Ice Hydrogen bonds are stable.

Question 57

Melting points

Answer 57

Water has a high melting point Ethanol has only one hydrogen that can interact with it. And it has some lone electrons so it can donate one hydrogen bond and accept a hydrogen bond. Not like water which can accept and donate a couple. Compare water and ethanol - ethanol is a tiny bit bigger in size - about the same size. Ethanol doesn't freeze in the freezer because it takes more effort to get the ethanol molecules to stick together as opposed to water. Ethanol has a lot higher melting point. Water: melts at 0˚C Ethanol: melts at -117˚C

Question 58

Boiling points

Answer 58

Boiling - separating molecules apart. Ethanol boils faster, because water molecules tend to stick together they have a higher boiling point than ethanol. Ethanol - high melting point and high boiling point and heat evaporation. Water boils at 100 ˚C. Ethanol boils at 78 ˚C.

Question 59

Water and energy.

Answer 59

Water can hold lots of energy due to all the hydrogen bonds in the water. The worst burns you can get are from steam or water because the energy involved in water is a lot higher than in other stuff. Joules - the energy to heat one ml of water by 1 degree C. to heat 1 kilogram of water it requires 4168kj. If we want to heat a kg of air, we require a lot less energy. Steel has a relatively low heat capacity so will heat faster than the water in the pot - only requires a tenth of the energy to heat a kg of steel → 450kj, compared to heating water. More energy is contained in the water so if you stick your hand in very hot water you will get quite badly burned as opposed to touching hot metals which has less energy. Specific heat of water is 4186 J/kg/K Specific heat of air is 718 J/kg/K Specific heat of steel is 450 J/kg/K

Question 60

Temperature represents...

Answer 60

the average kinetic energy of molecules. The reason we can hold all this energy is because of hydrogen bonds. When the molecules come together it can bind to four different molecules but it also varies - can be bound to 1, 2 or 3. They are constantly moving around and breaking and reforming these bonds. Because of the changing no. of hydrogen bonds it can form it can start absorbing and breaking lots of hydrogen bonds. 1 calorie is the amount of energy required to heat 1 g of water by 1˚C.

Question 61

Water and heat capacity.

Answer 61

As we are absorbing a lot of heat, hydrogen bonds are breaking apart, as things are cooling down the hydrogen bonds start forming. When water is heated they hydrogen bonds start breaking apart, when things are cooling down the hydrogen bonds start forming. The breaking and forming of hydrogen bonds means that a lot of energy is stored. Since we are mostly made of water (70%) it's easier for us to hold our temperature. On a hot or cold day we have a lot of potential energy stored in our body, thermal mass. Because we have water in our body, as water can absorb or release a lot of energy it's a lot easier for us to keep our body temp relatively stable. Heat is absorbed when hydrogen bonds break Heat is released when hydrogen bonds form Water’s high heat capacity is due to hydrogen bonding Water can absorb or release a large amount of energy with only a small change in temperature

Question 62

Evaporative cooling

Answer 62

Where water molecules start transitioning from a liquid to a gas. There are different speeds of water molecules - more active and less active molecules. As water starts evaporating the really high energy water molecules start leaving from the system (the temperature starts to drop) and the ones below have a lower average energy. We can release water by sweating.

Question 63

The small size and polarity of water...

Answer 63

make it a good solvent: With water → if we want to break some bonds, if we took some salt and melted it, you would need to get it really hot to break the bonds and turn the solid into a liquid just by doing it with heat alone. If we put salt in some water it helps the molecules to break apart. Solvents - the capability for other things to enter the system → dissolving. Water has a good capacity for things to dissolve in it. Important in our biological system: for us as blood, oxygen, carbon dioxide and sugars, amino acids and other ions can all dissolve in water. Water can interact with lots of things because water doesn't have a net charge, if we have some positively charged sodium then all our negatively charged oxygen can start associating with the sodium. If we have a negatively charged chloride then our slightly positively charged hydrogens can start interacting with it. Has a slightly negative and positive charge.

Question 64

Large molecules - dissolving.

Answer 64

Even large molecules such as proteins can dissolve in water if they have ionic and polar regions on the surface. If we have atoms, a protein, enzyme to dissolve in water. Because of the different charges of the molecule and the different charges of water means that we can have different interactions and can interact in water.

