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Biology · Inheritance

Genetic Variants and Phenotype (Higher tier)

A change in one base can have no effect, or it can switch a gene off or change an enzyme. This lesson is for separate Biology only, and for the Higher tier only: Combined Science and Foundation students do not need it. It explains how genetic variants in coding DNA and in non-coding DNA can influence the phenotype.

  • Separate onlyHigher
  • 9 key terms
  • All boards

Learning Objectives

  1. 1(Higher tier) Describe how genetic variants in coding DNA influence the phenotype by altering the activity of a protein.
  2. 2(Higher tier) Explain how mutations in coding DNA can affect protein structure, including the active sites of enzymes.
  3. 3(Higher tier) Describe how genetic variants in non-coding DNA influence the phenotype by altering how genes are expressed.
  4. 4(Higher tier) Explain how a variant can stop the transcription of mRNA.

Retrieval practice

  1. 1

    What is a gene?

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    A section of DNA that codes for a protein.

  2. 2

    What is the triplet code?

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    A group of three bases codes for one amino acid.

  3. 3

    What is the active site of an enzyme?

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    The part of the enzyme where the substrate binds.

  4. 4

    What is transcription?

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    The copying of the gene into mRNA in the nucleus.

A change in the DNA, a change in the organism

A genetic variant is a difference in the DNA of an organism that arose from a mutation. Not all of the DNA is the same. Some of it, called coding DNA, contains genes that code for proteins. Much of the rest, which is called non-coding DNA, does not code for a protein, but it has other jobs, and one of them is to control whether a gene is used. A variant can happen in either type, and the effects on the phenotype are different. Most variants have no effect, but those that do can have large effects.

Variants in coding DNA

A change inside a gene can change the protein that is made.

  • A different amino acid

    A change to one base can change a triplet, so that a different amino acid is put into the protein. The order of amino acids decides how the chain folds, so the shape of the protein can be altered.

  • Changing the activity of a protein

    If the shape is changed, the protein may work less well, or not at all, or it may do something new. This changes the phenotype.

  • A change to an enzyme

    If the protein is an enzyme, and the variant changes the active site, the substrate may no longer fit, and the enzyme cannot catalyse the reaction. Enzymes are specific because of the shape of the active site.

  • No change

    Some changes do not alter the amino acid, because more than one triplet codes for the same amino acid, so they have no effect on the protein.

  • A frameshift

    If a base is added or deleted, all of the triplets after it are changed, which usually makes a protein that does not work.

Variants in non-coding DNA

A variant outside a gene does not change the protein, but it can change how much of it is made.

  • Controlling the gene

    There are regions of non-coding DNA next to a gene that act like a switch. When the right proteins bind to the region, the gene is transcribed into mRNA, and the protein is made.

  • A variant in the switch

    A variant can stop the binding, so transcription of the mRNA is stopped, or reduced. The terms promoter and transcription factor are not required.

  • Gene expression

    The way that a gene is used, which means how much of its protein is made, and where and when, is called gene expression. A variant in non-coding DNA changes how the gene is expressed.

  • Phenotype

    The protein is normal, but less of it, or more of it, is made, which can change the phenotype.

Non-coding and coding variants

Variant in non-coding DNA

  • Outside the gene
  • Changes how the gene is expressed
  • May stop transcription of the mRNA
  • The protein is normal, but the amount may change

Variant in coding DNA

  • Inside the gene
  • Can change the amino acid sequence
  • Can change the shape and the activity of the protein
  • Can affect the active site of an enzyme

Explaining the effect of a variant

A variant in the gene for the enzyme amylase changes one amino acid in the active site. The enzyme no longer breaks down starch. Explain why.

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  1. 1 Coding DNA The variant is in the gene itself, so the amino acid sequence of the enzyme changes.
  2. 2 Shape The order of amino acids decides how the protein folds, so the active site has a different shape.
  3. 3 Specificity The substrate fits only an active site of the right shape, as in the lock and key model.
  4. 4 Result No enzyme-substrate complex forms, so the reaction does not take place, and the phenotype changes.

AnswerThe change in the coding DNA alters the amino acid sequence, so the shape of the active site changes. The starch no longer fits into it, so an enzyme-substrate complex is not formed, and the starch is not broken down.

Linking genotype to phenotype

These ideas explain how a small change in the DNA can have a large effect on the organism.

  • DNA to protein

    A gene codes for a protein, and the proteins an organism makes, and how much of each, decide its features.

  • Variants

    A variant that changes the protein, or the amount of the protein, may change a feature.

  • Many variants

    Most variants have no effect, so they are carried without any visible change, and they add to the genetic variation in the population.

  • Evolution

    A variant that gives a feature that suits the environment can be passed on, and spreads, by natural selection.

Case study

Sickle cell disease and lactase persistence

In sickle cell disease, a variant in the coding DNA for haemoglobin changes one base, so that one amino acid in the protein is changed. This alters the shape of the haemoglobin, so that the red blood cells can become sickle shaped, and block small blood vessels. In lactase persistence, a variant in the non-coding DNA near the lactase gene keeps the gene switched on in adults. The lactase protein is normal, but it is still made in adulthood, so that the person can go on digesting milk sugar. They show the two types of variant, and the way in which each can influence the phenotype.

Coding variant Changes the haemoglobin protein.
Non-coding variant Changes how much lactase is made, in adults.

Summary and exam focus

  • A variant in coding DNA can alter the structure and the activity of a protein, including the active site of an enzyme.
  • A variant in non-coding DNA can alter how genes are expressed.
  • A variant can stop transcription of the mRNA, so less protein is made.
  • Most variants have no effect on the phenotype.
  • The terms promoter and transcription factor are not required.

Exam focus

Describe how a genetic variant in the coding DNA of a gene, and a variant in non-coding DNA, can each influence the phenotype of an organism. (6 marks) (6 marks)

For coding DNA, say that the amino acid sequence changes, so the shape and the activity of the protein changes, for example the active site of an enzyme. For non-coding DNA, say that the protein is the same but gene expression changes, for example stopping transcription of the mRNA.

Key terms

The words this lesson expects you to use. Each one is linked from the first place it appears above.

Coding DNA
The parts of the DNA that code for proteins, which are the genes.
Non-coding DNA
Parts of the DNA that do not code for proteins, but may control how genes are used.
Gene expression
The way in which a gene is used to make its protein.
Transcription
The copying of the DNA of a gene into mRNA.
Active site
The part of an enzyme where the substrate binds.
Enzyme-substrate complex
The enzyme and its substrate joined together.
Frameshift
A change in all of the triplets after an addition or deletion of bases.
Variant
A different version of a gene, which arose from a mutation.
Protein structure
The shape of a protein, which depends on the order of its amino acids.

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