Chapter 12.1 Transcription Flashcards
Provide a molecular definition of the term gene
The entire nucleic acid sequence that is necessary for the synthesis of a functional gene product, which may be a polypeptide or any type of RNA
It’s an extremely specific sequence of nucleotide monomers that has the ability to control the expression of one or more traits in every type of living organism
Genes are made up of DNA (found in the cell nucleus of eukaryotes)
Two types of molecular genes: protein-coding genes and non-coding genes
Define the central dogma
The central dogma is a theory in genetics and molecular biology that describes the flow of genetic information in cells
The genetic information flows only in one direction, from DNA to RNA to protein
- Transcription: the process of transferring information from DNA to RNA
- Translation: the process of using RNA as a template for protein synthesis
proposed by Francis Crick
Discuss the three stages of transcription
Initiation: The beginning of transcription. It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can “read” the bases in one of the DNA strands. The enzyme is now ready to make a strand of mRNA with a complementary sequence of bases
Elongation: This is the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs. During this process, and adenine (A) in the DNA binds to a uracil (U) in the RNA
Termination: This is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA
Compare and contrast transcription in bacteria and eukaryotes
It’s fundamentally the same process, but there are some key differences:
1. Location: Bacteria and archaea perform transcription in the cytoplasm, while eukaryotes perform transcription in the nucleus
2. RNA processing: RNA transcripts can act as mRNAs right away in bacteria, while in eukaryotes, the transcript of a protein-coding gene is called a pre-mRNA and must go through extra processing before it can direct translation
3. RNA polymerases: eukaryotes use three different polymerases, RNA polymerases I, II, and III, all structurally distinct from the bacterial RNA polymerase
4. Simultaneity of Transcription and Translation: Transcription and translation occur at the same time in prokaryotes, while in eukaryotes, the RNA is the first transcribed in the nucleus and then translated in the cytoplasm
5. Post-transcriptional Modifications: RNAs from eukaryotes undergo post-transcriptional modifications including: capping, polyadenylation, and splicing
Describe transcription regulation in eukaryotes
A complex process that controls gene expression. It involves the combined effects of structural properties of DNA and the interactions of transcription factors
Eukaryotic DNA is packaged into chromatin, which affects the accessibility of genes to transcription machinery. Transcription factors are proteins that bind to specific DNA sequences and either activate or repress translation. Most eukaryotic genes require general transcription factors and RNA polymerase, as well as other regulatory factors, for high levels of transcription
Gene expression in eukaryotic cells is also regulated by repressors as well as by transcriptional activators. Like their prokaryotic counterparts, eukaryotic repressors bind to specific DNA sequences and inhibit transcription. In some cases, eukaryotic repressors simply interfere with the binding of other transcription factors to DNA
In eukaryotes, additional regulatory sequences called enhancers and the proteins that bind to enhancers are needed to achieve high levels of transcription. Enhancers are DNA sequences that regulate the transcription of genes.
Lastly, even after a gene has been transcribed, gene expression can still be regulated at various stages. Some transcripts can undergo alternative splicing, making different mRNAs and proteins from the same RNAs and proteins from the same RNA transcript. Some mRNAs are targeted by microRNAs, small regulator RNAs that can cause an mRNA to be chopped up or block translation. A protein’s activity may be regulated after translation, for example, through removal of amino acids or addition of chemical groups
Explain how genes within the same chromosomes vary in their direction of transcription
The transcription of a gene is controlled by a region of DNA called the promoter, which is located at the start of the gene. The promoter region determines the direction of the transcription.
The RNA polymerase enzyme, which carries out transcription, binds to the promoter region and separates the DNA strands. It then uses one of the strands as a template to synthesize a complementary strand of RNA. The strand that is used as a template to synthesize a complementary strand of RNA. The strand that’s used as a template is called the template strand and determines the direction of transcription
If the promoter is located at the left end of the gene, the gene is transcribed from left to right. If the promoter is at the right end of the gene, the gene is transcribed from right to left.
