Chapter 13: RNA and Protein Synthesis

13.1 RNA

The Role of RNA

• Ribonucleic acid (RNA) is a single-stranded nucleic acid that contains the sugar ribose

• @@There are three main differences between RNA and DNA@@

  • The sugar in RNA is ribose instead of deoxyribose
  • RNA is usually single-stranded and not double-stranded
  • RNA contains uracil in place of thymine

• Genes are made of instructions coded into DNA that tell cells how to build proteins

  • The first step in decoding these instructions is to copy part of the base sequence from DNA into RNA
  • RNA then uses these instructions to direct the making of proteins, which help to determine an organism’s characteristics

• @@The three main types of RNA are messenger RNA, ribosomal RNA, and transfer RNA@@

  • Messenger RNA carries instructions for making proteins from the nucleus to ribosomes in the cytoplasm
  • Ribosomal RNA forms an important part of both subunits of the ribosome
  • Transfer RNA carries amino acids to the ribosome and matches them to the coded mRNA message

RNA Synthesis

• Most of the work of making RNA takes place during transcription, the synthesis of an RNA molecule from a DNA template, or pattern
  • The order of the RNA bases complements the base sequences of the DNA
• In eukaryotes, RNA is made in the cell’s nucleus, and then it moves to the cytoplasm to help make proteins
• During transcription, the enzyme RNA polymerase uses one strand of DNA as a template to put together nucleotides to make a strand of RNA
  • The enzyme binds only to promoters, regions of DNA that have specific base sequences
  • Promoters are signals in the DNA that show RNA polymerase exactly where to begin making RNA
• In RNA editing, bits and pieces called introns are cut out and discarded from these RNAs; the remaining pieces, called exons, are then spliced back together

13.2 Ribosomes and Protein Synthesis

The Genetic Code

• The genetic code is a code for making proteins; @@it is a collection of codons of mRNA, each of which directs the incorporation of a particular amino acid into a protein during protein synthesis@@
  • The genetic code is read three “letters” at a time
  • Each “word” is three bases long and corresponds to a single amino acid
• Proteins are made of long chains of amino acids called polypeptides
  • Up to 20 different amino acids are found in polypeptides
• The shape and function of a protein are determined by its amino acids and their sequence
  • RNA contains four different bases: adenine (A), cytosine (C), guanine (G), and uracil (U), which are like the letters of a language called the genetic code
  • Each word in the genetic code is three “letters,” or three bases; each three-base set is called a  codon that specifies one amino acid
• There are 64 possible three-base codons in the genetic code, though most amino acids can be specified by more than one codon
• Special codons tell the cell where to start and stop translating RNA
  • The codon AUG acts as the “start” codon for protein synthesis
  • Translation continues until one of three different “stop” codons is reached; then, translation stops and the polypeptide is complete

Translation

• Translation is a process by which the sequence of bases of an mRNA is converted into the sequence of amino acids of a protein; it is the decoding of an mRNA message into a protein

• In eukaryotes, transcription occurs in the cell’s nucleus

• After transcription, mRNA leaves the nucleus, and translation takes place in the cytoplasm; the figure below shows this process:

  

  

  

• An anticodon is a group of three bases on a tRNA molecule that are complementary to the three bases of a codon of mRNA

• @@All three kinds of RNA are put to work in the ribosome during translation@@

  • The mRNA molecule carries the coded message that directs the process
  • The tRNA molecules bring the correct amino acid for each codon on the mRNA
  • The rRNA and many proteins make up the ribosomes

The Molecular Basis for Heredity

• Basically, proteins are tiny tools, each one designed to build or run a part of a living cell
• Molecular biology tries to explain living organisms by studying them at the molecular level; it uses molecules like DNA and RNA as tools to understand living things
  • The central dogma of molecular biology is that information is transferred from DNA to RNA to protein
  • Though there are many exceptions to this “dogma,” it is a useful rule that helps to explain how genes work
• Gene expression is the way DNA, RNA, and proteins are involved in putting genetic information into action in living cells

13.3 Mutations

Types of Mutations

• Sometimes cells make mistakes in copying their own DNA by inserting the wrong base or skipping a base as a strand is put together

  • These variations are called mutations, or, changes in genetic information that can be inherited

• @@All mutations fall into two basic categories@@

  • Mutations that make changes in a single gene are known as gene mutations
  • Mutations that make changes in whole chromosomes are known as chromosomal mutations

• @@Gene mutations that involve changes in one or a few nucleotides are known as point mutations@@