Question 65

Diffusion

Answer 65

Dye in water will spread out in the water. The universe doesn't like gradients, doesn’t like water. Diagram - if we have a high concentration of a particular molecule the overtime it will diffuse around. Low concentration uniformly spread out. If we want to diffuse something out - stir it around. To go the other way will require a whole lot of energy. Challenge in biology is to create order - requires energy. If we want to make a gradient of protons inside the cells, we want to bring sugar molecules from a low concentration to a high concentration inside the cell so we have to keep a lot of stuff moving and fight the laws of thermodynamics. “Diffusion is the net movement of molecules or atoms from a region of high concentration (or high chemical potential) to a region of low concentration (or low chemical potential).” (Wiki)

Question 66

Osmosis

Answer 66

If we have a high concentration of something (our cells are packed with sugars, ions, amino acids and lots of compounds), then they are in a high concentration. If we can't get the things inside the cell to diffuse out then the water is trying to come into the cell to dilute everything (the universe wants everything to be nice and diluted) and we have a movement of water from one side to the other. The cell has this challenge of having everything packed in the cell but also fighting water that wants to come inside the cells. “Osmosis is the movement of solvent through a semipermeable membrane into a region of higher solute concentration” (Wiki)

Question 67

Osmosis in red blood cells

Answer 67

In our blood we have calcium, sodium, electrolytes, hydrolytes, magnesium and lots of ions to help maintain our blood. Reasonably salty to try balance and stop the cells from losing too much water. To make it into a hypertonic solution (very salty) then all the water diffuses out of the cells from the high concentration inside the cells to the very salty concentration outside the cell and the cells start shrivelling up. If we stick it into a water solution with no salts in it all of the water rushes into the cell to dilute everything and the pressure builds up and the cell bursts (hypotonic). Trying to fight water potential is a challenge.

Question 68

All living things are made up of four classes of biomolecules:

Answer 68

carbohydrates, lipids, nucleic acids, and proteins

Question 69

Macromolecules are...

Answer 69

large polymeric structures made up of many repeating units (monomers)

Question 70

Each cells has...

Answer 70

thousands of different molecules inside, but they are precisely organised into a living unit

Question 71

Synthesis and hydrolysis of polymers

Answer 71

Polymers - repeating units, lots of bits. Long chains of repeating units. Monomer added onto the end of a chain → called a dehydration reaction because losing water. If we do the opposite so start with a polymer and go to something smaller, hydrolysis reaction → water comes in and breaks the bond. Polymers → big long strands, so can have something called polarity. Hydroxyl group and a hydrogen group at the other end - two distinct ends as they are going through

Question 72

Creating polymers...

Answer 72

helps create order and complexity.

Question 73

Creating order:

Answer 73

requires energy. Over time things are going to start decaying and breaking down because of the tendency towards disorder. Over time things breakdown. We don't want things to break down → we want polymers with a particular arrangement and order. Anytime we do this it requires energy. The food that we eat provides the energy to create order.

Question 74

Second law of thermodynamics.

Answer 74

there is a tendency towards disorder (maintaining order requires energy)

Question 75

Creating polymers also helps...

Answer 75

manage water potential If you have something with lots of salts, sugars and things dissolved in the cell (proteins, DNA, compounds). Creates a challenge for water potential because water wants to go inside the cell to dilute things creating pressure inside the cell. Polymers help to manage the water potential. Joining the molecules together reduces the osmotic potential. Creating polymers and sticking things together helps with complexity and order. It does require energy.

Question 76

Molecular shape and function.

Answer 76

Our cells need to be able to recognise themselves. Enzyme - substrate. One of the features of life is that it senses the environment. As soon as we start forming molecules we can start forming a 3D shape. Often we will get a complementarity between two molecules so that one can fit neatly (has a corresponding shape) so that the molecules can start recognising each other. Chemical functionality. A negatively charged region on one molecule and there can be a positively charged region on another molecule. We might have a hydrogen bond acceptor on one side and a hydrogen bond donor on the other.

Question 77

What are the two ways molecules can recognise each other?

Answer 77

3D shape and chemical functionality.

Question 78

COVID particle

Answer 78

If we are exposed to covid particles it wants to find a way inside our cells. On the surface of our cells particularly in our respiratory system we have a protein called the ACE receptor. Involved in regulating blood pressure, binds to a hormone and if our blood pressure is too high then we can release the hormone and signals to the cells by binding to the receptor and says release the vessels, dilate them → reducing our blood pressure. We have another compound which squeezes the blood vessels tightly to increase our blood pressure. ACE receptor is a protein → the spike protein starts interacting and recognising the ACE inhibitors on our body. Not targeting or designed to do this but is just binding. In our ACE receptors normally if we have one protein recognising the other so there is going to be a particular 3D shape and some chemical functionality, a bunch of hydrogen bonds and weak interactions that mediate the molecules recognising each other. Some strategies have been to see if we can block the ACE receptor, if we block the sites then we could stop the virus from infecting. There's a bunch of enzymes called ACE inhibitors for high blood pressure. But there may be a bunch of side effects. The covid spike recognises the ACE receptor of ours (also those ferrets and pangolins). The UK and Brazilian variants of COVID have a particular mutation called N501Y which is located in the particular part of the spike protein that interacts with our ACE receptor and increases the strength of binding. More infective - listen again if you want to know why. Recognising in these interaction is that weak hydrogen bonds and some form of weak molecular interactions between to molecules which can end up with a big biological effect.