DNA, genes and chromosomes — AQA A-Level Biology
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DNA, genes and chromosomes explained
DNA, genes and chromosomes covers 11 specification points, including In prokaryotic cells, DNA molecules are short,… and In the nucleus of eukaryotic cells, DNA….
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In prokaryotic cells, DNA molecules are short, circular and not associated with proteins.
A prokaryotic cell has no nucleus. Its DNA lies free in the cytoplasm as a single short, circular molecule, in a region sometimes called the nucleoid. This DNA is not wound around histone proteins, so it is often described as naked. Many prokaryotes also carry plasmids, which are small, separate circles of DNA holding extra genes such as those for antibiotic resistance, but a plasmid is not the cell's main DNA molecule. When the cell divides by binary fission, the circular DNA replicates and a copy passes to each daughter cell. The key features to remember are that the main DNA is short, circular, and not associated with proteins.
In the nucleus of eukaryotic cells, DNA molecules are very long, linear and associated with proteins, called histones.
In a eukaryotic nucleus each DNA molecule is very long and linear, meaning it has two ends rather than forming a loop, and it is wound around histone proteins. Histones are basic, positively charged proteins, and the negatively charged phosphate groups of the DNA backbone are attracted to them, so the DNA coils tightly around groups of histones. That coiling condenses what would be metres of DNA into a nucleus only a few micrometres across. The DNA and histone complex is called chromatin; it condenses further before nuclear division to form the chromosomes visible under a light microscope. The winding is not merely packaging. How tightly a region is wound determines whether transcription factors and RNA polymerase can reach the promoter of a gene, which is the basis of epigenetic control later in the course.
Together a DNA molecule and its associated proteins form a chromosome.
A chromosome consists of one long, linear DNA molecule wrapped around histone proteins. During most of the cell cycle, it exists as extended chromatin and cannot be resolved with a light microscope. In G₁, each chromosome is a single structure. After DNA replication in S phase, it consists of two identical sister chromatids joined at a centromere. During prophase, chromatin supercoils and condenses, making chromosomes visible. Therefore, seeing condensed chromosomes in a micrograph confirms the cell is dividing. Homologous chromosomes are pairs carrying the same genes at the same loci, one from each parent, though alleles may differ and sex chromosomes may differ in size.
The mitochondria and chloroplasts of eukaryotic cells also contain DNA which, like the DNA of prokaryotes, is short, circular and not associated with protein.
Mitochondria and chloroplasts contain their own DNA, which is structurally similar to prokaryotic DNA: it is short, circular, and not associated with histone proteins. These organelles also contain smaller 70S ribosomes and divide by a process resembling binary fission. These shared features support the endosymbiotic theory, suggesting these organelles evolved from free-living prokaryotes engulfed by ancestral eukaryotic cells. While this DNA codes for some organelle proteins, most are coded by nuclear genes. Mitochondrial DNA is typically inherited maternally via the egg's cytoplasm. Consequently, mitochondrial conditions often pass from mothers to offspring, though heteroplasmy can vary the severity.
A gene is a base sequence of DNA that codes for: the amino acid sequence of a polypeptide a functional RNA (including ribosomal RNA and tRNAs).
A gene is a length of DNA whose base sequence carries information. For most genes that information is read, by way of messenger RNA, as the sequence of amino acids in a polypeptide, which is its primary structure and which determines how the chain folds and therefore what it can do. But the definition deliberately has a second half. Some genes are transcribed into RNA molecules that are never translated and whose job is done by the RNA itself: ribosomal RNA, which combines with proteins to form ribosomes and is produced at the nucleolus, and transfer RNAs, which carry amino acids to the ribosome. These are called functional RNAs. So a gene is not the same thing as a sequence that codes for a protein, and a stretch of DNA coding only for a transfer RNA is still a gene. Alleles are different versions of the same gene, that is different base sequences at the same locus.
A gene occupies a fixed position, called a locus, on a particular DNA molecule.
The locus of a gene is its fixed position on a particular DNA molecule, and therefore on a particular chromosome. Because that position is fixed and is the same in every member of a species, the two chromosomes of a homologous pair carry the same genes in the same order, which is what makes them homologous, even though the alleles at those loci may differ. Fixed loci explain several later ideas. Crossing over in prophase one exchanges equivalent lengths of chromatid between homologous chromosomes, so no gene is lost or duplicated in the process. Genes at different loci on the same chromosome tend to be inherited together rather than assorting independently, which is linkage, and the closer their loci the stronger the linkage. Mapping loci is what genome projects do.
