Darwin's Findings

Biology Index

Where are we going with this? The information on this page should increase understanding related to this standard:  Identify chronological patterns of change and communicate that biological evolution is supported by multiple lines of empirical evidence that identify similarities inherited from a common ancestor (homologies).

Article includes ideas, images, and content from Troy Smigielski (2022-01)

Darwin's Findings

(Something was lost? What? What was it?)

Source, 2022-02

Charles Darwin was an English naturalist in the middle of the 1800s who became known as the “Father of Evolution.” 

Much of his work was based on what he learned while in the Galapagos Islands. Darwin noticed how finches on the islands had different beak types, and he described these as adaptations.

An adaptation is any inherited characteristic that increases an organism’s fitness in its environment. Adaptations can come from mutations in DNA or in response to the environment of the animal.

Darwin claimed that the generations of adaptations seen within the different species of finches were present because the finches had evolved into their observed characteristics. He cited how they accessed food as the environmental condition that had led to the adaptations that eventually evolved the birds into different species.

Evolution is the change in the characteristics of a species (or worldview, applications of technology, etc.) over several generations, and it relies on natural selection.

There are two kinds of evolution.

Macroevolution is the idea that all species can trace back to common ancestors. The idea is that adaptation within a species over time eventually leads to separate species that are both (or all) similar to the ancestor.

Microevolution is the process whereby adaptations over time lead to distinct changes within the species. Many examples of microevolution can be cited. As one example, within humans, the average height of eighteen year olds has increased over the last century. Access to nutrition has been pointed to as an environmental opportunity that humans have taken advantage of leading to the change within the species.

So, to summarize, macroevolution is the idea that species change into different species as generations of adaptations take place. Microevolution is the process whereby a species is altered (but remains the same species) by generations of adaptations.

At this point, it's probably worthwhile to define species. Within a taxonomic system, a species is considered to be the level above which reproduction is not possible. Except for a few exceptions wherein hybridization can occur, one species cannot reproduce with another species.

Within the bounds of that definition, Darwin's finches might be better seen through the lens of microevolution. Not only can they reproduce, they do. 

"A new article in Nature by Galápagos finch researchers Peter and Rosemary Grant, “Speciation undone,” confirms [that] Galápagos finch species are capable of interbreeding — but adds a new twist: they’re interbreeding so much that in multiple cases, two “species” may be fusing back into one species" (Source, 2022-02).

Regardless of how the process is defined, Darwin's finches clearly grouped according to how they adapted to (beak shape) the access to and restriction from resources in their environment. 

So, whereas an adaptation is any inherited characteristic that increases an organism’s fitness in its environment and adaptations can come from mutations in DNA or in response to the environment of the animal, we can see in all of creation how different adaptations have evolved to increase the ability of a species to thrive within its environment.

What adaptation did this little guy gain?

Adaptations occur as a result of something. When a resource needed by the organism becomes availalbe in greater quantities, some adaptations take advantage of the change. When something ceases to become readily available, some organisism will adapt in response to the change.

What color mice have the higher fitness?

Adaptations normally increase an organism’s fitness.

What is “fitness”?

Fitness describes the ability of an organism to survive and reproduce in its environment. It is a way to describe how well an organism can thrive.

Fitness is sometimes measured by the number of offspring an organism has.

Would a lion in South Africa with one baby or a lion in Kenya with ten babies show better fitness?

 

So, there is a mechanism within nature that leads to passing on traits that increase fitness. Natural selection is the survival of the fittest; this means that the best fit organisms are the ones that survive and reproduce. The less fit members of the population (possibly) die and do not produce. 

Think about it… if fitness leads to survival and if you have to survive to reproduce, less fit members of a population will not live long enough to reproduce, so the less fit traits will not get passed along!

Darwin was not the first person to use this term (Natural Selection).

Which one of these moths would most likely survive and reproduce in an environment with many trees?

Over time, what would you expect to happen to the green moths? The camouflaged moths?

Note a few things about natural selection…

Natural selection:

• Does not explain the origin of favored traits
  
  
• Takes place outside of human control
  
  
• Leads to an overall increase in a species’ fitness

Natural selection will only occur under specific conditions.

