Download (you should!). What exactly is the role of DNA and h

You have probably heard a lot about DNA and know something about it already
(you should!). What exactly is the role of DNA and how does it work within a
cell? How does DNA control life?
Learning Outcomes
You will be able to:

describe the structure of DNA by means of an annotated diagram

explain the function of DNA

safely carry out an experiment to extract DNA from some fruit

explain the role of mRNA

state how RNA is different than DNA

describe in detail the process of protein synthesis

State the basic structure of a protein
DNA Code
The letters we use is a form of a code. We can arrange the letters into a
particular arrangement to form words.
We can then arrange words into sentences and paragraphs so that we can
communicate with other people and pass on information.
This is the same with other codes.
Learning Task 1
Use the Morse code shown above to write a message to a friend. It must be
about something you have learnt in Biology. Get your friend to translate your
message.
DNA is a code and holds information. The order of the bases on the DNA
dictates the information that is passed on.
We've already learnt that DNA is located in the nucleus in the form of
chromosomes and these replicate during mitosis to ensure daughter cells have
the same quantity of DNA as the mother cell. But what is DNA, and what does it
do? In this topic we'll discuss the structure of DNA and how it codes for the
manufacture of proteins by cells. In the next topic we'll learn how these
proteins go on to perform many crucial functions in cells.
DNA Structure
DNA stands for Deoxyribonucleic Acid. It is a chemical molecule found in all
cells which consists of very long chains of repeating components (nucleotides).
The repeating unit which makes up a molecule of DNA consists of three
structures. Two of these are always the same, but one of these - the base - can
come in four different forms. So, a short section of a molecule of DNA could be
represented in the diagram below.
As you can see from the diagram, the DNA molecule consists of a long chain of
repeating units attached to a sequence of bases. There are four possible bases
in a DNA molecule: A, T, C & G. The diagram only shows a short length of DNA,
but one chromosome would be many millions of bases long. As we'll see later, the
sequence of these bases is crucial for the functions of the cell, and therefore
life itself.
If you're particularly observant, you will have noticed something about the
shapes of the bases in the diagram above. They have been drawn in such a way
as to represent the fact that the bases are complementary pairs. DNA in cells
is actually found as double stranded molecules with the two strands joining at
the bases. When the bases bond they can only do so in certain pairings. From
the diagram above, can you predict which base pairs with which?
As you can see the base A always pairs with T, and C pairs with G. This
results in two strands of DNA which are mirror images of each other. However,
this double stranded DNA molecule doesn't naturally exist as a straight ladder
as shown in the diagram above, it naturally coils to form a double stranded helix
instead.
Learning Task 2
Using the information you have just read, draw an annotated diagram to show
you understand the structure of DNA. Explain why DNA can be described as a
code.
Listen carefully as your teacher explains the process of Protein Synthesis.
This is quite a tricky subject so you should have some questions about it!
You are a weirdo if you don’t.
Now that you have listened to your teacher’s explanation, read through the
following section to help improve your understanding.
Making Proteins
So that's what DNA looks like, but what does it actually do? We've already
mentioned that DNA codes for the production of proteins but how does this
actually work? Before starting to explain this you need to know a little bit about
the structure of proteins. You'll know that there are different types of
proteins for example, such as the protein haemoglobin in your red blood cells
which not only makes your blood red, but more importantly binds to oxygen in
your lungs and carries it to all the tissues in your body. Another protein you
might have heard of is keratin. Keratin is an important structural protein in your
skin and is also the key protein in your hair and nails. Clearly these are two very
different proteins with very different functions which arise from their very
different structures. Amazingly, like all proteins, these two proteins are made
in exactly the same way using the same twenty ingredients.
Proteins consist of long chains of a repeating chemical unit called amino acids.
These chains can be hundreds or thousands of amino acids long. There are only
twenty naturally occurring amino acids and the order the amino acids are joined
together will determine which protein is produced. So the following two
sequences of amino acids would ultimately result in proteins which have very
different structures, and therefore very different functions also [amino acids
have quite complicated names so I've just used numbers instead to represent
the different amino acids].
An accidental change in one of the bases in the DNA code can have a dramatic
effect on the protein produced if it changes the sequence of the amino acids.
What decides the order of the amino acids in the protein molecule? Well, this is
when we come back to DNA. The sequence of bases on the DNA molecule is
what directs the sequence of amino acids in the protein molecule - that's how it
all links together!
mRNA
So, the sequence of bases in DNA codes for the sequence of amino acids of a
protein. But, there's a problem. In order to produce a protein you need
