Gene Expression

Eukaryotes (multicellular organisms) possess cells that contain a complete set of chromosomes (unless mutations occur). Cell genes in these chromosomes code for proteins and give commands on what cells will have to do in their life cycle. Gene expression will act as an "on" and "off" switch for proteins and their amounts that a specific cell will have to make. The cell will be controlled to make more if needed and less if not.

Gene Expression Gene Expression

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Table of contents

    What is gene expression?

    Gene expression is the translation and transcription of genetic information. It determines which genes are translated and transcribed and how many. The DNA of each of these cells includes genes needed to make all the proteins required. However, not every gene is expressed. Due to the expression of different genetic codes in cells, they become specialised and carry out specific functions.

    All the DNA in eukaryotic organisms contain less than 10% of the genes that code for proteins. The majority of the DNA is non-coding, essential for controlling gene activity. Non-coding DNA contains structural DNA, which helps maintain the structure of chromosomes in eukaryotes.

    Functional RNA does not code for proteins but plays an essential role in synthesising proteins, e.g. tRNA. The synthesis of particular proteins due to the expression of different genes determines an organism's phenotype, i.e. the physical characteristics of an organism. However, the base sequence of the DNA determines the organism's genotype.

    The function of gene expression

    Genes encode proteins, and proteins dictate cell function. Therefore, the combination of genes active in a particular cell determines the identity of a cell and its tasks. The activation of genes is called gene expression. It is tightly regulated at several points, from the initial stage of transcription to splicing and the translation of the proteins and the changes to the final protein structure. These processes are controlled to monitor and maintain cell types with required characteristics.

    Not all parts of a gene code for the amino acid sequence of a protein molecule. The gene is composed of coding sections called exons and non-coding sections called introns. After the gene is transcribed into RNA, the introns are spliced out of the RNA molecule. Then the exons reattached to each other, forming a single mature mRNA molecule. This is splicing. The inclusion of introns or disruption of the order of exons in the mature mRNA molecule would produce a dysfunctional protein.

    Splicing: Introns are removed, and exons are spliced together. Without this step, proteins would be non-functional.

    Introns: Non-coding sections of the RNA transcript.

    Exons: Coding sections of the RNA transcript.

    Therefore, gene expression uses information from genes to synthesise proteins or RNA molecules. The synthesis of proteins involves RNA in the processes of transcription and translation. You can read more about these vital processes in the Transcriptional Regulation and Translation Regulation explanations.

    RNA in gene expression

    Now, let's revise the structure and function of RNA, to understand its vital role in gene expression better.

    RNA differs from DNA in the following ways:

    Table 1. The main differences between RNA and DNA.

    RNADNA
    Single strand.Double helix (two strands).
    Ribonucleic acid in the nucleotide.Deoxyribonucleic acid (one less oxygen-containing hydroxyl group) in the nucleotide. Deoxyribonucleic acid makes DNA more stable than RNA.
    Base pairing: Cytosine bonds with Guanine (C-T) and Adenine bonds with Uracil (A-U).Cytosine bonds with Guanine (C-G), and Adenine bonds with Thymine (A-T).

    Three forms of RNA are involved in the translation and transcription of genes in a cell. These three forms are:

    • Messenger RNA (mRNA) carries a copy of the gene to be expressed from the nucleus to the ribosome, where it can be translated.
    • Transfer RNA (tRNA) consists of only one strand of RNA, which folds because of base pairing. Each tRNA molecule carries its specific amino acid to the ribosome.
    • Ribosomal RNA (rRNA), rRNA, together with proteins, forms ribosomes.

    Genes

    DNA in genes contains instructions, consisting of non-coding instructions (sequences of DNA) and code for RNA or proteins. Coding regions of a gene are called exons, and non-coding ones are called introns. The DNA code consists of nitrogenous bases: adenine, cytosine, guanine, and thymine. Different base pair combinations create different amino acids and therefore produce various proteins.

    A codon (three bases) codes for one amino acid. There are 20 amino acids and four bases (64 codons possible). Amino acids are specified by more than one codon, referred to as redundancy. Not all mutations will change the amino acid sequence of proteins; some mutations might still code for the same amino acid.

    Codon: A specific DNA or RNA sequence of three nucletides corresponding to a particular amino acid.

    Epigenetics: the study of how behaviour and environment contribute to the changes in your genes and affect the way they work.

    Cells that can express every one of their genes are stem cells. Stem cells can become any cell in the body because they can produce all the proteins needed to create a specific structure and carry out particular tasks. You can find more detail on this subject in the stem cells article.

    The development of stem cells into particular body cells can occur due to the factors involved in transcription and translation. This regulation of protein synthesis means that different genes are expressed, and various proteins are made, enabling the development of stem cells into different body cells. Epigenetic control of genes determines whether a gene is expressed via altering how proteins and enzymes involved in transcription can transcribe the DNA. Uncontrolled cell growth can create mutations, which may develop into tumours. Tumours can be harmful and non-harmful, but you'll find more information about tumours in the article on Epigenetics.