In order for natural selection to occur:

• Genetic variation must be present in a population.
  
  
• Reproduction must occur.
  
  
• Successful genes must reproduce (heredity).
  
  
• There must be a struggle to survive.

So, the if running faster than a lion helps increase fitness, and if some of the antelope slow (yellow to the right) they will not live to pass on their trait. The fast antelope (red to the right) will, and will reproduce, passing their "fastness" to the next generation. 

As adaptations occur, one of two things will happen.

A good adaptation will lead to a high level of fitness, which leads to natural selection.

Remember this guy?

What adaptation did this little guy gain?

His adaptation to blend in increases his ability to survive, and this trait will be passed on as a favorable trait leading to natural selection over many generations.

Snowshoe hare adaptation to change color as temperature gets colder.

The image above shows the progression of the change in coat color exhibited by the snowshoe hare as temperatures get colder.

A good adaptation will give a high level of fitness, which leads to natural selection.

Behaviors Can Also Adapt

Sharks have adapted the behavior to follow ships and boats.

Sharks have adapted the behavior to follow ships for two main reasons:

1. People often throw food/waste overboard.
   
   
2. During the slave trade, sick and/or deceased slaves were tossed overboard. This caused sharks to adapt their behavior to follow ships for food.

So, Back to Darwin…

From his findings, Darwin said that evolution happens through the principle of descent with modification. This says that organisms pass traits to their offspring that often include changes that happened due to mutations or environmental pressures and opportunities.

According to this principle, all species descended from one original species. The species from which all other species derived from is called the common ancestor.

Charles Darwin and His Influences

Biology Index

Where are we going with this? The information on this page should increase understanding related to this standard:  Identify chronological patterns of change and communicate that biological evolution is supported by multiple lines of empirical evidence that identify similarities inherited from a common ancestor (homologies).

Article includes ideas, images, and content from Troy Smigielski (2022-01)

Charles Darwin and His Influences

(This guy… I've heard of him!)

Evolution is the change in the characteristics of a species over several generations, and it relies on natural selection.

Charles Darwin was an English naturalist who became known as the “Father of Evolution.” As with most major figures, he had many people influence his thoughts. Darwin's work took place in the middle of the 1800s.

Two scientists who greatly influenced Darwin by helping him realize the apparent age of the Earth were Hutton and Lyell.

James Hutton proposed that rocks, mountains, and other formations change very slowly over time. This led him to believe that Earth must be more than a few thousand years old.

So… he got famous for saying rocks are old… Hmm…

Hutton's observations and his conclusion departed from the idea that all of the world was only a few thousand years old. 

Another of Darwin's influences, Charles Lyell argued that the shape of the Earth’s crust was the result of small changes over millions of years. (rivers and soil)

Lyell's views were congruent with those of Hutton, and they yielded more fodder for Darwin's ideas. Meanwhile, other scientists were taking not of other things.

Jean Baptiste Lamarck was one of the first scientists to recognize that living things have changed over time.

Lamarck also proposed that the selective use or disuse of certain organs caused organisms to acquire or lose certain traits over time. Organs that are very reduced in size or have evolved to have no use are called vestigial organs.

What are some organs humans have gained or lost function for over time?

The Appendix

Wisdom Teeth

Apparent “Tail” During Embryo Development

Another scientist, Thomas Malthus, studied population growth. He found that the human birth rate exceeded the death rate. If this continued, humans may run out of resources. Since resources, if renewable in the first place, are produced at a constant rate, if the number of resource consumers (population) increases, then the access to resources is limited.

If resources are limited, there will be competition. This could change a population over time. If the population relied on the resource, exhausting it would have in impact on the members of the population. 

This is observed frequently in numerous ecosystems as populations grow or shrink according available resources. Wildlife managers attend to this relationship regularly.

During the 2020-22 pandemic, as more people either got COVID-19 or were vaccinated, the resources for COVID-19 became limited. So, the original strain had to either change or die off.

