Pathophysiology 101-823

Unit 2Genetics & Genetic Disease

Molecular Genetics & The Genetic Control Of

Proteins

Paul Anderson Fall 2008

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Nucleotides - 1

1. DNA and RNA are NUCLEIC ACIDS (or POLYNUCLEOTIDES) i.e. POLYMERS made up of MONOMERS called NUCLEOTIDES.

2. Each NUCLEOTIDE has 3 parts, a 5 C or PENTOSE SUGAR, a P containing PHOSPHATE group and a N containing (NITROGENOUS) BASE.

3. The PENTOSE SUGAR in nucleotides of DNA is DEOXYRIBOSE while in RNA, ATP, ADP or AMP it is RIBOSE.

4. The N - containing BASE can be a single ring structure, called a PYRIMIDINE (bases CYTOSINE, THYMINE or URACIL) or a double ring structure, called a PURINE (e.g. ADENINE or GUANINE).

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Nucleotides - 2

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Nucleotides - 3

In each nucleotide the N base is bonded to carbon 1’ of the pentose while the phosphate group is bonded to carbon 5’ of the same sugar.

components of a nucleotide

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DNA Nucleotides

DNA is a DOUBLE POLYNUCLEOTIDE STRAND containing the bases ADENINE (A), GUANINE (G), CYTOSINE (C) and THYMINE (T).

DeoxyRibose

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RNA Nucleotides

RNA is a SINGLE POLYNUCLEOTIDE STRAND, containing the same bases as in DNA, except that THYMINE (T) is replaced by URACIL (U).

Ribose

U replaces T

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Mononucleotides

Single NUCLEOTIDES are called MONO NUCLEOTIDES and include AMP composed of RIBOSE, ADENINE and a PHOSPHATE group.

N base

Pentose

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Nucleic Acids - 1

NUCLEOTIDES join together to form a POLYNUCLEOTIDE strand by bonding between the PENTOSE SUGAR of one nucleotide and the PHOSPHATE group of another.

Since each sugar and each phosphate form 2 bonds between the HYDROXYL (ALCOHOL) group of the sugar and the ACIDIC PHOSPHATE these two ester linkages together form a PHOSPHO – DIESTER LINKAGE.

In the phosphodiester linkage each PHOSPHATE group is bonded to carbon 5’ of one sugar and to carbon 3’ of another sugar.

The "BACKBONE " of a POLYNUCLEOTIDE is thus composed of SUGARS and PHOSPHATES joined by PHOSPHO – DIESTER linkages while the N BASES project sideways from sugars.

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Nucleic Acids - 2

Fig. 5.26 Campbell & Reece

P

P

P

P

Phosphodiester linkage

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Nucleic Acids - 3

Direction of growth 5’-----------> 3’

Each POLYNUCLEOTIDE has a distinct polarity, with a “free-OH” group on C 3’ and a 5’ end which contains the terminal PHOSPHATE.

Elongation of a polynucleotide normally occurs by adding new nucleotides to the 3’ end so the chain elongates in a 5’----> 3’ direction.

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DNA Structure

DNA is a DOUBLE POLYNUCLEOTIDE STRAND containing the bases ADENINE (A), THYMINE (T), CYTOSINE (C) and GUANINE (G).

In any polynucleotide the percentage of PURINE BASES equals the percentage of PYRIMIDINE BASES. Also % ADENINE = % THYMINE and % CYTOSINE = % GUANINE.

Watson & Crick proposed (in 1953) that the 2 polynucleotide strands of DNA are coiled around each other into a into a DOUBLE HELIX with the N BASES connecting the two strands, like the rungs of a spiral staircase with the SUGARS and PHOSPHATES forming the sides

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DNA Structure - 2: Base Pair Rule

According to the Watson - Crick model of DNA the 2 polynucleotide strands of DNA are connected by HYDROGEN BONDS formed between the N BASES of each strand, ADENINE always pairing with THYMINE (each of which can form 2 H bonds) and GUANINE with CYTOSINE(each of which forms 3 H bonds).This pattern of base pairing is called the BASE PAIR RULE. Each base is said to be COMPLEMENTARY to its partner, thus ADENINE is complementary to THYMINE and GUANINE is complementary to CYTOSINE.

PURINE with PYRIMIDINEBASE A with TPAIR G with CRULE

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DNA Double Helix

3’ end 5’ end

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DNA Structure - 3

The 2 DNA strands are not identical. Each polynucleotide strand contains a set of bases COMPLEMENTARY to that of the other strand.