A sequence of three DNA bases, called a triplet, codes for a specific amino acid. The genetic code is universal, non-overlapping and degenerate.
Each sequence of three DNA bases, a triplet, codes for one amino acid. Three properties of this code matter. It is universal: the same triplet codes for the same amino acid in almost every organism, which is why a human gene inserted into a bacterium can yield the human protein, provided the gene is in a form the bacterium can express (for example cDNA without introns, or with suitable processing). It is non-overlapping: each base belongs to one triplet only and the bases are read in a fixed reading frame from a fixed starting point, which is why adding or deleting a base causes a frame shift that alters every triplet downstream, whereas substituting one base alters only that triplet. It is degenerate: most amino acids are coded for by more than one triplet, so a substitution may not change the amino acid sequence.
In eukaryotes, much of the nuclear DNA does not code for polypeptides.
In eukaryotes, a significant proportion of nuclear DNA does not code for polypeptides. This non-coding DNA exists in two main forms: between genes and within genes. Between genes, there are non-coding multiple repeats of base sequences, as well as regulatory sequences such as promoters. Within genes, there are non-coding sequences called introns, which separate the coding sequences called exons. During transcription, both introns and exons are transcribed into pre-mRNA, but introns are subsequently removed during splicing to form mature mRNA. This contrasts with prokaryotic DNA, which generally lacks spliceosomal introns. Some non-coding DNA also codes for functional RNAs like ribosomal RNA (rRNA) and transfer RNA (tRNA).
There are, for example, non-coding multiple repeats of base sequences between genes.
Between genes, eukaryotic DNA contains short base sequences repeated many times, known as variable number tandem repeats (VNTRs). The repeated sequence, for example AGAT, is common to everyone, but the number of repeats at a given position varies between individuals and is inherited. Because these repeats lie between genes and are non-coding, a change in repeat number often has no effect on a polypeptide, allowing variation to accumulate. This variation is exploited in genetic fingerprinting: DNA is cut with restriction endonucleases at specific recognition sequences, or amplified by PCR. The fragments are then separated by gel electrophoresis according to their length or size, moving towards the positive electrode due to DNA's negative charge.
Even within a gene only some sequences, called exons, code for amino acid sequences.
A eukaryotic gene is not one continuous coding stretch. Within the gene, exons are the sections whose base sequence is read as the amino acid sequence of the polypeptide; remember exons are expressed. The other sections, introns, do not code for amino acids. When the gene is transcribed, RNA polymerase copies the whole gene, exons and introns alike, producing pre-messenger RNA. Splicing then removes the introns and joins the exons, giving mature messenger RNA, which leaves the nucleus through a nuclear pore to a ribosome in the cytoplasm. Because splicing can join different combinations of exons from the same pre-messenger RNA, one gene can give rise to more than one messenger RNA and therefore more than one polypeptide. Prokaryotic genes are generally continuous, with no introns, so they need no splicing.
Within the gene, these exons are separated by one or more non-coding sequences, called introns.
Introns are non-coding base sequences lying between the exons of a eukaryotic gene. They are transcribed into pre-mRNA along with exons, then removed by splicing in the nucleus. Because they never reach a ribosome, their bases are not translated into amino acids. A mutation within an intron usually has no effect on the polypeptide, unless it alters a splice site. For genes containing introns, the gene is longer than the mature mRNA transcribed from it. This length difference is useful: complementary DNA (cDNA), made by reverse transcriptase from mature mRNA, contains only exons. Comparing cDNA to the original gene shows where the introns lay.
Your focus
- Give three features of the DNA of all prokaryotic cells that distinguish it from eukaryotic nuclear DNA.
- Explain why a plasmid is not the cell's main DNA molecule when describing where prokaryotic DNA is found.
- Compare the structure of prokaryotic DNA with eukaryotic DNA in terms of length, shape, and protein association.
Show all 33 objectives
- Describe how a very long DNA molecule is packaged with histones to fit inside a nucleus.
- Compare the DNA in a eukaryotic nucleus with prokaryotic DNA in terms of length, shape and associated proteins.
- Explain why the degree of coiling of DNA around histones affects whether a gene can be transcribed.
- Given a diagram or a stated stage of the cell cycle, say whether each chromosome is one chromatid or two, justifying the count by whether DNA replication has already happened.
- Distinguish between a chromosome, a chromatid and a homologous pair using a labelled diagram.