Before Darwin's publication in 1859, Alfred Russel Wallace published an essay covering the same topic and ideas that Darwin was interested in. This gave Darwin an incentive to publish his own work.

One of Darwin’s most significant works started on a voyage he took in the 1830s.

On this trip, he took a famous voyage around the world on the HMS Beagle to study the diversity of life.

From start to finish, this trip lasted for about 5 years. During his trip, he kept notes in a notebook. Some of his most influential notes came during his visit to the Galapagos Islands.

On the Galapagos Islands, Darwin noted that similar species of finches had different sizes and shapes of their beaks.

Why would these similar birds have different sized beaks?

To accommodate for different environmental factors and types of food based on where they lived.

So… Darwin gets back to England, and he realizes that Wallace has published work similar to what he just found.

Darwin published his most interesting notes in his book titled On the Origin of Species. This book detailed key terms for natural selection and contained his “evidence” for evolution.

Common Misconception: Darwin DID NOT argue that humans evolved from apes in this book, nor did he ever argue that.

Introducing Evolution

Biology Index

Where are we going with this? The information on this page should increase understanding related to this standard:  Identify chronological patterns of change and communicate that biological evolution is supported by multiple lines of empirical evidence that identify similarities inherited from a common ancestor (homologies).

Article includes ideas, images, and content from Troy Smigielski (2022-01)

Introducing Evolution

(This is a change…)

Evolution is the change in the characteristics of a species over several generations, and it relies on natural selection.

Evolution is a thing, not to be confused with the theory of evolution (which is also a thing). Evolution occurs within a species. And also within technology, for that matter.

If you stop for a moment, you can think of many things that have changed through generations, just within the last ten or so years.

By 2022, video game consoles had been through quite a few evolutions! Early consoles (e.g. Atari) relied on ROM chips inside cartridges and the controllers consisted of a joystick and ONE button.

Yeah… that's right!

Compared to the consoles of 2022, it was extremely elemental.

Within the context of biology, evolution is very notable, as well. 

For instance, the average height of humans has changed over the years.

Source, 2022

Why Do Things Evolve?

Many changes are the result of changes in the environment, access to nutrition, and various other factors influencing development.

Within a species or with regard to a concept or design of some object, adaptations to changes in what is present or what is not present lead to evolution. 

For instance, the automobile has evolved from the Benz's powered buggy, to the Stanley Steamer, to gas and diesel power to hybrids, and is moving toward more and more electric powered cars as of 2022.

The increase in production of gas and diesel led to the evolution to the cars of the late 20th Century. But, as the 21st Century progressed, the increase in problems related to carbon emissions and the decrease in access to fossil fuel sources pressured the "species" of automobile to "adapt" into electric utilization.

This, evolution can be thought of as sort of a push-me-pull-me system.

As access to a resource increases, an organism is pulled toward taking advantage of it. It will adapt to maximize into the available resource. The evolution of video games reflects this. As CPU and GPU

Source Google Images

power increased, the game systems adapted to incorporate those faster, more reliable components. Gone are the days when an adapter connected your game to the antenna inputs of a TV and have been replaced by HDMI connections!

If access to a resource decreases, the organism must also adapt. It can be thought of as the lack of resource pushing the organism into a change.

When habitat disappears, wild animals must migrate, and at times, it requires them to overcome innate fears of humans. Many suburban areas in the united states now is witness to populations of deer that have ceased being afraid to be close to humans. 

This generational adaptation opens up access to foraging. Deer too afraid would eventually be replaced by deer brave enough to venture into the neighborhood. 

Arguably, this stretches the idea of evolution; however, it illustrates how the members of the population that adapt will thrive while those that don't adapt will suffer. In the long run, the survivors within the species (or within a given population of the species) will be the ones able to adapt to the changing access to resources. 

In sum, evolution of things (species, technologies, worldviews, etc.) occurs when changes with regard to what is available or possible lead to adaptations which increase the ability of the thing to thrive.

Going back to video game systems, had one console refused to update graphics and move on to HDMI connections, it would not have been able to "thrive" in the market. Meanwhile, the games that took advantage of the new possibilities—the games that evolved into the new technologies would thrive. 

