Topic 1 – The building blocks of cells

PLANT AND ANIMAL CELLS The structure of cells can be studied using a light microscope:

o Light microscopes shine light on the specimen (i.e the cell to be studied)o The image is then passed through lensesis magnified (i.e made bigger)o the different parts of a cell can be seen

Plant and animal cells have some features in common: Cell membrane:

o It separates the contents of the cell and its surroundingscontrols the movement of substances (e.g oxygen, glucose, carbon dioxide) into and out of the cell

Cytoplasm:o This is where many of the cell’s chemical reactions take placeo It contains many organelles (tiny structures that carry out specific jobs)

Nucleus:o It’s an organelle that contains DNA (the genetic material)o It controls all the activities of the cell

Mitochondria: o These are organelles in which aerobic respiration (i.e respiration in the

presence of oxygen) takes place Plant cells also have some other structures: Cell wall:

o It’s made of tough cellulose, which supports the cell and gives it shape Large permanent vacuole:

o it’s filled with cell sap - helps support plants by keeping cells turgid (i.e filled with water)

Chloroplasts: o These are organelles that contain chlorophyll – a green substance that

absorbs light energy used for photosynthesis

INSIDE BACTERIA Light microscopes can magnify specimens more than 1500 times:

o this allows us to also see inside bacteria – single-celled organisms that are much smaller than animals or plant cells

o E.g light microscopes can show that bacteria don’t have nuclei In the 1930s the electron microscope was invented - this uses a beam of electrons

to magnify specimens up to about 2,000,000 times!

electron microscopes can allow us to study the structure of cells in even more detail

E.g electron microscopes have shown us that bacterial cells…:o have two types of DNA:

Chromosomal DNA – giant loop of DNA containing most of the genetic material

Plasmid DNA – comes in small loops and carries extra informationo have a cell wall:

It’s different to the cell wall in plants – it is not made of cellulose, and it is more flexible

However, it does a similar job (i.e provides support and shape)o (some) have flagella on the outside:

These are long, whip-like structures that bacteria can use to move themselves along

DNA Chromosomes inside nuclei (plural of ‘nucleus’) contain the genetic material –

they are made of DNA Sections of DNA are called genes:

o Each gene codes (i.e carries instructions) for a specific proteino Often, genes work together to produce what is needed for a particular

feature: E.g eye colour is determined by lots of different proteins that are

coded by several different genes The structure of DNA: A DNA molecule consists of two strands that are coiled together to form a spiral -

known as a ‘double helix’ The two strands of DNA are linked together at regular intervals by chemicals

called ‘bases’ Bases always pair up in the same way because they have complementary (i.e

matching) shapes:o Adenine (A) always pairs with thymine (T)o Guanine (G) always pairs with cytosine (C)o The matching bases are known as ‘complementary base pairs’

Base pairs are joined together by weak hydrogen bonds The order of the bases in DNA (i.e the ‘DNA sequence’) determines the proteins

that are made in the body We each have a slightly different order of bases in our DNA/genesall of us

make slightly different proteins – this is what makes us all different DNA DISCOVERY In the 1950s, Wilkins and Franklin were investigating the structure of DNA:

o They directed beams of x-rays at purified DNA and used photos to record how the DNA molecules scattered the x-rays

At the same time, Watson and Crick were trying to build a 3D molecular model of DNA, using data obtained by other scientists:

o The detailed x-ray images of Wilkins and Franklin gave Watson and Crick the clues they needed to come up with their double helix model

At the time, when Watson and Crick published their findings, Wilkins and Franklin were barely mentioned

Eventually, though, it became clear that all 4 scientists (i.e not just Watson and Crick) were key to the discovery of the structure of DNAthey were all (except for Franklin, who died beforehand) awarded Nobel Prizes

The human genome: The human genome project (HGP) involved finding out the sequence (order) of

the 3 billion base pairs that make up the human genome…o The HGP was a huge international effort, involving scientists in 18

different countries – it took 13 years Although each human being has a unique DNA sequence, everyone has at least

99.9% of their DNA in common (it’s that 0.01% that makes us different) Knowing the sequence of the human genome has many implications for science

and medicine - it is being used to develop…:o improved testing for genetic disorderso new ways of finding genes that may increase the risk of certain diseaseso new treatments and cures for disorders

e.g gene therapy, where scientists try to replace faulty genes that cause a disorder with normal genes

o new ways of looking at changes in the genome over time – i.e how humans have evolved

o personalised medicines – these are medicines that work best (i.e are more effective and have fewer side-effects) on certain people