ribosomes. Ribosomes catalyse the reactions of protein synthesis and if you can
remember back to the first topic you'll know that ribosomes are found in the
cytoplasm. And what's wrong with that? Well, the DNA remember is in the form
of large chromosomes inside the nucleus. Because the DNA code is in a
different part of the cell from the ribosomes, a messenger molecule is required
to carry the code from the nucleus to the cytoplasm. This molecule is called
messenger RNA, or mRNA for short. RNA is a bit like a smaller version of DNA.
RNA stands for Ribonucleic Acid so you'll see that it's quite a similar molecule.
RNA molecules are single stranded instead of double stranded and are much
much shorter than the DNA in the chromosome.
In order to produce a protein then your cells first make a copy of the code
from the DNA into an mRNA molecule in the nucleus. This mRNA molecules then
leaves the nucleus and enters the cytoplasm where it comes together with
ribosomes and uses the code to join amino acids together in a specific order to
produce a particular protein.
Protein Synthesis (in more detail)
Previously you learnt that the complimentary bases for DNA are that A always
pairs with T and C always pairs up with G. This is slightly different when DNA
and RNA come together.
RNA has a U base instead of a T base. Therefore, if the base on the DNA is A,
the complimentary base on the RNA would be U instead of T. C pairs with G as
usual.
mRNA is formed (transcribed) from one of the DNA strands found in the
nucleus. The detailed process of transcription is as follows:
Transcription (takes place in the nucleus of the cell)
1. The DNA strands become unwound.
2. The weak hydrogen bonds between the bases break causing the DNA
strands to separate.
3. Pairing of bases enables free RNA nucleotides to find complimentary
nucleotides on the DNA strand.
4. Weak hydrogen bonds form between the complimentary bases.
5. A strong chemical bond forms between the nucleotides.
6. The weak hydrogen bonds between the DNA and RNA bases break
allowing the transcribed mRNA to become separate from the DNA.
7. The transcribed mRNA can now leave the nucleus.
8. Weak hydrogen bonds between the 2 DNA strands reunite and the
molecule becomes wound into a double helix once more.
Translation (takes place at the ribosome)
Translation is the second stage of protein synthesis and is how the protein is
made from the mRNA. The process is as follows:
1. The ribosome holds the strand of mRNA in place.
2. Each triplet (3) of bases on the mRNA is called the a codon e.g. AUC
3. Each triplet of bases of the tRNA is called an anticodon e.g. UAG
4. The anticodon of the first tRNA molecule form weak hydrogen bonds
with the complimentary codon of the mRNA e.g AUC would pair with UAG.
5. The first tRNA brings with it a relevant amino acid.
6. The second tRNA molecule repeats the process and brings the first 2
amino acid molecules into line.
7. The amino acids become joined by a strong peptide bond.
8. The first tRNA molecule become disconnected and leaves the ribosome.
9. A third tRNA molecule joins the second tRNA molecule and it brings with
it an amino acid.
10. This continues along the chain of mRNA until a polypeptide chain is
formed.
11. This is the basic structure of a protein (phew!).
Don’t be confused by the diagram above. TYR, ASP, ARG and SER are examples
of amino acid that join together to form the protein.
Learning Task 3
Use the information above to answer the following questions:
1. Where is DNA located in the cell?
2. Name the bonds that hold the 2 strands of DNA together.
3. What sort of shape is DNA described as?
4. What is the function of DNA?
5. Where is mRNA made?
6. What is the function of mRNA?
7. What are 2 differences between DNA and RNA?
8. Where does the mRNA travel from and to?
9. If the DNA has a code ATTGCATGCTAT, what will be the code of
mRNA?
10. What is the role of tRNA?
11. Name the building blocks of proteins.
12. What is the name of the bond that forms between amino acids?
Learning Activity 4
Collect the experiment sheet ‘Extracting DNA’.
Focus on the following skills whilst carrying out this experiment:
Careful – work carefully without making any mistakes and ensuring that all
safety precautions are followed.
Group work – be a good team player. Help out others in your group if they need
help, do not dominate but get involved in carrying out the task.
Methodical – follow the instructions carefully.
Organisation – make sure everyone in the group gets involved and knows what
they are doing.
Learning Task 5
Collect the worksheet ‘Protein Synthesis’. Put the stages into the correct order
and then describe what is happening at each stage.
Let a friend assess your work and then show your work to your teacher for
some feedback.
We have actually taught you more detail than you actually need for your exam
because sometimes it helps to go into more detail in order to understand
something properly. Let’s run through the level of detail you will need for your
exam. Hopefully, you will feel a bit more confident after we have completed this
task.
Learning Task 6
Answer the following questions in full sentences:
1. What are chromosomes and where are they located in the cell?
2. How many strands are present in a DNA molecule?
3. What is the base pair rule?
4. How is the genetic code present in DNA transported from the nucleus to
the cytoplasm of the cell?
5. Where in a cell are proteins made?
6. What subunits make up a protein?
7. What determines the order in which the subunits are joined together?
8. Why is the sequence of the subunits in a protein molecule important?
Produce a poster explaining the 2 stages of protein synthesis, transcription and
translation.
Success Criteria:

Uses scientific terms

Use labelled diagrams

Show all the bonds (making and breaking)

Show where in the cell it takes place

Explain why the process is important

Explain what you think would happen if there was a mutation

Explain the role of mRNA and tRNA
Past Paper Questions
Complete the past paper questions on ‘Protein Synthesis’. Once you have
finished, get some feedback from your teacher and make any corrections.
Check your UNDERSTANDING
1. Think of an analogy to help describe the process of Protein Synthesis.
2. If you were teaching protein synthesis to someone else, what would you
say were the 5 most important points to remember?
3. Predict what would happen the DNA code for a particular protein
mutated (changed). Explain your answer.
Look at the following success criteria to assess how well you have learnt the
section on protein synthesis:
Success Criteria
Knowledge and Understanding
1. I can describe the structure of DNA
2. I can explain the function of DNA
3. I can explain the role of mRNA
4. I can state how RNA is different from DNA
5. I can explain the process of protein synthesis
6. I can state the basic structure of a protein
Skills
1. I can display the following skills when carrying out an experiment:
careful, organisation, methodical and group work.
2. I can read for information
3. I can extract relevant information from a passage
Use Didbook to note what you have learnt over this topic on protein synthesis
and also areas that you would like to improve your understanding. Copy and
complete the following sentences:
1. I think it is important to understand……….because…..
2. I will be able to use……..when I……
3. I would improve………..by…..
4. The skills I have developed over this topic are….and I know this because….
5. These skills will be useful…..
6. The skill I really need to work on is….because….
Choice Extension
Task
1
2
3
4
5
6
7
8
Choose at least 2 of the following activities to
complete.
Make a model of DNA that can be displayed in
your classroom (so not out of food this time!!)
Write a newspaper article about the discovery of
DNA
Find out about which genes have already been
identified in humans
Would it be a good thing if they found a 'fat'
gene? Discuss.
Was the human genome project worth spending
so much money on?
Write a short script for CSI where DNA
evidence helps out a case.
Everyone should have their DNA recorded at
birth so they can find out what might go wrong
with them later in life. Discuss.
Genetically Modified Olympics. Make a poster.
Completed
You have to accept that enzymes are VERY important. No, you do! Without
them you would not be the wonderful person you are! You would be very similar
to this person, but dead. Enzymes allow you to function at the high level you
currently operate at.
Learning Outcomes
You will be able to:

State what a catalyst is and give an example.

State what an enzyme is and give examples.

Describe the differences between catalysts and enzymes.

Describe how an enzyme works with the use of a diagram.

Explain why an enzyme is said to be specific in relation to its substrate.

Describe how a breakdown reaction and a synthesis reaction differ, and
give examples of each.

Explain how temperature affects enzymes and what denatured means.