It is worthwhile repeating something from above: evolution is not the same as the theory of evolution. 

It is important to realize that the theory of evolution is a theory, not a fact. A theory is a well-supported explanation of something that has occurred in the natural world, and it attempts to explain how or why something happens. A theory is neither undoubtedly true nor false.

With regard to the theory of evolution, who is the major figure in the origins of the topic?

Did you say Charles Darwin?

______________________

It is noteworthy that the topic of evolution does not exist apart from controversy. Within this collection of topics, the intent is to present the prevailing, related body of knowledge and history, as that information is considered to be integral to the field of biology.

Protein Synthesis: Translation and Mutation

Biology Index

Where are we going with this? The information on this page should increase understanding related to this standard:  Demonstrate how DNA sequence information is decoded through transcriptional and translational processes within the cell in order to synthesize proteins. Examine the relationship of structure and function of various types of RNA and the importance of this relationship in these processes.

Article includes ideas, images, and content from Troy Smigielski (2022-01)

Protein Synthesis: Translation and Mutation

(So, this seems like a thing…)

The goal of protein synthesis is to make a protein. In other places, we have discussed that proteins do a wide variety of functions in the body and/or are expressed as a trait. We have also explored how the protein synthesis process begins in the nucleus of a cell with the transcription process.

But, let's start with a quick review…

Okay, thanks!

In the nucleus of a cell, the first thing that happens is that the DNA elongates and opens up to make room for the RNA nucleotides to come in. The DNA is composed of a coding strand (which carries the code the mRNA will need to make the proteins) and a template strand made up of the complementary nucleotides found in the coding strand…

You know…

So… 

To summarize:

1. Transcription is the step in protein synthesis where DNA makes mRNA.

2. This process takes place in the nucleus.

3. After transcription, the cell has a long strand of mRNA that serves as a messenger between the nucleus (DNA) and the ribosome (protein).

4. But, before translation, the cell edits the mRNA sequence.

4a. Introns are the sequences that were cut out. (The invaders, intruders, the invasive code…)

4b. Exons are the sequences that were left in. (The expected code that will be expressed in the protein.)

5. When the strand has been edited, the cell splits up the bases into groups of three.

6. Each group of three bases is called a codon.

7. Each codon codes for an individual amino acid.

7a. When these are put together (in a specific order), they make up a specific protein.

That's pretty much it! But… Let's look at it again with pictures and more words! 

After transcription, it is time to begin the process called translation. 

You can think of it this way… in transcription, the DNA code is copied—transcribed. Then, the code has to be translated from the letters (A, U, C, and G) into a specific sequence of amino acids.

Okay… at the end of transcription, the cell has an edited strand of mRNA. Translation is the step that takes the mRNA code and turns it into a protein.

Translation occurs at the ribosome. (Sometimes, you'll see it described as "on" the ribosome.)

Wazzat?

1. mRNA travels to the ribosome to wait for tRNA.
2. tRNA transfers the anticodon and the appropriate amino acid to the mRNA sequence.
3. Amino acids are joined together with peptide bonds by the ribosome to make a protein.
   (Amino acids make up a protein)

tRNA acts as a molecular “bridge” that connects mRNA codons to the appropriate amino acid. One end has an anticodon and the other has the matching amino acid.

An anticodon is the complementary codon of the original mRNA codon. It is used to match up to the correct part of the sequence. Anticodons are like placeholders that allow tRNA to bind to the mRNA.

Hold on… What?

The mRNA is the important sequence that codes for the amino acid. It is the RNA version of the DNA coding strand. The tRNA has one job: to transfer the appropriate amino acid (that the mRNA coded for) to the ribosome. The ribosome then puts those amino acids together and creates a protein.

Hmm… could you be more specific?

Since the mRNA has a specific sequence of codons, then tRNA MUST line up in a specific sequence dragging their specific amino acid along with them. The result is that the amino acids line up in a specific sequence. And… that specific sequence determines which protein is made.

Woo… how about another picture?

Mutations

Do you think the correct base pair is brought every single time without error? Or that each codon is translated perfectly every time? A mutation is when the DNA sequence is changed.