According to the Watson - Crick model the two DNA strands are "ANTIPARALLEL" i.e. if one strand is 3’<---- 5' the other strand is 5’------>3'. If one DNA strand has the base sequence 5'TAAGCT3' its complementary DNA strand will have the sequence 3’ ATTCGA 5’.

Antiparallel DNA Strands

H bonds

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The Genetic Code

The function of the DNA molecule is to contain the GENETIC INFORMATION for the organism (i.e. information for making all PROTEIN molecules).

ALL GENETIC INFORMATION for the organism must be coded somehow in the structure of DNA. This code is called the GENETIC CODE. The GENETIC CODE is thus coded information in the molecular structure of DNA for making PROTEIN molecules.

The SUGAR and PHOSPHATE groups in each DNA nucleotide are always the same and therefore could not provide a code for PROTEINS which are composed of 20 different AMINO ACIDS.

The GENETIC CODE must therefore be in the only variable part of DNA, the NITROGEN BASES.

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The Genetic Code - 2

Only by using TRIPLET combinations of the four bases A, T, G and C could we form enough CODE "WORDS" (or CODONS) for the 20 different AMINO ACID building blocks in PROTEINS.

Code word (triplet of bases) corresponds to specific amino acid

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The Genetic Code - 3

Watson & Crick proposed (in 1953) that the GENETIC CODE consists of a SPECIFIC TRIPLET of BASES of NUCLEOTIDES (each specific triplet forming a code word (or CODON) along one of the two DNA strands.

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The Genetic Code - 4

Most GENES consist of a series of CODONS corresponding to the specific NUMBER, TYPE, and SEQUENCE of AMINO ACIDS in the PROTEIN controlled by that gene.

Therefore, the GENE dictates the STRUCTURE of the PROTEIN it controls.

A GENE which codes for a PROTEIN of 100 AMINO ACIDS would need to be at least 100 CODONS in length, i.e. contain at least 300 BASES.

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Relationship Between DNA and Protein

Primary Structure of Protein(number, type & sequence of amino acids)

Primary Structure of Gene (number, type & sequence of codons)

determines

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Protein Synthesis: Transcription

DNA is the molecule which stores the GENETIC CODE but since DNA never leaves the nucleus whereas protein synthesis occurs in the cytoplasm the information for making a protein must be conveyed from the nucleus to the cytoplasm by another molecule called messenger RNA or mRNA.

A molecule of mRNA is synthesised by base pairing between single mRNA nucleotides and DNA nucleotides from one DNA strand. This is the same as base pairing in DNA except that Adenine (A) in DNA base pairs with URACIL (U) in mRNA (instead of THYMINE (T).

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Transcription - 2

Requires RNA polymerase

DNA codons

mRNA codons

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Transcription & Function of mRNA

•After base pairing occurs, the free nucleotides are joined together (i.e. polymerise) to form an mRNA molecule. Formation of mRNA is called TRANSCRIPTION of the GENETIC CODE since the code is simply transferred (or transcribed) from the DNA molecule to mRNA using the enzyme RNA Polymerase. The newly formed mRNA molecule is complementary to the DNA strand from which it was formed.

•The function of mRNA is to receive GENETIC INFORMATION from one GENE in DNA and to carry this message out of the nucleus to the sites for protein synthesis (RIBOSOMES) in the cytoplasm.

•mRNA carries the GENETIC CODE in the form of a series of mRNA CODONS out of the nucleus to a ribosome particle.

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Overview of Protein Synthesis

Transcription

Translation

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Translation - 1•tRNA molecules bring AMINO ACIDS to the ribosome one by one. Each tRNA molecule has a triplet of bases (an ANTICODON) which can base pair with a specific mRNA CODON.

In this way tRNA molecules arrive in an order dictated by the order of codons in mRNA i.e. by the GENETIC CODE in mRNA.

Transfer RNA (tRNA)

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Translation - 2

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•The GENETIC CODE is said to be TRANSLATED into a PROTEIN when the AMINO ACIDS brought by tRNA polymerize to form a PROTEIN.

•The PRIMARY STRUCTURE of the PROTEIN (number, type and sequence of amino acids) is dictated by the PRIMARY STRUCTURE of the mRNA molecule (number, type and sequence of codons) which brought the GENETIC CODE to the ribosome and in turn by the GENE from which the mRNA was formed.

