DR. SAIDUNNISA Professor and chairperson

Department of Biochemistry

Lecture-Genetic code

“I thought if I’m going to work this hard, I might just as well have fun and by fun I mean I wanted to explore an important problem and I wanted to discover things.” Interview with Marshall NirenbergJuly 15, 2009

Learning Objectives

At the end of the session student shall be able to:

Define codon and the triplet nature of the genetic code.

Explain the degenerate, and Wobbling phenomena. Describe the unambiguous, non-overlapping and

universal nature of genetic code. Explain the reading frames of the code. Define and classify mutations and their

consequences with examples in human body.

Case study

A 28 years old female presented to the Medicine OPD with a history of abnormal movements of hands and face of one and a half year duration. These abnormal movements were of gradual onset with progressive course. She also had behavioral changes.

These findings were suggestive of early evidence of caudate lobe atrophy and are seen in Huntington’s chorea.

Case Study

Video

Introduction

Since RNA is constructed from four types of genetic alphabets (nucleotides) A, G, U and C.

These four nucleotides are arranged in a triplet sequence to produce triplet codon this is genetic code.

The three nucleotide (triplet) base sequences in mRNA that acts as a code for amino acids in protein constitute a codon.

Genetic code

So, there are 64 different combinations of bases (43).

Out of 64 codons: 61 code for 20 amino acids.

Which means most of the amino acids are represented by more than one codon.

3 codons act as termination (stop) codons.

Characteristics of the genetic code

1. Degeneracy

2. Unambiguous

3. Non overlapping

4. Non Punctuated

5. Universal

Codon and Anticodon binding

Degeneracy

Example:6 different codons specify: serine , leucine, Arginine. 4 different codons specify: Glycine ,Proline, Alanine ,Valine 1 codon codes: Methionine , tryptophan

"Wobble" position

If the amino acid has more than one codon, the first two bases in the codon will be same, only the third one is different.

This third position is known as the "wobble" position of the codon.

Example: Glycine: GGU ----- wobble" position GGC GGA GGG

Wobble hypothesis

Watson and crick noted that the paring between the 3’-base of the codon and the 5’-base of the anticodon does not always follow strict base pairing rules. This observation resulted in wobble hypothesis.

Wobble hypothesis

Example: codon for glycine

GCU/GCC/GCA—can pair with a single tRNA that contains the anticodon 5’-IGC (U can pair with unusual base hypoxanthine (I) found in tRNA.

1.The genetic code evolved in such a way as to minimize the deleterious effects of mutations.

2.Code degeneracy may serve as a safety mechanism to minimize errors in the reading of codons.

Th

e C

od

e Is

Deg

en

era

te

Minimize the deleterious effects of mutations-explanation

Unambiguous

Genetic code is unambiguous which means specific codon only a single amino acid.

AUG-codes for Methionine. UGG- codes for tryptophan.

Non-overlapping

Genetic code is non-overlapping, once the reading is commenced at a specific codon there is no punctuation between codons and message is read in a continuing sequence of nucleotide triplets until a non-sense codon is reached.

Three Rules

Codons are read in a 5’ to 3’ direction.

Codons are nonoverlapping and the message contains no gaps.

The message is translated in a fixed reading frame which is set by the initiation codon.

Reading Frames of genetic code

To illustrate the point using an analogy, consider the following set of letters:

Theredfoxatethehotdog Two reading frames that

produce nonsense:

t her edf oxa tet heh otd og

th ere dfo xat eth eho tdo g

 

If this string of letters is read three letters at a time, there is one reading frame that works:

the red fox ate the hot dog

Genetic messages work much the same way:

There is one reading frame that makes sense, and two reading frames that are nonsense.

Reading Frames

The genetic code is triplet based, there are three possible ways a particular message can be read, as shown in the following figure:

Clearly, each of these would yield completely different results.

Reading Frames

The start codon is AUG. codes for Methionine, signals for translation and sets the reading frame:

Translation continues until a stop codon is encountered which are UAA, UAG, and UGA.

Codon anticodon binding and amino acid translation

Reading Frames

First, the code is read in a 5' to 3' direction. The first AUG read in that direction sets the

reading frame, and subsequent codons are read in frame, until the stop codon, UAA, is encountered.

