What happens in cells (and what do cells need)?

What you'll learn

• How DNA is structured and why its order of bases matters.
• How cells use DNA instructions to make proteins.
• How enzymes speed up reactions in cells.
• How to investigate enzyme activity and calculate reaction rates.

The big picture: cells need instructions and reactions

Every living cell carries out thousands of chemical reactions. These reactions build molecules, break molecules down, release energy, and keep the cell alive.

To do this, cells need:

• DNA, which stores instructions.
• Proteins, which carry out many cell jobs.
• Enzymes, which control the speed of reactions.

DNA: the instruction molecule

DNA is not made of protein. It is a different biological molecule. It contains a sugar, phosphate groups, and bases.

DNA is a polymer

DNA is a polymer because it is made from many smaller units called nucleotides joined in a long chain.

For J247 separate Biology, you need the extra detail that each DNA nucleotide contains:

• a sugar
• a phosphate group
• one of four bases

The four bases are:

• A = adenine
• T = thymine
• C = cytosine
• G = guanine

DNA has a double helix structure

DNA is made of two strands twisted around each other. This shape is called a double helix.

The sides of the DNA molecule form a sugar-phosphate backbone. The bases point inwards and pair up between the two strands.

The base pairs are always:

• A pairs with T
• G pairs with C

These are called complementary base pairs because the bases fit together in specific pairs.

Genes and proteins

The order of amino acids in a protein affects how the protein folds. The shape of the protein affects what it can do.

For example:

• some proteins are enzymes
• some proteins help build cell structures
• some proteins are hormones or antibodies

Protein synthesis: making a protein from DNA

For J247 separate Biology, you need a simple description of protein synthesis, which means making a protein.

Protein synthesis happens in two main stages:

1. Transcription in the nucleus.
2. Translation in the cytoplasm.

Stage 1: transcription

In the nucleus:

1. The DNA molecule unzips around the gene.
2. A copy of the gene is made as mRNA.
3. The mRNA leaves the nucleus and moves into the cytoplasm.

Stage 2: translation

In the cytoplasm:

1. The mRNA attaches to a ribosome, which is the site of protein synthesis.
2. The ribosome reads the mRNA bases in groups of three.
3. Each group of three bases codes for one amino acid.
4. tRNA molecules bring the correct amino acids to the ribosome.
5. The amino acids join together in the correct order to make a protein.

Enzymes: biological catalysts

Enzymes are vital in metabolism because many reactions would be too slow without them.

Examples of enzyme-controlled reactions include:

• digestion of starch by amylase
• breakdown of hydrogen peroxide by catalase
• respiration reactions inside cells

How enzymes work

Each enzyme has a specially shaped region called an active site.

The lock and key hypothesis says that the substrate fits into the active site because their shapes are complementary. This makes enzymes specific, meaning one enzyme usually works with one type of substrate.

The steps are:

1. The substrate fits into the active site.
2. An enzyme-substrate complex forms.
3. The reaction happens.
4. Products leave the active site.
5. The enzyme is unchanged and can be used again.

Factors affecting enzyme activity

The rate of reaction tells you how quickly a reaction happens.

Enzyme-controlled reactions are affected by:

• temperature
• pH
• substrate concentration
• enzyme concentration

Temperature

As temperature increases, particles have more kinetic energy. Enzyme and substrate molecules collide more often, so the reaction rate increases.

At high temperatures, the enzyme can denature.

After denaturation, the rate drops quickly because fewer enzyme-substrate complexes can form.

pH

Each enzyme has an optimum pH, where it works fastest.

If the pH is too high or too low, the active site can change shape and the rate decreases. Extreme pH can denature enzymes.

For example, an enzyme in the stomach may work best in acidic conditions, but an enzyme in the small intestine may work best in alkaline conditions.

Substrate concentration

If substrate concentration increases, the rate usually increases at first because enzyme molecules collide with substrate molecules more often.

Eventually, the rate levels off. This is because all the active sites are occupied, so adding more substrate cannot make the reaction faster.

Enzyme concentration

If enzyme concentration increases, the rate usually increases because there are more active sites available.

This only works if there is enough substrate. If substrate becomes the limiting factor, the rate will stop increasing.

Investigating enzyme reactions

You need to be able to describe experiments that investigate enzyme activity.

A common example is the effect of temperature on amylase, an enzyme that breaks down starch.

Amylase and starch investigation

Amylase breaks starch into sugars. You can test for starch using iodine solution:

• iodine turns blue-black if starch is present
• iodine stays orange-brown if starch is absent

A simple method:

1. Place amylase and starch solutions in separate test tubes in a water bath at a chosen temperature.
2. Allow both solutions to reach the same temperature.
3. Mix the amylase and starch, then start a timer.
4. Every fixed time interval, place a drop of the mixture onto iodine on a spotting tile.
5. Record the time taken until iodine no longer turns blue-black.
6. Repeat at different temperatures.

Important control variables include:

• pH
• enzyme concentration
• substrate concentration
• volume of solutions
• time interval between tests

Calculating reaction rate

For some enzyme experiments, you measure the time taken for a reaction to finish. A shorter time means a faster rate.

A common GCSE rate equation is:

$$rate=\frac{1}{time\; taken}$$

If you measure product volume, you may use:

$$rate=\frac{volume\; of\; product}{time\; taken}$$

Other enzyme investigations

You may also meet other enzyme experiments, such as:

• Catalase and hydrogen peroxide: measure the volume of oxygen gas produced.
• Lipase and milk fat: measure pH change as fatty acids are produced.
• Amylase and baby rice paste: observe how starch is broken down by amylase.

The exact method may change, but the same logic applies: change one independent variable, measure the effect on rate, and control the other variables.