Uh oh… this shoulds bad!

The DNA sequence makes the mRNA, which provides the instructions to make a protein. Therefore, a change in the DNA sequence can completely change the protein being made.

For instance… 

Having used the analogy that a protein is a sentence and the amino acids are the alphabet, you can imagine what might happen if you switch some of the letters around.

Who is the girl going to marry?
How is the girl going to marry?

The boy was forced to give up his file.
The boy was forced to give up his life. 

In the cases above, the two "proteins" made are not the same!

Mutations can occur from environmental factors such as overexposure to:

• Chemicals
• Pollutants
• Radiation
• Sunlight

Mutations can also occur during:

• DNA replication
• protein synthesis.

Mutations can be classified in different ways.

Point Mutations

A point mutation is when one nucleotide is swapped out for another.

A point mutation can be a silent mutation if the resulting amino acid does not change as a result of the mutation.

Source, 2022-02

Silent Mutation Example

If the DNA sequence “GGT” gets changed to “GGG.” 

The mRNA sequence would change from “CCA” to “CCC.” 

“CCA” and “CCC” both code for Proline, so no harm would be done. 

A point mutation can also be a missense mutation if the amino acid changes as a result of the mutation.

If the DNA sequence “GGT” gets changed to “CGT.”

The mRNA sequence would change from “CCA” to “GCA.”

“CCA” codes for Proline; “GCA” codes for Alanine.

This changes the entire protein.

Frameshift Mutations

A frameshift mutation is when a nucleotide is either inserted or deleted in the DNA sequence.

Ex: ABCDEF       ABBCDEF

Ex: ABCDEF            ACDEF

Inversion Mutations

An inversion mutation is when a DNA sequence gets reversed.

Ex: ABCDEF          ABCFED

Hey… Could mutations be GOOD?

Sometimes, mutations help an organism out. 

Mutations can help increase an organism’s fitness and helps increase genetic variability within a species.

Transcription: Protein Synthesis

Biology Index

Where are we going with this? The information on this page should increase understanding related to this standard:  Demonstrate how DNA sequence information is decoded through transcriptional and translational processes within the cell in order to synthesize proteins. Examine the relationship of structure and function of various types of RNA and the importance of this relationship in these processes.

Article includes ideas, images, and content from Troy Smigielski (2022-01)

Protein Synthesis: Transcription

(So, this seems like a thing…)

The goal of protein synthesis is to make a protein. In other places, we have discussed that proteins do a wide variety of functions in the body and/or are expressed as a trait.

Therefore, as an organism grows, it is necessary to synthesize proteins—to make them within the cell. But, they have to be EXACTLY as designed.

How does this happen?

Keep in mind that proteins are complex.

Protein Review

Proteins are made up of amino acids sequenced together in a chain.

Thus, the monomer of proteins are amino acids. 

This is kinesin, a motor protein, thought
to be carrying an endorphin.

An amino acid is… complicated…

Amino acids consist of a basic amino group (―NH2), an acidic carboxyl group (―COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid is short for α-amino [alpha-amino] carboxylic acid. Each molecule contains a central carbon (C) atom, called the α-carbon, to which both an amino and a carboxyl group are attached. The remaining two bonds of the α-carbon atom are generally satisfied by a hydrogen (H) atom and the R group (Source, 2021-09-01). 

Amino acids are organic compounds that combine to form proteins (Source, 2021-09-01). 

The general form of an amino acid looks like this. 

There are 20 common amino acids used by all living things. In addition to proteins, amino acids form peptides and polypeptides, but… let's hold off on that for now.

Let's recap… before we press on…

Proteins are made of amino acids. 

Amino acids have four parts arranged around  a central carbon. Carbon has 4 places stuff can bond to it.

Part 1: One bond is usually just hydrogen (H).

Part 2: One bond is usually H2N, an amino group. 

Part 3: One bond is the carboxylic acid group (usually written as -COOH or CO2H).

