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7: Module 4- Prokaryotes - Biology
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: the plasma membrane, which functions as a barrier for the cell and separates the cell from its environment the cytoplasm, a jelly-like substance inside the cell nucleic acids, the genetic material of the cell and ribosomes, where protein synthesis takes place. Prokaryotes come in various shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilli (spiral-shaped) (Figure 1).
Figure 1. Prokaryotes fall into three basic categories based on their shape, visualized here using scanning electron microscopy: (a) cocci, or spherical (a pair is shown) (b) bacilli, or rod-shaped and (c) spirilli, or spiral-shaped. (credit a: modification of work by Janice Haney Carr, Dr. Richard Facklam, CDC credit c: modification of work by Dr. David Cox scale-bar data from Matt Russell)
- Describe the basic structure of a typical prokaryote
- Describe important differences in structure between Archaea and Bacteria
Antony van Leeuwenhoek improves microscopy
In the years immediately following, other scientists would build on the work of Hooke, including Antony van Leeuwenhoek (1632 – 1723), a cloth merchant in Delft, Nederland. Van Leeuwenhoek was not a scientist by formal training, but he was an industrious and curious individual who took great joy in observing the world around him (Anderson, 2009). While working in his haberdashery in the 1670s, van Leeuwenhoek began to experiment with glass-blowing and the construction of microscopes (Figure 2). Using the designs described by Hooke in Micrographia, van Leeuwenhoek built his own microscopes by hand, fabricating every element from the highly-refined lens to the screws used to hold the instrument together (Anderson, 2009).
Figure 2: van Leeuwenhoek's simple microscope. On the brass plate is a small magnifying lens mounted and a sharp point that would hold the specimen. Turning the screws would adjust the position and focus.
During his lifetime, van Leeuwenhoek constructed hundreds of microscopes and lenses by hand, each one unique. It was with these microscopes and improved lenses that he began to study the world around him and share these observations with institutions like the English Royal Society. One of his first important observations came in August 1674, when he looked at water samples from Berkelse Meer, a lake two miles outside of Delft. In a letter to Henry Oldenburg that September, and published in Philosophical Transactions of the Royal Society, van Leeuwenhoek noted:
I took up some of it [the water] in a Glass-vessel which having viewed the next day, I found moving in it several Earthy particles, and some green streaks, spirally ranged, . among all of which there crawled abundance of little animals some of which were roundish those that were somewhat bigger than others were of an Oval figure: On these latter I saw two legs near the head and two little fins on the other end of their body…. The motion of most of them in the water was so swift, and so various, upwards, downwards, and round about, that I confess I could not but wonder at it. I judge, that some of these little creatures were above a thousand times smaller than the smallest ones, which I have hitherto seen.
What van Leeuwenhoek was seeing, we can now presume, were some of the smallest forms of life: protozoa, rotifers, ciliates, and phytoplankton. Van Leeuwenhoek’s descriptions are among the first to identify the unique features of these different microscopic organisms and was the beginning of the discipline we now call microbiology – the study of microscopic organisms.
Antony van Leeuwenhoek's work led to the field of
In the years immediately following van Leeuwenhoek’s discovery of microorganisms in the Berkelse Meer water, his studies unearthed some very important cellular distinctions. Among them was the discovery of single-celled organisms (Figure 3) and structures existing within the walls of Hooke’s originally-thought-empty plant cells (large organelles called vacuoles).
Figure 3: Leeuwenhoek's drawing of protozoa.
Plants only have an innate immune response to protect themselves from pathogens.
An example is the hypersensitive response which detects pathogens and kills the infected cells through apoptosis.
Physical defences such as trichomes protect the plant from predation by insects or large herbivores.
Trichomes are spines found on plants such as the Gympie Gympie Tree of Queensland.
Australian stinging nettle or Gympie Gympie tree, Dendrocnide moroides.
Leaf dropping is another mechanism to eliminate the pathogen.
Leaf dropping is carried out in three steps:
- Nutrients are resorbed from the leaf.
- A protective layer of lignin forms at the site of leaf detachment.
- Cells at the detachment site are digested by enzymes to cause leaf dropping.
Plants can produce specific defensive chemicals such as caffeine which is toxic to fungi and insects.
If a pathogen defeats the plant’s physical defences and enters the cell, it can be detected by Pattern Recognition Receptors (PRR).
This triggers an immune response leading to thickening of the cell wall to prevent further spread.
In the next topic we will look at how animal cells undergo physical and chemical changes in response to pathogens.
Gene expression: DNA to protein
The Central Dogma
Francis Crick coined the phase “the Central Dogma” to describe the flow of information from nucleic acid to protein. Information encoded in DNA is transcribed to RNA, and RNA is translated to a linear sequence of amino acids in protein. Although information can flow reversibly between DNA and RNA via transcription and reverse transcription, no mechanism has yet been found for alterations in protein amino acid sequence to somehow effect a corresponding change in the RNA or DNA.
