Chapter 6: Genetic Control: DNA and RNA

Genetic control of protein structure and function

Structure of DNA and RNA

Nucleotides

DNA replication

Polynucleotides

DNA, RNA

Protein Synthesis

....the features of the “genetic molecule” • Ability to carry instruction (a blueprint) for the construction and behavior of cells • and the way they grow together to form a complete living organism

....the features of the “genetic molecule” • Ability to be copied (perfectly) over and over again • Whenever the cells divide it can pass on an exact copy of each “genetic molecule” to the nuclei of each daughter cells

The discovery of the DNA

(a) describe the structure of RNA and DNA and explain the importance of base pairing and the different hydrogen bonding between bases

Structure of DNA and RNA • DNA stands for deoxyribonucleic acid • RNA stands for ribonucleic acid • Both DNA and RNA are macromolecules like protein and polysaccharide. • They are polymers

• DNA and RNA are made of smaller molecules known as nucleotides. • DNA and RNA are therefore polynucleotides. • Refered simply as nucleic acid.

• Nucleotides have three parts to them: (i) a phosphate group, which is negatively charged.

• Nucleotides have three parts to them: (ii) a pentose sugar, which has 5 carbon atoms in it. In RNA the sugar is ribose. In DNA the sugar is deoxyribose.

Nucleic Acids Phosphate

Phosphate

Sugar

Sugar

The joined sugar is either ribose (RNA) or deoxyribose (DNA), and the only difference is that deoxyribose has one fewer oxygen atoms in its molecule

Pentose sugar • 5-carbon pentose sugar. • Nucleotides have 2 kinds of pentose; units of RNA contains “ribose” sugar and DNA contains “deoxyribose” sugar • The base of a nucleotide is covalently joined to C1 of the pentose through glycosidic bond (N-1 of pyrimidine ; N-9 of purine) •The phosphate of a nucleotide is covalently joined to C5 (-OH) of the pentose through phosphoester bond.

Nitrogenous base • Large, double ring molecule found in both DNA and RNA. •Adenine (A) and Guanine (G) •N-9 of the ring will form covalent bond (glycosidic bond) with C1 of the pentose in a nucleotide.

• Small, single ring molecule found in both DNA and RNA. •Cytosine (C), Thymine (T) [DNA] and Uracil (U) [RNA] •N-1 of the ring will form covalent bond (glycosidic bond) with C1 of the pentose in a nucleotide.

Nucleic Acids a.k.a Nucleotide Pyrimidine base

Phosphate

Purine base

Phosphate

Sugar

Sugar

There are two types of bases - purine and pyrimidine you only really need to know that adenine and guanine are the purine bases and that purine bases are larger.

Nitrogenous Base

Purine

Adenine

Pyrimidine

Thymine (DNA) Guanine

Cytosine

Uracil (RNA)

Polynucleotide • To form both DNA and RNA, many of these nucleotides are linked together in a polynucleotide chain. • The structure of this poly nucleotide chain is seen in this picture

As you can see, it is formed by alternating sugars and phosphates, and the nitrogen bases project sideways.

Polynucleotide • Nucleotides are connected to each other via the phosphate on one nucleotide (C5) and the sugar (C3)on the next nucleotide • A Polynucleotide • Sugar-phosphate bonds (backbone of DNA) • A-T(U) and G-C

Reading frame of DNA Phosphate grp covalently attached to C5 of the pentose sugar, hence -5’ end term is used.

Phosphodiester bond

Hydroxyl grp covalently attached to C3 of the pentose sugar, hence -3’ end term is used.

• In a leading strand (template) of a long polynucleotide chain (DNA), the reading frame is always from “ 5’ – 3’ ”. What does this means??? • As you start reading the nucleotides of a leading strand, you will realize a FREE phosphate grp is always attached to C5 of the pentose sugar. This group is called as the 5’ end of the chain • As you reach the end of the chain, you will see the final nucleotide has a FREE hydroxyl grp attached to the C3 of the pentose sugar. This group is called as the 3’ end of the chain. • Therefore we always read the leading strand of any given DNA as 5’ – 3’. It’s complementary strand is the reverse, we read as 3’ – 5’, because we start off a complementary nucleotide with a FREE –OH at C3 of the sugar.