Describe how pH affects enzymes.

Give examples of digestive enzymes and their optimum pH.
Quick review: What you should already know;
1. What is DNA important for?
2. What is DNA made of?
3. How does the information get out the nucleus?
4. Why does it need to do this?
5. Draw a diagram to show how a protein is made.
Enzymes
We have learnt how the code contained in DNA bases results in the production
of proteins. Proteins are crucial for the functions of cells and in this topic we’ll
discuss the variety of proteins in cells and focus in on one particularly important
group, enzymes.
TOP TIP – DNA base sequences determines the structure and function of a protein.
Variety of Proteins
There are many different proteins in cells, each carry out a particular function.
The shape of a protein is crucial to its function. If you change a proteins shape,
you change its function. The protein shape is dictated by the sequence of the
chain of amino acids which makes up the protein. There are 20 different amino
acids and the order they are arranged in determines the shape, and therefore
the function, of the protein. So, the following 2 chains of amino acids would
result in 2 very different proteins.
For life to exist, complex chemical reactions need to occur. You will learn more
about 2 such complex chemical reactions: respiration and photosynthesis.
In order for most of the chemical reactions which take place in living things to
occur, they need a catalyst. Catalysts are molecules which speed up the rate of
a chemical reaction, without being changed in the process. Enzymes are
catalysts and are made of proteins. DNA controls all of the chemical reactions
which take place in a cell through which enzymes are produced and when.
Learning Task 1
Find out what the following words mean (get a definition) and then use them in a
full sentence that makes sense! A biological context with regard to structure of
proteins would be great as well (use textbooks / laptops for this).
1. Enzyme
2. Hormone
3. Antibody
4. Haemoglobin
5. Collagen
Structure of Enzymes
A key component of the shape of an enzyme is its active site. This is the section
of the enzyme where the substrate (chemical the enzyme works on) combines
with the enzyme for the reaction to take place. The shape of the active site is
complimentary to the specific substrate it binds to in the reaction.
Therefore, amylase can only catalyse this reaction. This is why cells must
produce many different enzyme molecules, from the DNA code, for all the
different chemical reactions which are catalysed in cells.
Your teacher may well now talk to you about the Lock and Key model or even the
induced fit enzyme action (if you are lucky!). Pay attention.
Key words – active site, substrate, products, enzyme-substrate complex
Learning Task 2

Why is one enzyme not able to work on all substrates? For example
Amylase (previous diagram) cannot be used to break down fat. Why is
this called being specific?

Is this a good thing?

Why?

Draw yourself a diagram to show an enzyme working (Lock and Key model)
and label with key words from previous page.
Conditions affect Enzymes
As enzymes are chemical molecules, they can be affected by the conditions that
they are in. If the conditions change, it can change the shape of the enzyme. If
the active site of the enzyme changes shape, then the enzyme will not be able
to bind to its substrate which will prevent the enzyme from catalysing the
reaction. It is for this reason that each enzyme has its own optimum conditions.
These are the conditions which provide the right enzyme shape to allow it to
effectively catalyse its reaction.
Two particular conditions which can affect the rate of an enzyme catalysed
reaction are;


