Chapter 12: How Genes Work
Ribosomes in Translation:
- Composed of 2 subunits. - One is large and one is small. - Each consist of proteins and rRNA. - The 2 subunits bind together only during protein synthesis. - Have 3 binding sites for RNA: the A, P, and E sites, which bind in the order A-P-E.
Genes are made of:
- DNA, a nucleic acid. In Prokaryotes: - Uninterrupted stretch of DNA nucleotides whose transcript is read three nucleotides at a time to make a chain of amino acids. In Eukaryotes: - Genes are fragmented in exons and introns.
The Role of DNA Methylation in Eukaryotes:
- Eukaryotes control the long-term use of genes in a process called cell development.
The Six Stages of Eukaryotic Protein Synthesis:
1) Transcription. 2) RNA Processing. 3) mRNA travels to cytoplasm, binds to ribosome. 4) tRNAs bind to their appropiate amino acids, corresponding to their anticodons. 5) tRNAs bring amino acids to ribosome. 6) mRNA translated to polypeptide.
Transcription is the first step in "gene to protein" outlined in the central dogma. The main enzyme involved is RNA polymerase. Demonstrate your understanding of transcription by providing the template DNA sequence to the gene used by RNA polymerase to produce the mRNA: 5'-AUG ACU AAU GAU AGU CGC UGA-3'
3'-TAC TGA TTA CTA TCA GCG ACT-5'.
Ribosomes:
A cell structure composed of protein and RNA that translates RNA copies of genes into protein.
Ribosomal RNA (rRNA):
A class of RNA molecules found, together with characteristic proteins, in ribosomes; transcribed from the DNA of the nucleolus.
Activator:
A protein that binds to DNA and stimulates transcription of a specific gene.
Repressor:
A protein that suppresses the transcription of a gene.
Enhancers:
A site of regulatory protein binding on the DNA molecule distant from the promoter and start site for a gene's transcription.
Messenger RNA (mRNA):
A type of RNA, synthesized from DNA and attached to ribosomes in the cytoplasm; it specifies the primary structure of a protein. In other words: The RNA transcribed from structural genes; RNA molecules complementary to a portion of one strand of DNA, which are translated by the ribosomes to form protein.
RNA Interference: (AKA: Gene Silencing)
A type of gene silencing in which the mRNA transcript is prevented from being translated; small interfering RNAs (siRNAs) have been found to bind to mRNA and target its degradation prior to its translation. In other words: Introduction of double-stranded RNA into a cell to inhibit gene expression.
Operon:
A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions, like a group of genes operating together.
If lactose is added to their growth medium, bacterial cells that had contained no lactose-metabolizing enzymes abruptly possess them. How does this "enzyme induction" occur?
Activators and repressors work to respond to the environment. When lactose is present, it stimulates the chemical reactions to turn on the genes that produce the enzymes necessary to digest lactose in prokaryotic cells. Being able to respond to different food sources allows the cell to save energy and use its environmental resources most efficiently.
Alternate Splicing:
Building different proteins by combining exons of a gene in different ways
How do enhancers regulate gene expression in eukaryotes?
By using enhancer regions, genes have an increased likelihood to be amplified because of the variety of signals that can increase transcription levels
Exons:
Coding segments of eukaryotic DNA.
Transcription Factors:
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
If an enhancer is located far from a gene, how can it control that gene's transcription?
DNA bending and looping can shorten distances between activators and the initiation complex.
Central Dogma:
DNA → RNA → Protein. The theory that states that, in cells, information only flows from DNA to RNA to proteins.
What four roles does RNA play in gene expression?
Each type of RNA plays a specific role: 1) Messenger RNA (mRNA) is used to make a copy of the DNA during transcription. 2) Then, ribosomal RNA (rRNA) serves to initiate the translation of the mRNA copy into an amino acid sequence. 3) Individual amnion acids are carried to the site of translation via transfer RNA (tRNA). 4) Also, microRNA fine-tune a gene by influencing which mRNA transcripts are translated.
Is protein synthesis more complex in prokaryotes or eukaryotes?
Eukaryotes. (The reason being is eukaryotic cells have a nuclear membrane, making the process more complex. Part of the process takes place within the nucleus, and then the transcript is transferred to the cytoplasm to complete it.)
Why is protein synthesis more complex in eukaryotes?
Eukaryotic cells have a nuclear membrane, making the process more complex. Part of the process takes place within the nucleus, and then the transcript is transferred to the cytoplasm to complete it.
The process of gene expression occurs as:
Genetic transcription and genetic translation, where it is conversion of the information encoded in a gene first into messenger RNA and then to a protein
Cancers are caused by the expression of oncogenes (cancer-causing genes). Recent studies have linked the expression of some oncogenes to a change in chromatin configuration. When this occurs, the oncogene region of the DNA is released from the nucleosome. How would this release from the nucleosome result in the expression of the oncogenes?
If the nucleosome is released from the DNA that contains an oncogene, the RNA polymerase and transcription factors can gain access to the promotor and transcription can occur.
3' poly-A tail:
In eukaryotes, a series of 1-200 adenine residues added to the 3' end of an mRNA; the tail appears to enhance the stability of the mRNA by protecting it from degradation.
Initiation Complex:
In protein translation, a combination of a small ribosomal subunit, an mRNA molecule, and the tRNA charged with the first amino acid coded for by the mRNA; formed at the onset of translation.
