BINF6201/8201. Basics of Molecular Biology

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1 BINF6201/8201 Basics of Molecular Biology

2 Linear structure of nucleic acids Ø Nucleic acids are polymers of nucleotides Ø Nucleic acids Deoxyribonucleic acids (DNA) Ribonucleic acids (RNA) Phosphate Ø Nucleotide Ribose or deoxyribose Nucleoside Base Purines Adenine (A) Guanine (G) Thymine (T) RNA Pyrimidines Uracil (U) Cytosine (C)

3 Mono-, di-, and tri-phosphate nucleotides Base Nucleoside Nucleotide DNA RNA Adenine (A) Deoxyadenosine damp dadp datp Guanine (G) Deoxyguanosine dgmp dgdp dgtp Cytosine (C) Deoxycytidine dcmp dcdp dctp Thymine (T) Deoxythymidine dtmp dtdp dttp Adenine (A) Adenosine AMP ADP ATP Guanine (G) Guanosine GMP GDP GTP Cytosine (C) Cytidine CMP CDP CTP Uracil (U) Uridine UMP UDP UTP

4 The pairing rule of the bases in nucleic acids: A-T/U and G-C. Ø A-T/U pairing forms two hydrogen bonds--- weak bond. Ø G-C pairing forms three hydrogen bonds---strong bond. Ø Therefore, G-C pairing is more stable than A-T/U pairing.

5 Ø Two complementary DNA strands run in antiparallel, and are coiled around each other, forming a double helical structure. Ø There are two grooves on the surface of the double helix: the major groove and minor groove. Ø Regulatory molecules bind to DNA in these grooves, changing the structure and function of DNA. Ø Cytosine residues in some regions in DNA can be modified by methylation,thereby changing their functional states. The double helical structure of DNA

6 Higher level structures of DNA Ø In eukaryotic cells, DNA molecules are highly compacted by wrapping around the histone protein core, forming nucleosomes. Ø The histone core is made up of 2 copies of each of the four histone proteins (H2A, H2B, H3 and H4). Ø Nucleosomes are further coiled to form super coils. Ø The N-terminal tail of histones can be modified by methylation or acetylation on the lysine or arginine for controlling the open or close states of chromatin, and thus its functions. 3D structure of a nucleosome

7 Ø RNAs are single stranded. Ø However, the complementary parts in a RNA molecule can form local double-stranded structures, thus, causing loops in the non-complementary regions. Ø There are at least four major functional types of RNAs: Structure of RNAs 1. mrna 2. trna 3. rrna 4. Small regulatory RNAs, e.g., micro RNA (mirna) and small interfering RNA(siRNA) Structure of a trna-ala 5 3

8 Protein structure Ø Proteins are polymers of amino acids linked by peptide bonds; Ø There are twenty amino acids found in proteins; Ø Amino acids differ in their side chains: R groups; Ø The linear order of amino acid sequence of a protein is called its primary structure.

9 Classification of amino acids according to the structure of side chains

10 Classification of amino acids according to the structure of side chains

11 Classification of amino acids according to the structure of side chains

12 Classification of amino acids according to the structure of side chains

13 Higher level structures of proteins Ø Secondary structure: the ways that the linear amino acid sequence forms specific structures: α-helix and β-sheets. α-helix β-sheet Ø Tertiary structure: the ways that the linear amino acids of a polypeptide chain form a specific 3D structure for a specific function. Ø Prediction of the 3D structure of a protein from its sequence is a challenging problem in computational biology.

14 The Central Dogma of Molecular Biology Ø Genetic information is stored in DNA and passed from DNA to RNA to protein. Reverse transcription DNA mrna replication Transcription Translation Protein

15 What is a gene? Ø A gene is a segment of DNA that contains the information necessary to make functional RNA and peptide molecules. Ø According to this definition, a gene includes transcribed sequence and non-transcribed regulatory sequences that control the transcription and translation of the gene product. Ø Genes can be classified as protein coding genes and RNA-specifying genes. Ø In bioinformatics and computational biology, a gene often refers to the DNA sequence that specifies the sequence of a protein (open reading frame, ORF) or a RNA molecule, and its regulatory sequences are treated separately.