temperature and
pH.
If you were to carry out a series of experiments with the enzyme amylase
where you measured the rate of the breakdown of starch at different
temperatures and pH, you would get a set of graphs which would look something
like this:
Although these graphs look quite similar, the explanations for the graphs are a
little different. The first thing to notice is that from these graphs you can
deduce the optimum conditions for the amylase in your saliva. The optimum
temperature (B) is just below 40°C (your body temperature is 37°C) and the
optimum pH (E) is approximately 7 (the same as your saliva).
But how do we explain the other sections of the graph? Well...
A. At region A on the temperature graph, the rate of the reaction is increasing
as the temperature increases. This is to do with the effect of temperature on
chemical reactions...the rate is increasing because the molecules have more and
more energy causing them to collide more often.
C. Because enzymes are made of protein, there is a limit to how high you can
heat and enzyme-catalysed reaction. Once you've passed the optimum, some of
the enzyme molecules begin to change shape as the high energies break the
bonds which hold the molecules together. At very high temperatures all of the
enzyme active sites have lost their shape and it's as if there are no enzyme
molecules present, so the rate of the reaction is very low. Once an enzyme
molecule has lost its shape due to high temperature, it cannot return to its
functional shape. This is when we would describe an enzyme as being denatured.
Why do think then that biological washing powders only work at low
temperatures?
D. & F. The bonds which hold a protein's shape are quite sensitive to changes in
pH. At the optimum pH (E) the bonds are creating the right active site shape to
allow the enzymes to catalyse the reaction. However, as the pH is further from
this optimum, fewer and fewer enzyme molecules have the right active site
shape which reduces the rate of reaction. For many enzymes changes in shape
due to changes in pH are reversible.
REMEMBER
Describe and explain have different meanings. If asked to describe a graph,
give as much detail about the graph as you can, starting from the left and
working to the right. Also, use figures from the graph in your description. When
asked to explain the shape of a graph, you need to EXPLAIN WHY the graph
has the shape it does.
Denatured
The diagram below shows why a denatured enzyme molecule cannot catalyse a
reaction...the shape of the active site has changed which means it can no longer
bind to the substrate.
Learning Task 3
You will carry out a practical to look at the effects of conditions of an enzyme.
This will need to be added to your folio and the SQA may well ask to see this
work, so do it to the best of your ability.
From the three variables below work out a plan with your teacher as to how you
will carry out your experiment in a valid, reliable and accurate way.

Dependant variable – you will measure this

Independent variable – You need to choose this and you will change it over
a range of values.

Controlled variables – you will keep these the same for all your
experiments.
You will be given the success criteria to ensure you know what to put in you
write up once you have completed the experiment.
Application of Enzymes
In today’s world we use enzymes in biological washing powders. This would be a
good chance to find out a little about them. You can even do a 2.2/2.3 write-up
for your folio here if you want.
Find out;
1. What is the point of a washing powder?
2. What is in a biological washing powder?
3. How does it work?
4. Explain how conditions affect the washing powder from working?
5. Give two advantages of biological washing powders (think about energy
and its use here – pollution as well)
6. Why should you not use a biological washing powder with babies clothes?
Nearly done!
Learning activity 4. Some quick review questions;
1. Write down 4 different functions of proteins.
2. What do we call biological catalysts?
3. What do we call the molecule an enzyme acts upon?
4. What do we call the molecule(s) made at the end of an enzyme reaction?
5. Name 2 conditions which affect the rate at which an enzyme works.
6. The following table shows the results from an experiment set up to
investigate the effect of temperature on the rate of an enzyme reaction. In
this experiment they looked at how temperature affected the digestion of a
piece of muscle (protein) by pepsin (a protease).
Temperature (oC)
0
5
10
15
20
25
30
35
40
45
50
55
60
65
Mass of protein digested by pepsin (g)
0
3
10
16
24
31
40
52
48
42
23
8
0
0
(a) Present the results from the table as a line graph.
(b) What is the optimum temperature for this enzyme?
(c) Explain why there is no substrate broken down at 60oC
(d) Predict the mass of substrate broken down at 33 oC
(e) By how many times was the rate of activity greater at 40 oC
You have now used Didbook as a tool for reflecting on your learning a few times.
It is important that you think carefully about your learning, have a clear idea
about what you have achieved, what you haven’t yet achieved, future goals, next
steps to make sure you keep improving and identifying strategies you are going
to use to improve your learning.
Think carefully and answer the following questions:
1. Look at your previous targets. What skills have you developed over the
last three topics? How do you know and how could you prove it to
someone?
2. What targets have you found difficult to achieve? What strategies are
you going to use to overcome these problems?
Choice extension
Task
1
2
3
4
5
6
Choose at least 2 of the following activities to
complete.
Make a diagram to show all enzymes are catalysts
but not all catalysts are enzymes.
Devise an experiment to show an enzyme is
specific.
Find out what a thermophile is and where it lives.
Try to find out why Bulimia can lead to tooth
damage
What effect would indigestion remedies have on
enzyme efficiencies?
Plan an experiment to show that a denatured
enzyme no longer works even when returned to
optimum conditions.
Completed