How can attacking double-stranded DNA provide a defense against RNA viruses?
It can silence the gene whose sequence is complementary to the double stranded DNA and then stop the transcription process.
Do you think methylated genes would be found in nucleosomes?
Likely yes, since this form of DNA is not intended for replication.
Each amino acid genetic code is complementary to an anticodon on a tRNA molecule. If the codon UCU is read by a tRNA containing the anticodon AGT, would the amino acid added to the growing polypeptide be changed?
No, the amino acid that corresponds to the codon, UCU, is serine. The codon that is complementary to the anticodon AGT is UCA which also codes for serine.
Introns:
Noncoding segments of nucleic acid that lie between coding sequences.
How many different activating enzymes does a cell require?
One activating enzyme per each type of amino acid is needed.
Your body maintains constant internal conditions. Why may prokaryotic gene regulation not be suitable for you?
Prokaryotic gene regulation exploits transient resources of rapidly changing environments; human gene regulation does not need to be so rapidly responsive because of more sophisticated ways of maintaining homeostasis.
Activating Enzymes:
Specific amino acids are attached to tRNA molecules by these enzymes.
Promoter:
Specific region of a gene where RNA polymerase can bind and begin transcription.
Tetracycline is a common antimicrobial drug used to treat many bacterial infections. It works by binding to the A site in the large portion of the prokaryotic ribosome. Discuss how blocking this site would interfere with protein synthesis, which would eventually result in the death of prokaryotic cells.
The "A" site in the large ribosomal subunit is the "attachment" site where amino-acid bearing tRNA molecules enter to be incorporated in a growing polypeptide chain. If the "A" site is blocked, these tRNA molecules cannot bring in amino-acids. If no amino-acids are brought in, the polypeptide chain would cease. When the cell can no longer make proteins essential for growth and reproduction, it will eventually die.
Genetic Code:
The "language" of the genes. The mRNA codons specific for the 20 common amino acids constitute the genetic code.
The chemical direction in which an mRNA chain is assembled during transcription is:
The 5' to 3' direction.
How RNA Interference Works:
The RNA molecules uses synthetic double-stranded RNA molecules matching the sequence of a particular gene to trigger the breakdown of the gene's messenger RNA.
Codons:
The basic unit of the genetic code. A sequence of three adjacent nucleotides in DNA or mRNA that codes for one amino acid or for polypeptide termination. In other words: A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.
RNA Polymerase:
The enzyme that transcribes RNA from DNA. In other words: Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription.
How does an RNA transcript differ in prokaryotes and eukaryotes?
The gene in prokaryotes is an uninterrupted stretch of DNA nucleotides; the transcript then is read three nucleotides at a time to make a chain of amino acids. Eukaryotic genes are fragmented; the DNA nucleotide sequences encoding the amino acid sequence of a polypeptide, called "exons," are interrupted frequently by extraneous nucleotides, called "introns." Therefore, the eukaryotic RNA transcript first contains the extra DNA and later it is excised out with the help of enzymes.
In what order are the sites of a ribosome occupied by a particular amino acid?
The order is A-P-E.
Transcription (Genetics):
The organic process whereby the DNA sequence in a gene is copied into mRNA. In other words: The first stage of gene expression in which the RNA polymerase enzyme synthesizes an mRNA molecule whose sequence is complementary to the DNA.
Gene Expression:
The process in which an RNA copy of each active gene is made, and the RNA copy directs the sequential assembly of a chain of amino acids at a ribosome.
Translation (Genetics):
The process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm. In other words: The second stage of gene expression in which a ribosome assembles a polypeptide, using the mRNA to specify the amino acids.
Anticodon:
The three-nucleotide sequence of a tRNA molecule that is complementary to, and base pairs with, an amino acid-specifying codon in mRNA.
If RNA is not double-stranded, how can microRNA bind to mRNA?
These small RNA fragments bind to any mRNA molecules in the cell that have a complementary sequence.
How do activators and repressors work together to control transcription?
They bind to DNA close to the promoter and either activate or repress the activity of RNA polymerase.
Why is an mRNA chain assembled in only one direction?
Though DNA is double-stranded, its strands are complementary, not identical. Thus, RNA polymerase recognizes a promoter site on one strand, binds at the promoter site, and moves along this strand only.
The goal of transcriptional control in prokaryotes:
To adjust the cell's activities to its immediate environment (to achieve exploitation of transient resources, and respond quickly to changes in their environment).
The three stop codons do not code for:
an amino acid.
Primary RNA transcript:
the original unmodified RNA product corresponding to a transcription unit
Summary of Chapter 12, How Genes Work:
• DNA carried hereditary information that can passed on in the form of genes. • DNA's structure is a uniform double helix with complementary base-pairing (A=T, G=C). • DNA replication occurs in three stages: initiation, elongation, and termination. • DNA replication can make mistakes, leading to changes in the sequence called mutations. • The central dogma is the passage of information from DNA to RNA to protein. • Transcription is the process of creating a mRNA strand from the DNA template strand. • Translation is the process of creating a polypeptide (protein) from the mRNA strand. • Gene expression is the use of genetic information in DNA to produce proteins in the cell. • Understanding how genes work has revolutionized the world and will continue to do so.