The two DNA strands are antiparallel, meaning they run in opposite directions. This allows the genes on the two strands to be transcribed in opposite directions
Transcribe an mRNA sequence from a DNA strand:
5’ -ATGCGTACGT- 3’
5’ -AUGCGUACGU- 3’
Discuss the three mRNA modification in eukaryotes
These modifications are necessary to turn pre-mRNA into a mature mRNA molecule that can leave the nucleus and be translated
Splicing: the removal of introns, or “junk” sequences, and the pasting together of the remaining, good sequences - exons. Introns are non-coding sequences that must be spliced out of mRNA so that its translation leads to a functional protein
5’ Capping: A 5’ cap is added to the beginning of the RNA. This cap is a modified guanine (G) nucleotide, and it facilitates binding of the ribosome to the mRNA, increases mRNA stability, and improves intron splicing
3’ Poly(A) tail: a poly-A tail, which is a tail of adenine (A) nucleotides, is added to the end of the RNA. This tail protects the mRNA from degradation, assists in the export of the mature mRNA to the cytoplasm, and aids in translation
DNA
- Information storage: DNA stores the genetic information of an organism. This information is used to construct functional products such as proteins
- template for transcription: during transcription, the DNA sequence of a gene is copied to make an RNA molecule. This process is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand using a DNA strand as a template
- Regulation of Gene expression: the DNA contains promoter sequences near the beginning of a gene. These promoters control the binding of RNA polymerase and the initiation of transcription. So, DNA plays a key role in regulation gene expression
- Coding for proteins: the transcribed DNA message, or RNA transcript, is used to produce proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA
Double helix
- The unwinding of DNA: the double helix must unwind to allow an enzyme called RNA polymerase to transcribe the DNA. This unwinding separated the DNA strands, enabling one strand to serve as a template for transcription
- Directionally: The antiparallel nature of the double helix allows transcription to occur in a specific direction, from 5’ to 3’. This directionality is essential for the correct sequence of the resulting mRNA
- Regulation of transcription: Certain proteins can bind to specific areas of the double helix, influencing the rate and timing of transcription. These regulatory proteins can either promote or inhibit the binding of RNA polymerase to the DNA
- Protection of Genetic information: the double helix structure helps protect the genetic information from damage. This is crucial because any errors in the DNA sequence could lead to the production of faulty proteins
- Role of helicase: the enzyme helicase plays a key role in unwinding the double helix by breaking the hydrogen bonds between the paired nucleotides. This is important during both DNA repair and the process of transcription
Genes
- Information storage: genes are segments of DNA that store the genetic information of an organism. This information is used to construct functional products such as proteins
- Template for transcription: During transcription, the DNA sequence of a gene is copied to make an RNA molecule. This process is performed by enzymes called RNA polymerase, which link nucleotides to form an RNA strand using a DNA strand as a template
- Regulation of gene expression: the DNA contains promoter sequences near the beginning of a gene. These promoters control the binding of RNA polymerase and the initiation of transcription. DNA plays a key role in regulating gene expression
- Coding for proteins: the transcribed DNA message, or RNA transcript, is used to produce proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA
Gene expression and regulation
- Information Transfer: Transcription is the first step in gene expression, where the information from a gene is used to construct a functional product such as a protein. The DNA sequence of a gene is transcribed to make an RNA molecule
- Control of Protein Synthesis: By controlling the level of transcription, gene expression and regulation can determine when and how much protein product is made by a gene. This is crucial because the types and amounts of proteins synthesized in a cell determine its structure and function
- Response to Environmental Signals: Signals from the environment or from other cells can activate proteins called transcription factors. These proteins bind to regulatory regions of a gene and increase or decrease the level of transcription. This allows the cell to respond to changes in its environment
- Regulation of Cell Identity: The genes that a cell turns on largely determine its identity and properties. For instance, a photoreceptor cell in your eye can detect light because it expresses genes for light-sensitive proteins
- Post-Transcriptional Regulation: Even after a gene has been transcribed, gene expression can still be regulated at various stages. Some transcripts can undergo alternative splicing, making different mRNAs and proteins from the same RNA transcript. Some mRNAs are targeted by microRNAs, small regulator RNAs that can cause an mRNA to be chopped up or block translation. A protein’s activity may be regulated after translation, for example, through removal of amino acids or addition of chemical groups
Central Dogma
The Central Dogma of molecular biology, which states that information flows from DNA to RNA to protein, is fundamental to the process of transcription. Here’s why:
- Information Transfer: Transcription is the first step in the Central Dogma, where the information from a gene (DNA) is used to construct a functional product such as a protein. The DNA sequence of a gene is transcribed to make an RNA molecule
- Template for Transcription: During transcription, the DNA sequence of a gene is copied to make an RNA molecule. This process is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand using a DNA strand as a template
- Regulation of Gene Expression: The Central Dogma provides the basic framework for understanding how genetic information flows from a DNA sequence to a protein product inside cells. This flow of information is followed through three different processes: replication (DNA is duplicated), transcription (a DNA segment is read and transcribed into RNA), and translation (the RNA sequence is translated into a sequence of amino acids as the protein is formed)
- Coding for Proteins: The transcribed DNA message, or RNA transcript, is used to produce proteins. The information in DNA is not directly converted into proteins, but must first be copied into RNA
Summary: It describes the normal flow of biological information: DNA can be copied to DNA (DNA replication, DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in the mRNA as a template (translation)
Transcription and RNA transcript
Transcription is the process in which a gene’s DNA sequence is copied to make an RNA molecule. This process is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand using a DNA strand as a template. The RNA molecule produced can be messenger RNA (mRNA) or non-coding RNA (ncRNA)
The major steps of transcription are initiation, promoter clearance, elongation, and termination. RNA polymerase binds to a promoter sequence near the beginning of a gene to initiate transcription. Transcription is the first part of the central dogma of molecular biology
The RNA transcript is the product of transcription. It carries the genetic instructions of a gene from the nucleus to the ribosome in the cytoplasm. If the gene that’s transcribed encodes a protein (which many genes do), the RNA molecule will be read to make a protein in a process called translation.
In eukaryotes, RNA molecules must be processed after transcription: they are spliced and have a 5’ cap and poly-A tail put on their ends. Transcription is controlled separately for each gene in your genome
RNA polymerase
RNA polymerase binds to the promoter sequence of DNA near the beginning of the gene and unzips the two DNA strands. This marks initiation
It then synthesizes a complementary RNA strand in the 5 to 3 direction on the template strand. The RNA strand is called the primary transcript and needs to be processed before it can be functional
It interacts with many proteins, in which the proteins help in enhancing the binding specificity of the enzyme, aid in unwinding the double helix, modulate the activity of the enzyme based on the requirements of the cell, and alters the speed of transcription
RNA polymerase is involved in the production of molecules that have a wide range of roles, one of its main functions is to regulate the number and kind of RNA transcripts formed in response to the cell’s requirements
The key enzyme involved in creating an equivalent RNA copy of a DNA sequence. This transcription is the first step leading to gene expression
Elongation and termination
Elongation: the stage where the RNA polymerase moves along the DNA template and synthesizes a complementary RNA strand. In eukaryotes, RNA polymerase II transcribes the major share of genes. During the elongation, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. Transcription elongation occurs in a bubble of unwound DNA, where the RNA polymerase uses one strand of DNA as a template to catalyze the synthesis of a new RNA strand in the 5 to 3 direction
Termination: the stage where the RNA polymerase reaches the end of the gene and releases the newly synthesized RNA molecule. In eukaryotes, RNA polymerases I and II terminate transcription in response to specific termination sequences in either the DNA being transcribed (RNA polymerase I) or in the newly-synthesized RNA (RNA polymerase III). RNA polymerase II terminates transcription at random locations past the end of the gene being transcribed. The newly-synthesized RNA is cleaved at a sequence-specified location and released before transcription terminates
Promoters
A DNA sequence that controls the initiation of transcription of a gene by binding transcription factors and RNA polymerase. The promoter is usually located upstream of the gene and its specific sequence determines how often and under what conditions the gene is transcribed. Promoters are essential for regulating gene expression in response to environmental stimuli or cellular needs
Binds transcription factors that control the initiation of transcription. The promoter region can be short or quite long; the longer it is, the more available space for proteins to bind. To initiate transcription, a transcription factor binds to the TATA box, which causes other transcription factors to subsequently bind to the TATA box
Promoters control the binding of RNA polymerase to DNA
Each gene has its own promoter, and a promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the DNA
TATA box
a DNA sequence that helps initiate transcription. It’s a type of promoter sequence that specifies to other molecules where transcription begins. The TATA box is the binding site of the TATA-binding protein (TBP) and other transcription factors in some eukaryotic genes
It’s recognized by one of the general transcription factors, allowing other transcription factors and eventually RNA polymerase to bind
Found in the core promoter region of genes in archaea and eukaryotes