The triplet must be in the same reading frame as the start codon.

5’ and 3’ UTR

Nucleotides at either end that are outside of the open reading frame are not used to code for amino acids.

The region at the 5' end is called the 5' untranslated region, or 5' UTR and at 3' end is called the 3' UTR.

These regions typically contain regulatory sequences.

Reading Frames

Note that there are three nucleotides, UAG (indicated by asterisks) that would otherwise constitute a stop codon, except that the codon is out of frame and is not recognized as a stop.

Brainstorming Question

Let's see how a sequence would be translated by considering the following sequence:

5'-GUCCCGUGAUGCCGAGUUGGA-3'

Universal

Genetic code is universal with few exceptions. Genetic code has been highly preserved

during evolution.

All Laws will have exceptions

Codon Translated in cytoplasm as

Translated in mitochondria as

AUA Isoleucine Methionine

UGA Termination Tryptophan

AGA Argnenine Termination

AGG

UGA is stop codon but under special circumstances it codes for Selenocysteine the 21ST amino acid

Argenine Termination

Learning check

Mutations

Definition: An alteration in the genetic material results in a mutation resulting in an abrupt spontaneous origin of a new character.

Statistically out of every 106 cell divisions one mutation takes place

Mutagens: substances which induce mutations.

Effect of mutation: reflected in

Replication, Transcription, and Translation. Classified :

1. Point Mutations

2. Frame Shift Mutations

Point Mutations

purine is replaced by purine or Pyrimidine by

pyrimidine.

Replacement of purine by pyrimidine or vice

versa

Transition Trans version

Point mutation

Consequences of point mutation

Silent mutation: change in the 3rd base still codes for serine due to degeneracy no detectable effects.

Nonsense mutation: some times the codon with the altered base may become a termination code leading to termination of protein synthesis.

Missense mutation : changed base may code a different amino acid.

Learning check Name the type of mutations

Missense mutation acceptable

Missense mutation : can be acceptable or partially acceptable or unacceptable.

Missense mutation but acceptable: change in the amino acid sequence in a protein affects the physical characteristics (eg: electrophoretic mobility) but not the functions of the protein.

Example: Hb sydney and Hb Bristol Normal HbA at 67th position is valine (GUU) Is replaced by Alanine(GCU) in Hb Sydney and Asparate (GAU) in Hb bristol

Missense mutation but Partially acceptable:

Change in the amino acid sequence in a protein affects the physical characteristics (eg: electrophoretic mobility) as well as partially affects the functions of the protein.

Example: HbS mutation in the beta chain at 6th position

of HbA glutamic acid (GAG) normal is replaced by Valine (GUG) is transversion.

Missense mutation un acceptable:

change in the amino acid sequence in a protein affects the physical characteristics (eg: electrophoretic mobility) and seriously affects the functioning of the protein is incompatible to life.

Example: HbM results from histidine substitution at 58th position for tyrosine (CAU to UAU).

HbM: results in oxidation of ferrous iron to ferric in hemoglobin results in decrease oxygen carrying capacity.

Learning check

A 53- year old man sees his family physician he suspects Hemochromatosis and finds the patient carries a mutation where tyrosine is substituted for cysteine at position 282 of the HFE gene. What is the type of mutation seen in this disorder?

Frame Shift Mutations

Frame-shift mutation Insertion

mutation

One or more base pair inserted to the gene

One or more base pair deleted from gene

Deletion mutation

Insertion (Huntington’s chorea)

CAG trinucleotides are repeated 30-300 times.

It is a neurodegenerative disorder named after the American physician George Huntington characterized by repetitive abnormal movements called chorea.

Deletions (Cystic fibrosis One AA at 508th phenylalanine is missing )

Consequences of frame shift mutation

The insertion and deletion of a base in a gene results in an altered reading frame of mRNA hence the name frame shift.

The machinery of mRNA containing codons does not recognize that the base was missing or a new base was added, since there are no punctuations in reading of codons translation continues.

The result is that the protein synthesized will be garbled (completely irrelevant) having several altered amino acids or prematurely terminated protein.