16 Structure of genes in prokaryotes Ø Adjacent genes of the same orientation in prokaryotes can be transcribed simultaneously, forming a structure, called an operon. Ø A typical operon contains the following elements: 1. Open reading frames; 2. Upstream regulatory elements 3. A downstream transcriptional terminator FT binding site Promoter region TSS Ribsome binding site Terminator Upstream regulatory region Ø Prediction of genes (ORFs) in prokaryotes has reached a high accuracy using machine learning algorithms.

17 Structure of genes in eukaryotes Ø Due the complexity of gene structures in eukaryotes, accurate prediction of genes in these organisms is still a challenging problem.

18 Ø Although both polymerase III and I have the capability of proofreading, incorrectly paired bases can still be incorporated, which is a major source of mutations. DNA replication Ø Chromosomes are replicated before each cell division; Ø DNA replication is semi-conservative: each of the two newly synthesized DNA molecules contains an original strand of DNA and a newly synthesized complementary strand; Ø The leading strand is synthesized continuously, while the lagging strand is produced in fragments (Okazaki fragments), which are later jointed; Ø Major enzymes involved: 1. Primase for the synthesis of RNA primers; 2. DNA polymerase III for extension; 3. DNA polymerase I for the excision of primers and filling the gaps; 4. Ligase for joining fragments.

19 Transcription Ø Transcription is catalyzed by RNA polymerase using one of the DNA strands as the template template strand or non-coding strand; Ø The opposite strand is called non-template stand or coding strand, because it has the same sequence as the transcribed RNA with a T replaced by a U. Coding strand Non-coding strand

20 Transcription Ø Transcription is controlled by the interaction of trans-acting elements called transcription factors (TFs) and cis-acting elements of DNA. Ø Prediction of cis-acting elements or TF binding sites is a challenging problem in computational biology. Regulation of transcription in prokaryotes TF binding site TF1-300 TF2 Promoter region α α β β σ RNA TSS +1 Ribosome binding site 5 UTR Terminator Transcription 3 UTR

21 RNA processing in eukaryotes Ø A cap is added to the 5 end, consisting of a methylated guanosine and cap-binding proteins Ø A string of bout 200 adenosines are added to the 3 end. This poly-a tail is bound by poly-a binding proteins. Ø Splicing: introns are cut out, and exons are linked. There can be many forms of splicing, generating different mrnas alternative splicing, so a gene can code for many proteins. Splicing can be mediated by spliceosome or the RNA itself. Prediction of alternative splicing sites is a challenging problem in computational biology.

22 Translation Ø Translation starts by the association of ribosome with the ribosome binding site in the mrna molecule, and the following components are involved : 1. Ribosome: consisting of a small and a large subunit, each is composed of a few rrna and hundreds of protein molecules. 2. trna: carrying a specific amino acid, and recognizing a codon using its anti-codon through base paring. 3. Amino acyl-trna synthetase: attaching an amino acid to its trna.

23 Transcription and translation are two highly coupled process in prokaryotes TF binding site TF1-300 TF2 Promoter region α α β β σ RNA TSS +1 Ribosome binding site Proteins Ribosome binding site 5 UTR Terminator Transcription 3 UTR Translation

24 Standard genetic codons Ø There are 61 sense codons and 3 non-sense (stop) codons; Ø Degeneracy of codons; Ø Some codons for the same amino acid are more frequently used than the others, a phenomenon called codon bias; Ø Mutations in the 1st and 2nd nucleotides in a codon often result in changes in amino acids, while a mutation in the 3rd nucleotide does not, thus it is called a wobble base.