- Explain why a chromosome is only visible under a light microscope during cell division.
- Compare the DNA of a mitochondrion with the DNA in the nucleus of the same cell.
- Explain how the features of mitochondrial DNA support the idea that mitochondria evolved from prokaryotes.
- Deduce from family data whether a condition is caused by a mitochondrial or a nuclear mutation.
- Define a gene in a way that covers both polypeptide-coding genes and functional RNA genes.
- Explain how a change in the base sequence of a gene can change the tertiary structure of the polypeptide it codes for.
- Distinguish between a gene and an allele using the idea of base sequence at a locus.
- State what is meant by the locus of a gene and relate it to homologous chromosomes.
- Explain why crossing over between homologous chromosomes neither adds nor removes genes.
- Explain why two genes at different loci on the same chromosome may fail to assort independently.
- Explain why a bacterium given a human gene can produce the human protein, noting the need to remove introns or use cDNA.
- Explain how the code being non-overlapping causes an insertion to have a greater effect than a substitution.
- Use the degeneracy of the code to explain why a substitution mutation may leave the polypeptide unchanged.
- State that much of eukaryotic nuclear DNA does not code for polypeptides.
- Describe the location and nature of non-coding multiple repeats and introns.
- Explain the difference between eukaryotic and prokaryotic DNA regarding non-coding sequences within genes.
- Explain why variation in the number of repeats between individuals is often tolerated, in terms of the repeats being non-coding.
- Give features of DNA fragments that allow them to be separated by gel electrophoresis.
- Describe how restriction endonucleases are used to cut DNA at specific recognition sequences.
- Describe what happens to a pre-messenger RNA molecule before it leaves the nucleus.
- Explain how a single gene can code for more than one polypeptide.
- Explain why a gene taken directly from a human chromosome may not be expressed correctly in a bacterium.
- Describe the position and the fate of introns from transcription through to translation.
- Calculate the number of amino acids in a polypeptide from the number of bases in the exons of its gene.
- Explain why complementary DNA produced from mature messenger RNA is shorter than a gene containing introns.
DNA, genes and chromosomes exam tips
Marking Points
- Prokaryotic DNA is circular and free in the cytoplasm, not enclosed within a nucleus.
- The main DNA molecule is short compared to eukaryotic DNA.
- Prokaryotic DNA is not associated with proteins or histones.
- Plasmids are small, separate circles of DNA carrying extra genes, distinct from the main circular DNA molecule.
- Nuclear DNA is linear rather than circular.
- The DNA is associated with proteins called histones, forming chromatin.
- The DNA is very long, so it must be coiled or condensed to fit inside the nucleus.
- Replication of linear DNA is associated with a cell cycle involving mitosis.
- This DNA is enclosed within a nuclear envelope containing pores.
- Credit depends on the wording of the actual question; the points above are teaching guidance, not an official question-specific mark scheme.
- One mark for stating a eukaryotic chromosome consists of DNA and associated histone proteins.
- One mark for explaining that after S phase, a chromosome consists of two identical sister chromatids.
- One mark for identifying that sister chromatids are joined at a centromere.
- One mark for defining homologous chromosomes as a pair carrying the same genes at the same loci.
- One mark for stating the DNA of mitochondria and chloroplasts is short and circular.
- One mark for specifying this organelle DNA is not associated with histone proteins.
- One mark for noting these organelles contain smaller 70S ribosomes, supporting prokaryotic origins.
- One mark for identifying that mitochondrial DNA is typically inherited maternally via the cytoplasm of the egg.
- one mark for a gene being a sequence of DNA bases
- one mark for stating that it codes for the amino acid sequence, or primary structure, of a polypeptide
- one mark for recognising that a gene may instead code for a functional RNA, naming ribosomal RNA or transfer RNA
- one mark for associating the production of ribosomal RNA with the nucleolus
- one mark for an allele being a different base sequence of the same gene
- one mark for a locus being the fixed position of a gene on a DNA molecule or chromosome
- one mark for homologous chromosomes carrying the same genes at the same loci but possibly different alleles
- one mark for explaining that crossing over exchanges equivalent lengths because the loci on the two chromosomes correspond
- one mark for linked genes being at different loci on the same chromosome and so not assorting independently
- one mark for using the term allele correctly as one version of a gene at a given locus
- one mark for the genetic code being universal, that is the same triplets code for the same amino acids in almost all organisms
- one mark for non-overlapping meaning that each base is part of only one triplet, read in one fixed frame
- one mark for degenerate meaning that most amino acids are coded for by more than one triplet
- one mark for using degeneracy to explain why a substitution may not change the amino acid sequence
- one mark for explaining that a frame shift alters every triplet downstream, whereas a substitution alters only one triplet
- one mark for stating that a human gene inserted into a bacterium can produce the human protein because the code is universal, with the caveat that introns may need to be removed or the gene supplied as cDNA
- State that much of eukaryotic nuclear DNA does not code for polypeptides.