This video gives a highly simplified overview of the central dogma of molecular biology:
And this video provides an animated overview of gene expression in a eukaryotic cell:
Transcription: DNA to RNA
Transcription is the process of using DNA as a template to make an RNA molecule:
- The enzyme RNA polymerase reads the template strand of DNA and synthesizes an RNA molecule whose bases are complementary to the template strand of DNA.
- RNA is synthesized 5′ –> 3′ (same direction as DNA synthesis) RNA polymerase reads the template strand of DNA 3′ –> 5′.
- The sequence of bases in RNA is the same as the sequence of bases in the “coding” strand of DNA, except that RNA has uracil (U) instead of thymine (T).
- RNA polymerases in both prokaryotes and eukaryotes depend on DNA-binding proteins, called transcription factors, to bind to special sequence motifs in the DNA called promoters, to recognize where genes start.
- Transcription factors recruit RNA polymerase to bind to the promoter sequence and begin transcription just “downstream” of the promoter.
This video gives a simplified overview of transcription. The narrator makes a mistake at 3:45 (which he later catches and corrects!) which serves as a really important reminder of one of the major differences between DNA and RNA.
See a more advanced molecular animation of transcription, with narration, here: https://www.dnalc.org/resources/3d/13-transcription-advanced.html
Translation: RNA to Protein
Translation is the process of using an mRNA molecule as a template to make a protein:
Translating a sequence of bases in the RNA to a sequence of amino acids in proteins requires 3 major components:
- messenger RNA (mRNA): mRNAs are transcribed from protein-coding genes. (There are other types of genes which do not encode proteins, such as genes encoding rRNAs and tRNAs.)
- Ribosomes:Ribosomes are large assemblies of ribosomal RNA molecules (rRNAs) and dozens of proteins. When they are not working, they fall apart into the small subunit and large subunit, each consisting of a rRNA and numerous proteins. When the structures of prokaryotic ribosomes were determined at high resolution, researchers were astonished to discover that the catalytic site for the peptidyl-transfer reaction (attaching new amino acids to the growing polypeptide chain) consists entirely of rRNA. Thus the ribosome is actually an immense ribozyme, or a catalytic RNA molecule stabilized by numerous proteins, rather than an enzyme.
- transfer RNAs (tRNAs) that are “charged” with their corresponding amino acids (meaning the tRNAs are attached to/carrying their corresponding amino acids). tRNAs match the amino acid to the codon in the mRNA. The bases in the anticodon loop are complementary to the bases in an mRNA codon. The 3′ end of the tRNA has a high-energy bond to the appropriate amino acid. Cells have a family of enzymes, called amino-acyl tRNA synthetases, that recognize the various tRNAs and “charge” them by attaching the correct amino acid.
Secondary structure of phenylalanyl-tRNA from yeast, from Wikipedia
Tertiary structure of tRNA, from Wikipedia. The anticodon loop (in gray) base-pairs with the codon in the mRNA in anti-parallel orientation. The amino acid attachment site (yellow) is the location where the tRNA is covalently bonded to its amino acid.
Translation begins near the 5′ end of the mRNA, with the ribosomal small subunit and a special initiator tRNA carrying the amino acid methionine. In most cases, translation begins at the AUG triplet closest to the 5′ end of the mRNA. In eukaryotes, the small subunit of the ribosome typically just “scans” along from the 5′ end of the mRNA until it finds the first AUG codon. In prokaryotes, there is typically a specific sequence that the ribosome binds to, which “positions” the ribosome at the starting AUG. In either case, the large ribosomal subunit then docks and translation begins, always starting with an AUG codon (methionine) in both prokaryotes and eukaryotes. The ribosome moves along the mRNA 3 bases at a time, from the 5′ to the 3′ direction, and new tRNAs whose anti-codons are complementary to the mRNA codons arrive with their corresponding amino acids. A peptide bond forms to join the amino acid to the carboxyl end of the growing polypeptide chain. The ribosome moves another 3 bases, and the empty tRNA is ejected to make room for a new amino-acyl tRNA.
Image modified from “Translation: Figure 3,” by OpenStax College, Biology (CC BY 4.0).
The polypeptide chain made by the ribosome also has directionality one end has a free amino group and the other end of the chain has a free carboxyl group. These are called the N-terminus and the C-terminus, respectively. New amino acids are added only to a free carboxyl end, so polypeptide chains grow from the N-terminus to the C-terminus.