  • Point mutations happen at a single point in the DNA sequence and include substitutions, insertions, and deletions; they usually happen during replication
  • In a substitution, one base is changed to a different base
    • Substitutions usually affect a single amino acid, and sometimes they have no effect at all
  • An insertion adds a new base to the DNA sequence, and a deletion removes a base from the DNA sequence
    • The effects of these changes can be dramatic; after a change, the sets shift in every codon that comes after the mutation
    • Insertions and deletions are also called frameshift mutations because they shift the “reading frame” of the genetic code; this change can alter a protein so much that it cannot do its job

  

• @@A chromosomal mutation is a change in the number or structure of chromosomes@@

  • There are four types of chromosomal mutations: deletion, duplication, inversion, and translocation
  • Deletion happens when part or all of a chromosome is lost
  • Duplication happens when an extra copy of all or part of a chromosome is made
  • Inversion happens when parts of a chromosome change direction
  • Translocation happens when part of one chromosome breaks off and attaches to another one

  

Effects of Mutations

• Some mutations are caused by mutagens, chemical or physical agents in the environment
  • Chemical mutagens include some pesticides, tobacco smoke, and pollutants
  • Physical mutagens include X-rays and ultraviolet light
• Sometimes the cell can repair the DNA, but when the cell cannot fix the DNA, the sequence changes become permanent
• @@Mutations can help or harm organisms, though most mutations have little or no effect on genes@@
  • Some of the changes made by mutations can help an organism or species; these mutations make genes with functions that are useful to organisms in different environments
  • For example, the condition in which an organism has extra sets of chromosomes is called polyploidy; polyploid plants are often larger and stronger than diploid plants
  • Some of the most harmful mutations make big changes in protein shape or gene activity; the proteins made by these mutations can get in the way of biological activities
• @@Mutations are important because they promote genetic variation@@

13.4 Gene Regulation and Expression

Prokaryotic Gene Regulation

• @@Most bacteria transcribe only the genes they need at any one time@@

  • For example, some genes produce enzymes used to digest certain types of food molecules; if these food molecules are not present, there is no need for these enzymes

• One way bacteria control making proteins is through operons; an operon is a group of adjacent genes that share a common operator and promoter and are transcribed into a single mRNA

  • For example, in the case of the lac operon, when lactose is not present, the repressor protein binds to the operator, blocking RNA polymerase from transcribing the lac genes
  • When lactose is present, it binds to the repressor, causing the release of the repressor, which then moves away from the operator; transcription can then take place

• On one side of the operon’s three genes are two control regions

  • The first is a promoter (P), the site where RNA polymerase can bind to begin transcription
  • The other region is called the operator (O), a short DNA region, adjacent to the promoter of a prokaryotic operon, that binds repressor proteins responsible for controlling the rate of transcription of the operon

  

Eukaryotic Gene Regulation

• Transcription factors control the expression of eukaryotic genes by binding DNA sequences in regulatory regions

  

• Complex gene regulation is what makes specialization possible

• Using a silencing complex to block gene expression is called RNA interference (RNAi)

  • MicroRNAs attach to mRNA molecules and stop them from passing on their protein-making instructions

  

• The discovery of RNAi has made it possible for researchers to switch genes on and off by inserting double-stranded RNA into cells

  • RNAi technology may also provide a way for medical scientists to turn off genes from viruses and cancer cells; RNAi may provide new ways to treat, and maybe even cure, diseases

Genetic Control of Development

• Controlling gene expression helps shape the way a multicellular organism develops
  • This kind of cell change and development is called cell differentiation
• Homeotic genes are a class of regulatory genes that determine the identity of body parts and regions in an animal embryo
  • Mutations in these genes can transform one body part into another
• All homeotic genes share a similar DNA sequence, called the homeobox sequence
  • Homeobox genes code for transcription factors that turn on other genes
  • These genes are important in cell differentiation, as they control features such as the presence of wings or legs
  • Other animals, including humans, also have Hox genes; so, nearly all animals share the same basic tools for building the different parts of the body

Environmental Influences

• @@In all kinds of organisms, environmental factors like temperature can change gene expression@@
• Metamorphosis is another example of how organisms can alter gene expression in response to environmental changes
  • Metamorphosis involves a series of changes from one life stage to another and is usually regulated by factors inside and outside of the body
  • Environmental changes are translated into hormonal changes
  • The hormones act to regulate gene expression, which controls the speed of metamorphosis
  • Temperature and population size can also affect the speed of metamorphosis
• @@Master control genes are like switches that trigger particular patterns of development and differentiation in cells and tissues@@