GENETIC ENGINEERING Scientists can remove a gene from one organism and insert it into the DNA of

another organism – this process is called ‘genetic engineering’ E.g production of human insulin by genetically modified bacteria: Scientists can insert the gene for human insulin into bacterial plasmid DNA… Stages of process:

o 1. Bacterial plasmid DNA is removed from bacteriao 2. Bacterial plasmid DNA is cut by ‘cutting enzymes’o 3. Bit of the chromosome that contains the human insulin gene is cut by

‘cutting enzymes’o 4. The human insulin gene is stuck onto the bacterial plasmid DNA by

‘sticking enzymes’o 5. The bacterial plasmid DNA, with the additional human insulin gene, is

reinserted into bacteria The genetically modified (GM) bacteria now have the human insulin gene in their

plasmid DNAcan make human insulin, which is used by people with diabetes Organisms like these GM bacteria are known as genetically modified organisms

(GMOs) Advantages of producing human insulin using GM bacteria:

o In the past, insulin used to be extracted from dead cattle and pigs: Although similar, the insulin from dead cattle and pigs is not the

same as human insulin The supply of the animal insulin could be affected by animal

diseases or by the numbers of animals slaughteredo Human insulin produced by GM bacteria doesn’t have these drawbacks:

It is the same as the insulin produced by body cells in the pancreas It can be used by vegans (vegans don’t eat any animal products

would not take animal insulin)

It can be made in vast quantities and more cheaply The slight disadvantage of producing human insulin using GM bacteria is that

different bacteria produce insulin slightly differentlythis may not suit everyone E.g2 beta-carotene in golden rice to reduce vitamin A deficiency in humans: Lack of vitamin A:

o can cause the immune system to stop working properlycan lead to deatho can cause blindness

Beta-carotene is needed by humans to make vitamin A Two extra genes can be inserted into normal rice plants to make them produce

beta-carotene in their grains…o Rice plants that make beta-carotene in their grains are called ‘golden rice

plants’ and they make yellow rice Disadvantages of this process:

o 1. Some people are concerned that the GM rice will crossbreed with wild rice plants and contaminate the wild rice DNA

o 2. Others worry that eating GM organisms might be harmful (though there is no evidence for this)

o 3. Some people say the levels of beta-carotene in golden rice are not high enough to make much of a difference

o 4. GMOs can be expensive E.g3 production of herbicide-resistant crop plants: Herbicides are used to kill weeds Scientists have added genes to some plants to make them herbicide resistant

o This means farmers can use one large spray of herbicide rather than several smaller doses (reduces the amount of crop spraying needed)

Possible disadvantages of this process:o 1. Cross-pollination can take place between plants and weeds (i.e they

fertilise each other) some weeds may inherit the herbicide resistance genes weeds can become herbicide resistant (i.e they’re no longer

killed by herbicides)o 2. Fewer weeds surviveloss of food and shelter for animals

MITOSIS AND MEIOSIS Mitosis: All human body cells (i.e all cells except sperm and egg cells) contain two sets of

23 chromosomes (46 in total) in their nucleus…o One set of 23 chromosomes comes from the father and the other set of 23

chromosomes comes from the mother o So human body cells contain two copies of each chromosomethey’re

said to be ‘diploid’ To make more cells during growth and/or to repair damaged cells, body cells

divide by a process called mitosis:o 1. Chromosomes first make copies of themselves - this process is called

DNA replicationo 2. The copies of the chromosomes separate and then the cell divideso 3. This division produces two daughter cells, which are…:

diploid (each daughter cell has 46 chromosomes in their nucleus…so they have two copies of each chromosome)

genetically identical to each other and to the parent cell

Note: n = 23 chromosomes in nucleus…2n = 46 , 4n = 92

o Diploid cell has 46 chromosomes2no 1st stage: diploid cell replicates46x2 = 92 chromosomes4no 2nd stage: chromosomes separate but no further division occursstill 4no 3rd stage: cell divides to form two diploid daughter cells, each containing