    Protein Synthesis/Stage 1 of Gene Expression

    DNA helicase unwinds the DNA double helix, and the hydrogen bonds between base pairs are broken. RNA polymerase creates a complementary template strand. The result of this process is a molecule called pre-mRNA.

    This pre-mRNA molecule is 'spliced', where introns are removed, and the remaining exons are re-joined. The molecule is referred to as mRNA after spicing.

    1. During translation, the mRNA leaves the nucleus. The template strand travels to the ribosome to which it attaches.
    2. Transfer RNA (tRNA) brings free amino acids from the cytoplasm to the mRNA in the ribosome. The codon on mRNA forms complementary base pairs with the anticodon of the tRNA molecule allowing the tRNA to specify the amino acid. The specific amino acid is bound to the other end of the tRNA molecules.
    3. tRNA molecules are attached to the mRNA via the ribosome, which moves along the mRNA strand. As the ribosome covers two codons, two tRNA molecules are attached, and a peptide bond forms between them.
    4. The amino acids form a polypeptide chain, and as each amino acid is attached, they separate from the tRNA. This allows the tRNA molecule to return to the cytoplasm and bring another amino acid.
    5. The protein (polypeptide chain) formed can be changed by combining polypeptide chains or adding a phosphate or carbohydrate group.

    Every protein has a unique shape designed to carry out a specific function. The primary structure, i.e. the sequence of amino acids, allows every protein to have a unique shape as there is nearly an unlimited number of possible amino acid combinations. The secondary structure of proteins can take one of two shapes: the alpha-helix or beta-pleated sheets.

    The tertiary structure integrates alpha-helices and beta-pleated sheets, establishing a unique three-dimensional structure.

    If you want to learn about the tertiary structure of proteins, you can find it in the article on protein structure.

    The quaternary structure of proteins consists of multiple polypeptide chains. The quaternary structure might contain prosthetic groups. These are non-protein groups that become integrated into the chains. This forms what is called a conjugated protein, e.g., haemoglobin. The primary structure dictates the secondary, tertiary and quaternary structures.

    The disturbance of the primary structure completely changes the protein's function, highlighting the importance of the amino acid sequence.

    Gene expression, the different levels of protein structure, Study SmarterFig. 1 - Protein structure

    Regulation of gene expression

    Many of the genes in humans code for factors that regulate the transcription and translation of different genes. These factors control which genes are expressed and used to make proteins, and control which genes are not. The sequences that do not create a protein have the essential function of regulating the expression of other genes.

    One such factor involved in gene regulation is an activator. Proteins must bind to the promoter region at the start of the DNA to be transcribed. Activator proteins such as RNA polymerase bind to the promoter legion and activate transcription.

    Regulatory elements can have general or specific effects. These effects are described in the article on regulating transcription and translation. The regulation of translation involves RNA interference, which causes mRNA not to be translated into proteins. RNA interference uses siRNA (small interfering RNA in mammals) and miRNA (micro interfering RNA in mammals and plants). Refer to the article on regulation of translation for more detail.

    Gene Expression - Key takeaways

    • Regulation of gene expression patterns in eukaryotic cells is a complex process that occurs at various levels, from elements within the DNA of modifications to complete proteins.
    • Not every piece of DNA holds instructions to make a protein; some sequences exist to regulate the expression of other genes.
    • Genes are made up of introns and exons. Introns are removed from the final mRNA. Promoters and enhancers are regulatory elements that do not code for proteins but regulate the expression of genes.
    • RNA is essential in the synthesis of proteins as it allows a template to be made (mRNA) of the original strand. It also allows specific amino acids to be brought together to form the polypeptide chain (tRNA).
    • Haemoglobin is a protein with a quaternary structure called a conjugated protein. The disturbance of its amino acid sequence would cause a completely different protein to be formed, and it would not carry out the function of haemoglobin.
    Gene Expression Gene Expression
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    Frequently Asked Questions about Gene Expression

    What is gene expression?

    Gene expression affects the activation of genes in a cell. It affects whether all the genes in a cell are expressed and controls which genes are switched off (not expressed). This dictates the proteins produced and influences what functions the cell carries out.

    How does epigenetics affect gene expression?

    Epigenetic changes do not affect the base sequence of DNA; however, they affect whether genes are expressed or how much some genes are expressed.

    How does gene expression occur?

    Many factors influence the expression of genes, such as intracellular structures (molecules within the cell). Transcription factors affect which genes are expressed, and epigenetic changes influence how much gene expression occurs or whether some genes are expressed or not.

    How do you read a gene expression heat map?

    A heat map is how gene expression data is illustrated. The data is displayed in a grid in which there are rows and columns. Each column represents a sample, and each row represents a gene. The colors and their intensity varies according to changes in gene expression.

    How do you measure gene expression levels?

    The levels of the gene product (proteins produced) are quantified and displayed in a heat mat to measure the gene expression levels. From the data, the level of gene expression can be interpreted. Western blotting (Southern blotting involves identification of DNA, whereas western blotting identifies proteins) can be used to quantify gene products as well as the ELISA test.

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