Tutorial: Gene Expression
Index
RNA vs DNA Nucleotides | RNA vs DNA Polymer | RNA Types | tRNA with Amino Acid | 3 tRNA with Amino Acids | 3 tRNA with Valine | Ribosome Structure | Gene Expression Overview | Animation Symbols | Gene Expression Procedure | Gene Expression Animated | Start and Stop Codons | Translation Box | Gene Decoder | Quiz


Copyright © Steve Kuensting, 2004, All Rights Reserved.
This web tutorial may not be distributed by any means
without the expressed permission of the author!




Introduction

Because of the complex nature of gene expression, you should have already viewed the tutorial titled "Genetic Code".
This program explores the details of transcription and translation, which is gene expression.

Cell



RNA

Before you can view the processes, RNA structure must be understood. RNA is a nucleotide polymer much like DNA but there are 3 main differences:
  1. RNA is always single stranded, never double stranded.
  2. RNA contains all N-bases except thymine, it contains another N-base, URACIL, instead.
  3. RNA contains a different sugar - RIBOSE - instead of deoxyribose which is found in DNA.

DNA and RNA Differences
RNADNA
Single strandedDouble stranded
Has N-bases A,G,C,UHas N-bases A,G,C,T
contains ribose sugarcontains deoxyribose sugar



RNA vs DNA Nucleotides

To compare, look at the N-bases of the nucleotides below.

RNA vs DNA



RNA vs DNA Polymer

To compare again, look at the nucleotide polymers below.
Note the differences.

RNA vs DNA polymers



3 Types of RNA

There are three types of RNA, distinguished on the basis of their function. (All RNA molecules are polynucleotides).

  1. mRNA - messenger RNA - carries copies of the DNA code to ribosomes.
  2. tRNA - transfer RNA - brings amino acids to the ribosome and mRNA so polypeptides can be made.
  3. rRNA - ribosomal RNA - found in ribosomes and holds the ribosome structurally intact.



RNA Types

The three types of RNA are drawn below, tRNA and rRNA differ from mRNA only because they fold or roll up instead of staying linear. Remember - they all are "strings" of nucleotides, but they have different shapes.

RNA types



tRNA

tRNA molecules are critical in the translation process because they carry amino acids to the ribosomes. There are 61 different tRNA molecules --- they differ in the types of ANTICODONS they have. The anticodon of the tRNA below is labeled.

Anticodons



Anticodon

An anticodon is really just a codon, made of three nucleotides. The entire tRNA molecule below is actually a strand of nucleotides, but the only ones distinguished are those of the anticodon --- they are the only ones that are important.

tRNA



Cloverleaf tRNA

The cloverleaf shape of a tRNA is caused by hydrogen bonding between complementary nucleotides (A-U,G-C). This cloverleaf shape is important to its interaction with ribosomes. Although the molecule below is hypothetical, the anticodon is structured as shown.

tRNA



tRNA with Amino Acid

At the other end of the tRNA away from the anticodon is another important part --- the amino acid attachment site. At this site is where amino acids are picked up by tRNA molecules (acylation) to be carried to a ribosome.

tRNA acylation



3 tRNA's

Three different tRNA's are drawn below, note that the only differences between them are the anticodons they have and the amino acids they carry.

Different tRNA's



3 tRNA with Amino Acids

Each tRNA can only carry a specific amino acid depending on the type of anticodon it has. Therefore, a given tRNA CANNOT carry different amino acids at different times. This is crucial to the process of gene expression or protein synthesis.

tRNA's and amino acids



3 tRNA with Valine

It is possible for two different tRNA molecules to carry the same amino acids --- there are 61 different tRNA's but only 20 different amino acids. Generally, for every amino acid type there are about three different tRNA's that can carry it. Three are shown below.

tRNA types



Ribosome Structure

Ribosomes are actually made of 4 pieces of rRNA. Three of the pieces make up what is called the large subunit (belly) and the remaining piece makes up the small subunit (cap). The pieces are names by centrifuge-derived units that indicate their movement in centrifugation. The larger the number, the more dense (bigger) they are. A ribosome is pictured below. Each piece also has polypeptides that serve as enzymes. The nucleotides A,C,U,G could not be drawn below, but each square represents one of them.