• DNA molecules are simply two of these strands next to each other, running in opposite directions held together by hydrogen bonds.

• The bases do not take part in the polymerisation

• Adenine always pairs with thymine, cytosine always pairs with guanine (A-T, C-G, and in RNA, it is A-U, since thymine does not appear).

Base pairing of Nucleotides In 1940s, Erwin Chargaff calculated a “rough equivalent” between adenine and thymine molecules and between cytosine and guanine molecules Chargaff’s DNA Database Composition in Various Species (%) Species

A

T

G

C

Homo sapiens (Human) Drosophila melanogaster (fruit fly) Zea mays (Corn) Neurospora crassa (fungus) Escherichia coli (bacteria)

31.0 27.3 25.6 23.0 24.6

31.5 27.6 25.3 23.3 24.3

19.1 22.5 24.5 27.1 25.5

18.4 22.5 24.6 26.6 25.6

Base pairing – Conclusion of Chargaff’s experiment

Polynucleotides DNA molecules forms a 3D double helix shape, bonded by hydrogen, whereas RNA remains as single strands of polynucleotide.

The Rule: • Adenine always base pairs with Thymine (or Uracil if RNA) • Cytosine always base pairs with Guanine. • This is because there is exactly enough room for one purine and one pyramide/pyrimidine base between the two polynucleotide strands of DNA.

Types of RNA There are three major classes of RNA. Each class of RNA has its own unique size, shape and function in protein synthesis • Ribosomal RNA (rRNA) – alone with ribosomal proteins, makes up the ribosomes, where proteins are synthesised. • Messenger RNA (mRNA) – takes a message from DNA in the nucleus to the ribosomes in the cytoplasm • Transfer RNA (tRNA) – transfers amino acid to the ribosomes

RNA vs DNA RNA is a nucleic acid like DNA, but with 4 differences: • RNA has the sugar ribose instead of deoxyribose • RNA has the base uracil instead of thymine • RNA is usually single stranded • RNA is usually shorter than DNA

(b) explain how DNA replicates semi conservatively during interphase;

Nature of the Genetic Material • Property 1 - it must contain, in a stable form, information encoding the organism’s structure, function, development and reproduction • Property 2 - it must replicate accurately so progeny cells have the same genetic makeup • Property 3 - it must be capable of some variation (mutation) to permit evolution

Dianne Chabira

• The discoverers of DNA, Watson and Crick suggested that the two polynucleotide strands of DNA could spilt apart, and • new nucleotides (the correct, complimentary ones) could line up along each strand, making a new DNA molecule.

• This process is known as semiconservative replication, since half of the original molecule is conserved in each of the new molecules.

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DNA Replication

dispersive model

dispersive model

• Semi-conservative: Each new molecule would contain one old strand and one new strand.

dispersive model

• Conservative model: One completely new double helix would be made from the old one

dispersive model

• Dispersive model: Each new molecule would be old bits and new bits scattered randomly through the molecules

Experimental proof • Nitrogen is a major constituent of DNA, and there are two different isotopes - 14N and 15N. • 14N is by far the most abundant isotope of nitrogen, but DNA with the heavier 15N isotope also works.

The conditions of DNA replication

1. 2. 3. 4. 5. 6. 7. 8.

Replication fork Helicase Continuous synthesis DNA polymerase III Discontinuous synthesis RNA primer DNA polymerase I DNA ligase

(c) state that a gene is a sequence of nucleotides as part of a DNA molecule, which codes for a polypeptide and state that a mutation is a change in the sequence that may result in an altered polypeptide;

DNA, RNA and Protein Synthesis How can a single type of molecule like DNA control all the activities of a cell?

What are proteins made of? Strings of amino acids

The triplet code • The sequence of bases or nucleotides in a DNA molecule is a code for the sequence of amino acids in a polypeptide. • A sequence of amino acids is coded for by the sequences of nucleotides in a DNA molecule three bases form a triplet code or the codon on the mRNA strand.