- Identify that non-coding DNA between genes includes multiple repeats of base sequences, and may also include regulatory sequences.
- Explain that non-coding sequences within genes are called introns and they separate exons.
- Describe how introns are transcribed into pre-mRNA but are removed during splicing before translation.
- Contrast eukaryotic DNA with prokaryotic DNA by stating that prokaryotic DNA generally lacks spliceosomal introns.
- The repeated sequences are non-coding and lie between genes, so variation in repeat number often does not alter a polypeptide.
- The number of repeats varies between individuals while the repeated sequence itself is common to all.
- Fragments differ in length, size or mass, which allows them to be separated by gel electrophoresis.
- DNA fragments carry a negative charge, causing them to move towards the positive electrode.
- Restriction endonucleases cut DNA at specific recognition sequences, not at random positions.
- one mark for exons being the sections of a gene whose base sequence codes for amino acids
- one mark for introns being non-coding sections within the gene
- one mark for pre-messenger RNA containing both exons and introns, because the whole gene is transcribed
- one mark for splicing removing introns and joining exons to form mature messenger RNA
- one mark for contrasting this with prokaryotic genes, which are generally continuous and need no splicing
- Introns are non-coding sequences within a gene, lying between the exons.
- Introns are transcribed into pre-messenger RNA and then removed by splicing.
- Splicing occurs in the nucleus, before the messenger RNA reaches a ribosome.
- For genes with introns, the DNA sequence is longer than the mature messenger RNA transcribed from it.
- Complementary DNA made from mature messenger RNA contains no introns.
Examiner Tips
- 💡When asked for features of prokaryotic DNA, explicitly state that it is short, circular, and not associated with proteins.
- 💡The phrase 'not associated with proteins' or 'not associated with histones' is the standard way to describe prokaryotic DNA lacking nucleosomes.
- 💡Two words carry the marks here: linear and histones.
- 💡If the question asks for a difference from prokaryotes, put both sides of it in the same sentence.
- 💡Remember chromatin, chromosome and chromatid describe the same DNA at different stages, not different substances.
- 💡A complete definition of a eukaryotic chromosome must include both DNA and histone proteins.
- 💡When counting chromosomes, count the centromeres; a chromosome may consist of one or two chromatids depending on the cell cycle stage.
- 💡Memorise the three key features shared with prokaryotes: short circular DNA, no histones, and smaller 70S ribosomes.
- 💡If a pedigree shows a trait passing from mothers to offspring but never from fathers, consider mitochondrial inheritance.
- 💡Learn the definition with both halves; a one-sided definition loses the mark.
- 💡Write polypeptide rather than protein where the gene codes for a single chain.
- 💡Use base sequence rather than genetic information, which examiners often ignore.
- 💡Answer a definition question in one clean sentence: position, gene, chromosome.
- 💡If a question tells you two genes are on the same chromosome, it is asking about linkage.
- 💡Write alleles as upper and lower case of the same letter so their shared locus is obvious.
- 💡Write universality out in full as the same triplets coding for the same amino acids in almost all organisms; the bare word is not enough.
- 💡Keep triplet, codon and anticodon straight by naming the molecule each one sits on.
- 💡When using the human gene in bacterium example, mention that introns may need to be removed or the gene supplied as cDNA.
- 💡When asked for examples of non-coding DNA, specifically name multiple repeats between genes or introns within genes rather than using vague terms like 'spacer DNA'.
- 💡Be precise with terminology: state that introns are removed from pre-mRNA during splicing, not from the DNA itself.
- 💡When explaining separation in gel electrophoresis, clearly distinguish that negative charge causes movement, while differences in length or size cause the actual separation.
- 💡State early in any fingerprinting answer that the repeats are non-coding.
- 💡Name restriction endonucleases and recognition sites rather than writing 'cutting enzymes'.
- 💡Remember that exons are expressed; the mnemonic has rescued a great many marks.
- 💡Use pre-messenger RNA and mature messenger RNA as separate terms in any eukaryotic transcription answer.