Translation - 3

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Overview of Protein Synthesis - 2

Transcription

Translation

tRNA molecules (bind to large ribosome subunit)

First amino acid

Next anticodon will be

AAA

phenylalanine

Next amino acid will be

5'

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The Genetic Code

Note that the genetic code is•a triplet code•redundant (only 20 amino acids but 64 codons- 3rd base of many codons can vary so a mutation here is not damaging)

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Semi - Conservative DNA Replication•When DNA replicates prior to cell division each strand acts

as a “template” for making one new strand. •Thus each new double helix consists of one “old” or

parent strand and one “new” or daughter strand.

•For this reason the process is called SEMI - CONSERVATIVE DNA REPLICATION.

•DNA REPLICATION begins when DNA uncoils.

• Free DNA NUCLEOTIDES then base pair with nucleotides in each of the parent DNA strands using the enzyme DNA Polymerase.

•These nucleotides then join together to form a new daughter strand that is complementary to the parent strand from which it was formed.

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DNA Replication - 2

Step 1: Parent DNA strands separate.

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DNA Replication - 3Step 2: Each parent strand acts as a template for a new DNA strand growing antiparallel to the old strand in a 5 ’----> 3’ direction.

Each new DNA strand grows in 5’------> 3’ direction

5’

3’ 5’

3’

Base pairing

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DNA Replication - 4

New DNA molecule

New DNA molecule

Two new identical DNA molecules are formed, each with one old strand and one new strand.

Parent DNA strands

New DNA

strands

3’

5’

3’

5’ 5’

3’5’

3’

H bonds between base pairs

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DNA Replication - Summary

Parent DNA molecule “unzips at Origin of Replication

“Replication Fork”

New “leading” DNA strand grows continuously in a 5’--->3’ direction towards replication fork

New “lagging” DNA strand grows in fragments in a 5’--->3’ direction away from replication fork

Campbell & Reece, fig. 17.27

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Gene (Point) Mutations

•According to the ONE GENE ONE PROTEIN THEORY for each PROTEIN in the body there is a GENE which controls it. There is therefore a ONE -TO-ONE RELATIONSHIP between PROTEINS and GENES and between CODONS in a GENE and AMINO ACIDS in the PROTEIN controlled by the GENE.

•A single GENE (POINT) MUTATION consists of a CHANGE in one BASE within a CODON. This, in turn, will change the AMINO ACID SEQUENCE in the PROTEIN controlled by the GENE.

•A single BASE SUBSTITUTION in a gene will change ONE CODON only and may therefore affect only ONE AMINO ACID in the protein.

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Base Substitution Mutations

If a STOP CODON results from a base substitution a NONSENSE MUTATION occurs forming a shortened polypeptide.

Normal mRNA

Base substitution at 3rd position of codon usually has no effect on protein

A single BASE SUBSTITUTION in a gene will change ONE CODON only and may therefore affect only ONE AMINO ACID in the protein.

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Sickle Cell Gene: A Base Substitution Mutation

Normal DNA codon for glutamic acid

(Beta chain)

Abormal DNA codon for valine instead of glutamic acid

(Beta chain)

Normal RBCSickle cell

Hydrophobic valine less soluble

HbS sickles when blood O2

is low

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Base Insertion or Deletion Mutations

• BASE ADDITION or BASE DELETION MUTATIONS are “frame shift” mutations and will affect every codon after that point in the gene.

• These mutations are therefore more serious since they may change every amino acid after that point in the protein

Normal mRNA

Base addition - Reading “frame” shifts to left

Base deletion - Reading “frame” shifts to right

Normal reading “frame”

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Enzyme Deficiency Diseases (Inborn Errors of Metabolism)

•Since almost all ENZYMES are PROTEINS, each ENZYME must be controlled by a GENE.

•A GENE MUTATION in this case would result in the ABSENCE of the ENZYME, a condition called an ENZYME - DEFICIENCY DISEASE.

•These inherited diseases were first described by Garrod in 1909 and called “INBORN ERRORS OF METABOLISM”.

• Inborn Errors of Metabolism include - PKU disease- Galactosemia- familial hypercholesterolemia- von Gierke’s disease (and other glycogen storage diseases)

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Somatic vs Germ Cell Mutations

• Since DNA is faithfully copied during DNA REPLICATION, SOMATIC CELL MUTATIONS are passed on to all daughter cells.

• However, only MUTATIONS in GERM CELLS (i.e. GAMETES) can be passed on to OFFSPRING.