The Codon??? • A triplet of bases that codes for a specific amino acid is called a codon. • Hence, the complementary set of triplet bases for the codon is knows as the anticodon.

• Each triplet code (codon) codes for one amino acid • E.g.: T-T-T, thyminethymine-thymine stand for the amino acid lysine and it is always read in the same direction.

• Short piece of DNA carries the instruction to the cell. • Deciphering the codes of life!!

The nature of genetic codons • Triplets • Non-overlapping • degenerate

Genes and Genomes • A gene is a part of a DNA molecule that codes for just one polypeptide, and in humans alone there is an estimated 140,000 genes.

• • • •

One DNA molecule contains many genes. One gene = one polypeptide One codon = one amino acid In human it is estimated that there are about 30 000 genes. • Total DNA of a human cell is 3 x 109 base pair long • Only 3% of this DNA actually code for protein. • The rest are known as junk DNA.

• The total set of genes in a cell is called the genome. • The genome is the total information in one cell. • All cells in the same individual contain the same information, the genome represents the genetic code of that organism.

Human Genome Project • A global project to sequence the complete human genome which launched in 1990. • The human genome contain about 3 billion bases • To Identify every human gene and find out how at least some of them affect human health.

mRNA

RNA in protein synthesis rRNA ribosome

tRNA

(d) describe the way in which the nucleotide sequence codes for the amino acid sequence in a polypeptide with reference to the nucleotide sequence for HbA (normal) and HbS (sickle cell) alleles of the gene for the β-haemoglobin polypeptide;

Sickle Cell Anemia • If even one amino acid in the sequence is changed, that can potentially change the protein’s ability to function. • Sickle cell anemia is a blood disorder that affects hemoglobin

Sickle Cell Anemia • It is caused by a change in only one nucleotide in the DNA sequence that causes just one amino acid in one of the hemoglobin polypeptide molecules to be different. • Because of this, the whole red blood cell ends up being deformed and unable to carry oxygen properly.

One amino acid change • • • •

Clumping of cells in bloodstream Spleen concentrates sickle cells Rapid destruction of sickle cells Anemia, causing weakness,fatigue, impaired development, heart chamber dilation • Spleen enlargement • Heart failure, paralysis, pneumonia, rheumatism, gut pain, kidney failure

(e) describe how the information on DNA is used during transcription and translation to construct polypeptides, including the role of messenger RNA (mRNA), transfer RNA (tRNA) and the ribosomes;

Protein Synthesis • There is a direct relationship between the base sequence of DNA and the sequence of amino acids that makes up a protein DNA


mRNA


tRNA


protein

triplet

codon

anticodon

Amino acid

CCA

GGU

CCA

Glycine

AAA

UUU

AAA

phenylalanine

GTG

CAC

GUG

histidine

Transcription • Transcribe means to copy – using DNA as a template, complementary RNA nucleotides are joined to make mRNA

Transcription • RNA polymerase unwinds a short section of the DNA double helix near the start of the gene. • This unwound section is known as the transcription bubble.

Transcription • The RNA polymerase, and therefore the transcription bubble, travels along the coding strand in the 5' to 3' direction, and along the noncoding strand in the opposite, 3' to 5', direction,

Transcription • as well as polymerizing a newly synthesized strand in 5' to 3' or downstream direction. The DNA double helix is rewound by RNA polymerase at the rear of the transcription bubble. • Like how a zipper works, only it unzips it and rezips it without going back and forth.

Transcription • Where the helix is unwound, the coding strand consists of unpaired bases, whilst the template strand consists of an RNA:DNA composite, followed by a number of unpaired bases at the rear. • This hybrid consists of the mostrecently-added nucleotides of the RNA transcript, complementary base-paired to the template strand

Transcription • mRNA can now leave the nucleus. • Each triplet code of bases from DNA is now represented by three bases on mRNA called a codon.

Stages of Translation

Structure of tRNA

An aminoacyl-tRNA synthetase joins a specific amino acid to a tRNA

Anatomy of a ribosome

Initiation of translation Sequence in mRNA is complementary to a sequence in the tRNA anticodon in the small ribosomal subunit

Translation elongation

Termination of translation