- 💡If a question puts a eukaryotic gene into a bacterium, say the bacterium cannot splice, so complementary DNA made from mature messenger RNA must be used.
- 💡When calculating amino acid number, use only the exon bases and divide by three.
- 💡State explicitly that splicing happens in the nucleus.
Common Mistakes
- Naming plasmids as the cell's main DNA. Correction: plasmids are small separate circles; the main DNA is the short circular molecule free in the cytoplasm.
- Writing nucleosome when nucleoid is meant. Correction: nucleoid is the region containing the main DNA; a nucleosome is DNA wound around histones in eukaryotes.
- Stating that a prokaryote contains no protein at all. Correction: say the DNA is not associated with proteins or histones, which is the accepted wording.
- Answering that the DNA is in the nucleus when the question asked about its shape or its associated proteins.
- Describing histones as enzymes, or as molecules that code for proteins.
- Treating chromatin and chromosome as different molecules rather than the same DNA at different degrees of condensation.
- Claiming all eukaryotic DNA is linear and forgetting mitochondrial and chloroplast DNA.
- Writing genetic material where the mark scheme ignores it and requires DNA with histones.
- Saying a chromosome is made only of genes or DNA, omitting the essential histone proteins.
- Assuming all visible chromosomes always have two chromatids; during anaphase, sister chromatids separate to become individual chromosomes.
- Confusing a homologous pair (one maternal, one paternal) with a pair of identical sister chromatids.
- Stating these organelles contain no DNA and rely entirely on the nucleus.
- Describing mitochondrial or chloroplast DNA as linear, confusing it with nuclear eukaryotic DNA.
- Assuming maternal mitochondrial inheritance guarantees all offspring will be equally affected, ignoring heteroplasmy and threshold effects.
- defining a gene only as a section of DNA that codes for a protein, so functional RNA is left out
- saying a gene codes for a characteristic rather than for a polypeptide
- using gene and allele interchangeably
- saying the gene itself leaves the nucleus to be translated at a ribosome
- describing transfer RNA and ribosomal RNA as being made of protein
- using locus and allele as though they meant the same thing
- saying homologous chromosomes are identical, when the alleles at their loci can differ
- claiming that genes can move to new positions during ordinary inheritance
- describing two genes on different chromosomes as linked
- saying crossing over swaps whole chromosomes rather than equivalent sections of chromatids
- answering that the code is degenerate when asked why a bacterium can make a human protein, which is rejected
- writing that DNA is universal without qualifying it, which gains nothing
- saying degenerate means one triplet can code for several amino acids, which is the reverse of the truth
- confusing the triplet on DNA with the codon on messenger RNA and the anticodon on transfer RNA
- explaining a frame shift as affecting only the triplet in which the base was added or lost
- claiming that transcription and translation are identical in all species, ignoring differences such as splicing and coupled transcription-translation in prokaryotes
- Stating that DNA is translated into polypeptides. Correction: DNA is transcribed into mRNA, which is then translated at the ribosomes.
- Confusing introns and exons. Correction: Remember that introns are the non-coding intervening sequences that are removed, while exons are the coding sequences that are expressed.
- Suggesting prokaryotes have introns. Correction: Prokaryotic DNA generally lacks spliceosomal introns, which is a key difference from eukaryotic nuclear DNA.
- Giving 'they are short' on its own as the reason fragments separate; link separation to differences in length, size or mass.
- Stating that DNA fragments are positively charged; DNA is negatively charged and moves to the positive electrode.
- Claiming the repeats code for a protein; they are non-coding sequences located between genes.
- Saying restriction enzymes cut DNA at random positions; they cut at specific recognition sites.
- saying messenger RNA is transcribed from the exons only, so the pre-messenger RNA stage disappears
- confusing an exon with a codon; an exon is a section of a gene, a codon is three bases on messenger RNA
- saying splicing happens at the ribosome or in the cytoplasm rather than in the nucleus
- claiming that removing the introns changes the amino acids coded for by the exons
- applying splicing to a bacterial gene in a recombinant DNA question; bacteria cannot splice eukaryotic introns
- Saying introns are cut out of the DNA itself; correction: they are spliced out of the pre-messenger RNA.
- Describing introns as having no function; correction: mutations at splice sites can alter which sections are removed.
- Assuming all eukaryotic genes have introns; correction: some, like histone genes, are intronless.
- Calculating the number of amino acids from the whole length of a eukaryotic gene; correction: use only the exon bases.