Part 4: The fourth bond is the "organic side chain" called the "-R Group"

How do amino acids differ from one another? Amino acids differ in their -R groups. There are 20 different -R groups, which allows for a wide variety of proteins. The -R group determines what amino acid it is.  

So, there are 20 different amino acids, and they combine to form proteins (and peptides and poly peptides, but we're overlooking that, here). 

You can think of a protein as a sentence. The amino acids are the letters. The letters form words (peptides) and phrases (poly peptides) to create the protein. But… there are only 20 different letters (amino acids).

The order in which the amino acids combine determines what protein is made.

So, how do we replicate these things? This has to be difficult!

Let's take a look at a process by means of an illustration!

Suppose a biology teacher who may or may not also coach soccer wanted to build a nightstand… but, he doesn't know how. Luckily, his friend has detailed instructions on how to build it.

The friend sends over a copy of the instructions. But… The biology teacher doesn't have tools or wood.

Since he's lazy, he send his wife to Home Depot with the instructions to pick up the materials I need. Being the great wife she is, she returns home with everything needed. Now he can get to work and make the nightstand.

So, does it work out?

 Does it look exactly the same? Pretty much!

From analogy to reality…

1. The ribosome wants to build a protein, but it doesn’t know how.
   
   
2. Luckily, DNA in the nucleus has detailed instructions on how to build it.
   
   
3. Those instructions get sent to the ribosome through mRNA.
   
   
4. With the instructions, tRNA brings the building blocks (amino acids) to the builder (ribosome).
   
   
5. The ribosome builds the protein according to the instructions (DNA).

That doesn't look too bad! Wow!

Looking Closer

There are a lot of moving parts in making a protein. There are 3 kinds of RNA involved in making a protein.

Messenger RNA (mRNA) carries a copy of the code for a protein from the nucleus to the ribosome.  mRNA serves as a “runner” or a “messenger” between the nucleus (DNA) and the ribosome (protein factory).

Ribosomal RNA (rRNA) makes up ribosomes. Remember, ribosomes make proteins.

Transfer RNA (tRNA) transfers the appropriate amino acid to the ribosome so that a protein can be made.

Remember, proteins are made out of amino acids—long, complex chains of amino acids.

So, how does your body use those RNAs to make a protein? Before the RNAs can be used, the process actually starts with DNA.

DNA makes RNA in a process called transcription.

RNA makes proteins in a process called translation.

This is the central dogma of biology. All life revolves around this process.

Every organism on here depends on 

DNA   -->    RNA  -->   Protein

Overviewing The Process

Step 1: Transcription

Get the instructions for how to build the protein.

Step 2: Translation

Get the building blocks and build the protein.

Looking In More Detail

Step 1: Transcription

REMEMBER: DNA is a code of instructions, but it cannot leave the nucleus because of the nuclear envelope. mRNA can leave the nucleus. How?

Nuclear pores!

Transcription is the process where DNA makes mRNA. This happens in the nucleus. Remember, DNA is stuck in there.

About the Coding Strand and the Template Strand…

DNA, being a double helix, is two stranded. One strand, called the Coding Strand. This strand is in the actual order that will eventually identify the protein being made.

The other strand, called the Template Strand, is the opposite nucleotide to the coding strand.  

So, the mRNA connects to the Template Strand, and thus, becomes an exact copy of the DNA coding strand. The proteins are recognized by the code on THIS strand, which is a copy of the DNA coding strand. (But, there are charts and tables the use the DNA code to identify the protein, too.) 

 

Next, (to be discussed elsewhere), tRNA comes along dragging the amino acid that corresponds to the code on the mRNA. But, that's jumping ahead…

Why Uracil instead of Thymine in RNA? 

The short answer is that it is easier for a cell to make Uracil, but Thymine is more stable. (Source, 2022)

Three steps…

1. Initiation - the promoter sequence in the DNA lets the process know where to begin; it serves as a template for the mRNA.
   
   
2. Elongation - mRNA nucleotides (bases) are added by RNA polymerase.
   
   
3. Termination - mRNA synthesis stops at the terminator sequence, and the mRNA strand leaves the nucleus.

REMEMBER: mRNA is able to leave the nucleus but DNA is not.