46 chromosomes (2n) Asexual reproduction: As well as in growth and repair, cell division by mitosis also occurs in asexual

reproductiono Asexual reproduction is when organisms reproduce by themselves (i.e

without a partner) Bacterial cells often reproduce asexually by splitting in half Some plants can also reproduce asexually Sexual reproduction: Sex cells (i.e sperm cells and egg cells) are called ‘gametes’…

o Gametes are different to body cells as they only contain one set of chromosomes in their nucleus (so have a total of 23 chromosomes)

o gametes are haploid cells When a sperm cell fertilises an egg cell, the gametes fuse to produce a diploid

body cell (with 46 chromosomes – two sets of 23) called the zygote…o The zygote develops into a ball of cells called the embryo, which then

develops to form a new individual Note: it is important that gametes only have 23 chromosomes, because if they had

46, then after fusion, the body cells formed would end up with 92 chromosomes in their nuclei!

Meiosis: In order for haploid gametes to be produced, a different type of cell division called

‘meiosis’ is required…o 1. First step is DNA replication (this first step is the same as in mitosis) o 2. This is followed by two cell divisions - i.e the cell is first divided into

two and then divided again into fouro 3. This produces 4 haploid daughter cells, each containing one set of (23)

chromosomes (i.e the haploid daughter cells have half the number of chromosomes in the nucleus than diploid cells)

Chromosome pairs in a diploid cell contain the same genes but may have different versions of the genes (i.e different ‘alleles’) because they come from different parentschromosomes in a pair are slightly different

In meiosis, these slightly different chromosomes are split between the daughter cells in a random waythe haploid gametes produced in meiosis are genetically different from each other

Note: n = 23 chromosomes in nucleus…2n = 46 , 4n = 92

o Diploid cell has 46 chromosomes2no 1st stage: diploid cell replicates46x2 = 92 chromosomes4n o 2nd stage: two cell divisions split the cell into two and then into fouro four haploid cells are produced each containing 23 chromosomes (n)

CLONES Clones are individuals that are genetically identical (i.e that have the same DNA

sequence) The process of cloning – producing an identical individual – is an example of

asexual reproduction Benefits and risks of cloning mammals: Cloning animals isn’t easy because it’s not possible to make a whole new animal

from an arm or a leg It wasn’t until 1996 that the first large animal (a sheep called Dolly) was cloned Unfortunately…

o very few embryos produced during cloning develop successfully (Dolly was the only lamb produced after 237 attempts!)

o Dolly grew older much more quickly than normal and died young… Scientists aren’t sure whether this was due to health problems

caused by the cloning or whether it just happened by chance However, cloning can also be useful… It can be used to make a genetically identical copy of an adult organism that has a

desirable trait:o This can be a desirable natural trait - e.g bulls whose sperm produces high

quality calves are valuableare worth cloningo This can be a desirable genetically engineered trait - e.g cows engineered

to produce human insulin in their milk can be cloned…two clones can then be bred together so that their offspring will also have this engineered trait

How to clone a mammal: 1. A diploid nucleus is removed from a body cell of the animal that is going to be

cloned

2. The diploid nucleus is inserted into an enucleated egg cell (i.e a cell that has had its nucleus removed)

3. The egg cell is stimulated to start dividing by mitosis 4. It is then implanted into the uterus (womb) of a surrogate mother where it will

develop into a new individual o Note: the ‘surrogate mother’ hosts the embryo but isn’t actually the mother

because the organism being produced doesn’t have any of the surrogate mother’s DNA/genes

STEM CELLS When stem cells divide, they not only produce more stem cells but they can also

develop into specialised (‘differentiated’) cells - e.g muscle cells, skin cellso Once a cell becomes specialised, it cannot turn into another type of cell

There are two types of stem cells:o Embryonic stem cells – these can develop into nearly all types of cellso Adult stem cells - these can develop into only a few types of cells

The ability of embryonic stem cells (in particular) to develop into lots of different types of cells means they could be used to treat many medical problems...