Ribosomes



Gene Expression Overview

The entire protein synthesis process superficially works something like this:
  1. RNA polymerase unzips DNA and an mRNA COMPLEMENTARY COPY is made.
  2. The new mRNA moves to cytoplasm and attaches to ribosome.
  3. A ribosome allows different tRNA's bringing amino acids to attach to mRNA as their anticodons match the mRNA codons.
  4. The ribosome bonds the amino acids together to produce the polypeptide.

Animation Symbols
In the following demonstration, we will use the following figures to represent the DNA, mRNA, tRNA, amino acids, and ribosomes.

Gene expression animated



Gene Expression Procedure

The entire gene expression process will be demonstrated.
First, TRANSCRIPTION consists of 3 steps:
  1. RNA polymerase attaches to DNA and unzips it.
  2. RNA polymerase attaches RNA nucleotides to the exposed DNA N-bases of one DNA strand only.
  3. The mRNA detaches and moves to cytoplasm.

TRANSLATION consists of 6 steps:
  1. The ribosome attaches to the first two codons of mRNA.
  2. The appropriate tRNA molecules (with correct anticodons) attach to mRNA bringing their amino acids.
  3. The ribosome bonds amino acids together.
  4. The ribosome moves down the mRNA molecule, one codon at a time, allowing more tRNA's to bring more amino acids.
  5. The ribosome continues to bond amino acids together.
  6. Finally, a "stop" codon is reached, the ribosome detaches and a finished polypeptide is released.
Gene Expression Animated:

Below is the starting frame of the animation. Be sure to write the nucleotide sequence down!
Identify the parts before you use the start the animation.

Gene expression start
This animation is Copyright © 1989, Steve Kuensting, All Rights Reserved.
Speed = | Delay = milliseconds | Frame # =
Loop
Use the controls above to control the animation. You can play forward, stop, play reverse, and adjust the speed (actually the delay between images). The higher the speed (delay) values, the slower the animation. Reasonable delay values fall between 200 and 2000.





Protein Function

The protein formed may become an enzyme for a chemical reaction, a hormone to act as a messenger, or a structural "piece" of the framework of your body!

Finished protein



Details of Translation

As you can see, the process has many steps but it occurs very rapidly in a cell. In order to supply the process, there must be RNA nucleotides for RNA polymerase to put together in transcription, amino acids for the tRNA's to pick up in translation, and fuel energy to run just about every step of the process.

Gene expression steps



Start and Stop Codons

The ribosome knows where to first attach to the mRNA because of the "start codon" AUG, and when it hits the "codon" UGA it knew that the mRNA message was ended and it was time to release to find other mRNA molecules.

Start and stop codons



Codon Sequence Determines Amino Acid Sequence

If a different DNA codon sequence had been used, a different mRNA molecule would have been made which would have produced a different polypeptide consisting of different amino acids.

Different DNA codes make different proteins

Codon wheel


Translation Box

Step 1: Please enter a DNA codon in the "DNA Codon Box"
Step 2: Click on the "Decode" button.
Step 3: Read the mRNA codon.
Step 4: Read the tRNA anticodon.
Step 5: Read the amino acid carried by the tRNA.
DNA Codon Box:
mRNA codon:
tRNA anticodon:
Amino Acid:




Gene Decoder

Step 1: Type a gene sequence into the "Gene Box" below.
NOTE: Type only letters A, G, C, or T.
NOTE: Codons must be separated by SPACES. Ex: AAA CCC GGG TTT
Step 2: Click the "translate" button below.
Step 3: Read the mRNA codon sequence in the "mRNA" box below.
Step 4: Read the amino acid sequence in the "Polypeptide" box below.
NOTE: A result of "---" indicates an invalid gene entry!"
NOTE: Click the "Clear" box to clear all fields and start over.
Gene Box:
mRNA:
Amino Acid Sequence:



Quiz

  1. What type of RNA copies the genetic code?

  2. What type of RNA brings amino acids to ribosomes?

  3. What type of RNA is found within ribosomes?

  4. What is the shape of a tRNA molecule?

  5. What is the shape of an mRNA molecule?

  6. What is the shape of an rRNA molecule?

  7. What critical 3 nucleotides do tRNA's possess?

  8. By what do all tRNA's differ?

  9. What molecules do tRNA's carry?

  10. Can different tRNA's carry the same type of amino acid?

  11. How many different parts make up a ribosome?

  12. How do different polypeptides differ from one another?

  13. What mRNA codon would complement the DNA codon ATC?

  14. What tRNA anticodon would bond to the mRNA codon UAG?

Diagram
Name the numbered structures below.
Quiz pictures

Answers