About those promoter and terminator sequences…

The promoter sequence is a special sequence of nucleotides that indicate where to start the process to build a protein. The terminator sequence indicates where to stop. If we go back to the metaphor of proteins being a sentence with amino acids as the letters, you could think of the promoter sequence as the "shift key" to make a capital letter to begin the sentence and the terminator sequence could be thought of as a period to end the sentence.

After termination, the cell has successfully copied the code from DNA to mRNA and has left the nucleus. But, does anyone actually read all of the directions? 

Maybe not!

Having successfully copied the code from DNA to mRNA, the mRNA then leaves the nucleus. At this point, the cell has this looooong strand of mRNA, but it does not need it all. What do you think happens next?

The cell edits the sequence so that it only has the necessary information that is specific to the protein being built.

The unnecessary bits of the mRNA that get cut out are called introns. Think: Introns are invasive. Introns are intruders!

The necessary sequences of the mRNA that are left in are called exons. Think: Exons are expressed. Exons are expected.

 

So, how about another picture!

Making Sense of RNA Code

At this point, you have your shortened sequence of mRNA.  BUT it is still pretty long. What could you do to make it easier to read?

mRNA is read in base groups of 3, which help decode the instructions piece by piece. A sequence of 3 bases is called a codon. Each codon codes for an amino acid.

DO NOT FORGET: the mRNA codes for these amino acids.

And chaining the amino acids together results in a protein.

How do you figure out which amino acid the mRNA codon is coding for? Basically, it's just magic?

Each amino acid is identifiable by a particular codon. The codons are made up of 3 nucleotides, and there are 4 versions of the RNA nucleotide: A, U, G, and C.

So, AAA is a codon. AAU is a codon. AAG is a… you get the idea… 

Plot twist! Some amino acids are coded by more than one codon. Naturally…

So… here's a chart. You can begin with any of the 4 nucleotides in the center, then work outward to find what amino acid is coded by the resulting codon. 

Source, 2022-02

Say you start with the A, then move out to the U, then out to the G, you get AUG, which is Methionine. 

The only codon that codes for the START of protein synthesis is AUG. Methionine is the ALWAYS the first amino acid in ALL proteins! That sort of deserves a mnemonic! 

AUG = Starts proteins. (School starts in August!) Nicely done!

If you look close, you'll find that there are three codons for "Stop": UGA, UAG and UAA.

And since there's always more than one way to do things, here's another matrix for charting codons to proteins…

How about a list? Sure!

Inverse RNA codon table

Amino acid	RNA codons			Amino acid	RNA codons
Ala, A	GCU, GCC, GCA, GCG			Ile, I	AUU, AUC, AUA
Arg, R	CGU, CGC, CGA, CGG; AGA, AGG			Leu, L	CUU, CUC, CUA, CUG; UUA, UUG
Asn, N	AAU, AAC			Lys, K	AAA, AAG
Asp, D	GAU, GAC			Met, M	AUG
Asn or Asp, B	AAU, AAC; GAU, GAC			Phe, F	UUU, UUC
Cys, C	UGU, UGC			Pro, P	CCU, CCC, CCA, CCG
Gln, Q	CAA, CAG			Ser, S	UCU, UCC, UCA, UCG; AGU, AGC
Glu, E	GAA, GAG			Thr, T	ACU, ACC, ACA, ACG
Gln or Glu, Z	CAA, CAG; GAA, GAG			Trp, W	UGG
Gly, G	GGU, GGC, GGA, GGG			Tyr, Y	UAU, UAC
His, H	CAU, CAC			Val, V	GUU, GUC, GUA, GUG
START	AUG			STOP	UAA, UGA, UAG

(Source, 2022-02)

Well… well… well… That's a lot of letters!

Okay, let's look at an example…

This sequence codes for the following protein:

REMEMBER: 

• Each amino acid has a different -R group.
• The order of amino acids determines the protein.

It would seem as if we’re done because we know the amino acids needed to build the protein.

Translation is the process that will deliver these amino acids to the ribosome, and we will talk about that tomorrow.