Two steps:o 1. Embryonic stem cells first need to be extracted (see below for problems

associated with this)o 2. They are then put wherever in the body they are needed so that they can

develop into the appropriate specialised cell e.g if the patient has a heart problem, embryonic stem cells are put

in the heart so they can develop into a specialised heart cell General risks of using stem cells:

o If stem cells are put into the body, they could produce the wrong kind of cells or even create cancer cells…more research is needed to make sure stem cells are safe

o People may try to use embryonic stem cells to produce human clones – this is illegal

Problems associated with extracting embryonic stem cells: One way of extracting embryonic stem cells is to use leftover embryos created for

couples having fertility treatment…o However, extracting the embryonic stem cells kills the embryoo This is controversial because some people think that because embryos go

on to develop into people, destroying embryos is the same as murder Two ways scientists are trying to solve this issue:

o 1. Use adult stem cells to make cloned embryos - the embryonic stem cells could then be extracted from the clones without any natural embryos having to be killed

o 2. Turn specialised body cells into stem cells by reprogramming them – if this works, it will help to completely avoid the ethical problem of using embryos

Treating leukaemia: Due to the ethical issues associated with extracting embryonic stem cells, most

established methods use adult stem cells, which are easier to extract e.g adult stem cells are used in bone marrow transplants to treat leukaemia (a

cancer of white blood vessels)

Note: remember, though, that adult stem cells can’t develop into as many different types of cellsthe number of diseases they can treat is limited

PROTEIN MANUFACTURE (SYNTHESIS) Protein synthesis takes place in two stages – transcription and translation… Transcription: Transcription takes place inside the nucleus The DNA is first unzipped by breaking the weak hydrogen bonds between the

bases in the double helix – this separates the two strands of DNA One of the DNA strands then acts as a template…:

o RNA bases that are complementary (i.e that match) to the bases on the DNA strand link together

o This forms a strand of messenger RNA (mRNA) that is complementary to the DNA template strand - see diagram below

RNA vs DNA:o RNA only has one strand (not two like DNA has)o RNA has a base called uracil (U) instead of thymine (T)…

in RNA: adenine (A) bases pair with uracil (U) bases in DNA: adenine (A) bases pair with thymine (T) bases in the diagram above…

an adenine (A) base on the strand of DNA is matched by a complementary uracil (U) base on the mRNA strand

a thymine (T) base on the strand of DNA is matched by a complementary adenine (A) base on the mRNA strand

Translation: Translation takes place on ribosomes (an organelle found inside the cytoplasm) mRNA is small enough to leave the nucleus, enter the cytoplasm and then attach

itself to a small structure called a ribosome In the ribosome are also transfer RNA (tRNA) molecules:

o These each have attached a triplet of bases (i.e 3 bases) and an amino acido The triplet of bases on the tRNA controls which amino acid is attachedo tRNA (like mRNA) contains uracil (U) bases instead of thymine (T) bases

Process:o The ribosome moves along the mRNA, decoding it in groups of 3 – these

base triplets on the mRNA strand are known as ‘codons’o As the ribosome moves along the mRNA, the tRNA with complementary

triplet of bases lines up with the codono The tRNA then releases the amino acid it was carrying…

The amino acid joins on to the growing amino acid chain The tRNA is now free to collect another amino acid

o The ribosome then moves onto the next codon and the process continues until the chain of amino acids is long enough

The chain of amino acids is called a polypeptide (chain) Most proteins are made of many polypeptide chains, linked up Note:

o It’s important to realise that the order of bases in DNA decides the order of amino acids in a protein…

o This is because order of bases in DNA decides the mRNA sequence, which then decides how tRNA molecules carrying amino acids line up along the mRNA strand

MUTATIONS Each protein is made up of a different sequence (i.e different number and order) of

amino acids The sequence of amino acids affects the way the polypeptide chain folds up

gives the protein its specific 3D shape…o Some proteins form long fibrous molecules (e.g keratin - found in human

hair and nails)o Other proteins have a round ‘globular’ shape (e.g insulin, haemoglobin,

enzymes) The shape of proteins is important for their function:

o E.g the round shape of haemoglobin helps it move around inside cells and around the rest of the body easily

o E.g2 enzymes are specific to one reaction - their shape determines which reaction this is (see enzyme sections below for more details)