This video gives a solid overview of translation. It is a little longer than the typical videos we use on this site, but it does a really nice job of breaking down step-by-step what happens during translation:
Watch a much shorter molecular animation of translation here:
The Genetic Code
The universal genetic code. AUG (methionine, highlighted green) is the “Start” codon. The three codons labeled “Stop” in red are “nonsense” codons that signal termination of translation. From http://biology.kenyon.edu/courses/biol114/Chap05/Chapter05.html
This genetic code is universally used by all living organisms, whether Archaea, Bacteria or Eukarya, with only minor modifications in the mitochondria of a relatively few species. If you do the math, you can see that there are 64 possible codons (4^3), but we know that there are only 20 amino acids. Thus the code is “degenerate,” because the same amino acid can be specified by 2, 3, 4 or 6 different codons. For example, glycine can be specified by codons GGU, GGC, GGA, and GGG. Methionine is unusual in that it is specified only by a single codon: AUG. (Tryptophan is the only other amino acid specified by a single codon.)
Mutations can have vastly different effects depending on where they occur in a gene or in a codon
If we consider just single nucleotide changes (substitutions, deletions or insertions of single bases), these can have very different consequences depending on whether they occur in the gene.
Often a DNA base substitution will have no effect if they change the 3rd base in the codon, due to the degenerate nature of the genetic code. For example, changing GAG to GAA has no effect on the protein because both codons specify alanine. Such “silent” mutations are called “synonymous” mutations.
Other base substitutions in the first or 2nd position will cause amino acid changes these are “nonsynonymous” mutations, and also mis-sense mutations.
Even among nonsynonymous mutations, the exact amino acid change matters. A change of one hydrophobic amino acid to another hydrophobic amino acid will be less disruptive to the structure of the protein than a change of a hydrophobic amino acid to a polar or charged amino acid. Finally, some parts of a protein are more important than others, such as the catalytic site of enzymes, or sites that bind other proteins, DNA, or regulatory molecules.
Some mutations create a new stop codon (UAA, UAG, or UGA). These are called “nonsense” mutations and cause truncated polypeptides to be made.
Insertions or deletions (“indels”) of single nucleotides cause a change in the reading of all downstream codons they are shifted by one base. Such “frameshift” mutations will alter most or all amino acids downstream (towards the 3′ end of the mRNA, towards the C-terminus of the protein) of the mutation.
Differences between prokaryotes and eukaryotes
Much of what is discussed above was originally discovered in bacteria, and then found to be true of archaea and eukaryotes as well many of the core features of molecular biology are evolutionarily conserved. However, there are a few key differences as outlined below.
Prokaryotes: transcription and translation are coupled
In prokaryotic cells, ribosomes begin to translate even while the mRNA is still being transcribed. DNA, RNA polymerase, and ribosomes are all in the same location. This coupled transcription and translation can occur because prokaryotes have no nucleus. (In eukaryotes, the nucleus separates the transcription machinery from the translation machinery.)
Eukaryotes: transcription and translation are separated in space and time, and nuclear pre-mRNA undergoes processing to become mature mRNA
In eukaryotes transcription occurs in the nucleus, whereas translation occurs outside the nucleus, in the cytoplasm by free cytoplasmic ribosomes or by ribosomes docked to the ER.
The RNA transcribed from a protein-coding gene in the nucleus is called the pre-mRNA. Pre-mRNA has to undergo at least two, and usually 3, processing steps before they can be exported to the cytoplasm as mature mRNA. These are, in order:
- The 5′ end of the pre-mRNA is modified by the covalent attachment of a 7-methylG nucleotide, called the 5′-cap. The 5′ cap is required for eukaryotic ribosomes to initiate translation.
- The majority of eukaryotic genes contain sequences which do not actually code for protein. These sequences are called introns (“intervening” sequences), and they “interrupt” the protein coding sequences, which are called exons (“expressed” sequences) in the gene. These non-protein coding intron sequences are removed by RNA splicing, leaving just the protein-coding exons in the final mRNA.
- The 3- end of the pre-mRNA is modified by the addition of hundreds of adenine nucleotides, called the polyA tail. The polyA tail is important for nuclear export, mRNA stability, and translation.
All of these processing steps actually happen while the mRNA is being transcribed that is, they occur co-transcriptionally. So in reality, a full-length “pre-mRNA” never actually exists.
Eukaryotic pre-mRNAs are processed in the nucleus by adding a 5′ cap, 3′ polyA tail, and removal of introns via RNA splicing to create a mature mRNA consisting only of exons, ready for export to the cytoplasm for translation. From http://www.biology.arizona.edu/molecular_bio/problem_sets/mol_genetics_of_eukaryotes/03t.html
This video gives a nice quick overview of these differences between prokaryotes and eukaryotes:
Dr. Choi’s video lecture on this topic, in one 32-min chunk:
Test your knowledge with these questions & problems: B1510_module4-6_DNA_to_protein_questions