The effect of mutations: A mutation is a change in the sequence of bases in the DNA (‘genetic code’) Some mutations (i.e some changes in the genetic code) have no effect on the

amino acid sequenceshape of the protein produced is not affected Other mutations result in one amino acid being replaced by anotherprotein folds

up differently (different 3D shape)this affects the way the protein works...o E.g sickle cell anaemia:

mutation in the gene that produces haemoglobin causes red blood cells to become ‘sickle-shaped’ and pointy

they stick together in long fibres and get stuck in small blood vessels

Mutations can sometimes be beneficial to the organism:o E.g some mutations make bacteria resistant to the effects of antibiotics (i.e

they’re not killed by antibiotics) ENZYMES What are enzymes? Each reaction that is going on in the body is controlled by a particular group of

proteins called enzymes A substance that helps a chemical reaction go faster without itself being changed

by the reaction is called a ‘catalyst’ – enzymes are ‘biological catalysts’o Without enzymes, the reactions may still happen, but at too slow a rate for

cells to do all they need to do to stay alive Some enzymes help break a large substance into smaller molecules (e.g in

digestion) Other enzymes help smaller molecules join together to make larger ones

(synthesis) Enzymes catalyse (i.e speed up) reactions inside cells: During DNA replication in mitosis and meiosis:

o The weak hydrogen bonds holding the two strands of DNA together are broken downthe DNA double helix unwinds – this reaction is catalysed (i.e sped up) by a specific enzyme

o As new bases line up along each separate DNA strand, a different enzyme catalyses the reaction joining the complementary base pairs together

o This makes two DNA molecules that are identical to each other and to the original DNA molecule

o The enzymes are unchangedthe process can be repeated when needed

Enzymes are also used to speed up reactions during protein synthesis – e.g the reaction that joins one amino acid to another (in the formation of a polypeptide chain) is catalysed by a specific enzyme

Enzymes catalyse reactions outside cells: Food molecules (e.g carbohydrates, proteins and fats) are too large to pass across

the cell membranes of the gut wall and into the bloodthey first need to be broken down in a process called digestion…

o The reactions that take place during digestion are catalysed by different enzymes that are released into the mouth, stomach, and small intestine

Microorganisms and fungi also release digestive enzymes: o However, microorganisms and fungi don’t have a gutthey grow on the

food they’re digesting – this can be seen as mould on e.g fruits After the enzymes have digested the food, microorganisms absorb the small food

molecules through their cell walls Some of the enzymes that are involved in digestion are now used in laundry

detergents to help digest (remove) food and other large molecules on dirty/stained clothes

ENZYME ACTION Enzymes work by binding to molecules called ‘substrates’ – once bound, enzymes

catalyse the change of substrate molecules into product molecules Each enzyme only works with a particular substrate or a small group of similar

substratesenzymes are highly specific for their substrate Explanation using the ‘lock and key’ hypothesis:

o Substrates bind to an enzyme’s active site – this is where the reaction turning the substrates into products takes place

o The active site has a different shape in different enzymeso In order for substrates to bind to the enzyme’s active site, they must have a

complementary (i.e matching) shape…all substrates that fit into a particular enzyme’s active site have the same 3D shape

o The analogy is the that the enzyme’s active site is the ‘lock’ and the substrate is the ‘key’ – only the substrate (key) with the right shape can fit into the active site (lock)

Factors affecting enzyme action: There are 3 main factors that affect how well an enzyme works (i.e how well it

can catalyse/speed up a chemical reaction) 1. Temperature:

o Most enzymes work best at normal body temperature - i.e they have an ‘optimum’ temperature of around 40°C (37.5°C to be exact)

2. pH: o Most enzymes work best at about pH7 (neutral)

o However, some enzymes work best at other pH values e.g enzymes in the stomach have a much lower optimum pH

Small changes in pH or temperature (away from optimum conditions)…: o change the shape of the enzyme’s active sitesubstrates don’t fit as well

enzyme activity is reducedrate of reaction is reduced This is partly what happens when you get a fever (body

temperature risesenzymes don’t work as wellreactions take place more slowlyyou feel ill)

Large changes in pH or temperature (away from optimum conditions)…:o can cause bonds within the enzyme to breakactive site is destroyed (it

completely loses its shape)substrates can no longer fit into the active site An enzyme that has lost its specific 3D shape/structure (under conditions of

extreme temperatures and pH) is said to be ‘denatured’ 3. Substrate concentration:

o As the substrate concentration increases, there are more molecules that can bind to the active sites of enzymesrate of reaction increases

o However, at very high substrate concentrations, all the active sites of the enzymes are occupied all the time…

the enzymes can’t work any faster adding more substrate will make no difference to the rate of

reaction