1. Basics of Molecular Biology
BINF6201/8201
Basics of Molecular Biology

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

3. Mono-, di-, and tri-phosphate nucleotides
Base
Nucleoside
Nucleotide
DNA
Adenine (A)
Deoxyadenosine
dAMP
dADP
dATP
Guanine (G)
Deoxyguanosine
dGMP
dGDP
dGTP
Cytosine (C)
Deoxycytidine
dCMP
dCDP
dCTP
Thymine (T)
Deoxythymidine
dTMP
dTDP
dTTP
RNA
Adenosine
AMP
ADP
ATP
Guanosine
GMP
GDP
GTP
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.
A-T/U pairing forms two hydrogen bonds---weak bond.
G-C pairing forms three hydrogen bonds---strong bond.
Therefore, G-C pairing is more stable than A-T/U pairing.

5. The double helical structure of DNA
Two complementary DNA strands run in anti-parallel, and are coiled around each other, forming a double helical structure.
There are two grooves on the surface of the double helix: the major groove and minor groove.
Regulatory molecules bind DNA in these grooves, changing the structure and function of DNA.

6. Higher level structures of DNA
In the cell, DNA molecules are highly compacted by association with proteins, forming nucleosomes and super coils in eukaryotes.
3D structure of a nucleosome

7. Structure of a tRNA-Ala
Structure of RNAs
RNAs are single stranded.
However, the complementary parts in a RNA molecule can form local double-stranded structures, thus, causing loops in the non-complementary regions.
Structure of a tRNA-Ala 5’ 3’
There are at least four major functional types of RNAs:
mRNA
tRNA
rRNA
Small regulatory RNAs, e.g., microRNAs and siRNAs

8. Protein structure
Proteins are polymers of amino acids linked by peptide bonds;
There are twenty amino acids found in proteins;
Amino acids differ in their side chains: R groups;
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
Secondary structure: the ways that the linear amino acid sequence form specific structures: a-helix and b-sheets.
a-helix
b-sheet
Tertiary structure: the ways that the linear amino acids of a polypeptide chain form a specific 3D structure for a specific function.
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
Genetic information is stored in DNA and passes from DNA to RNA to protein.
replication
DNA
Reverse
transcription
Transcription
mRNA
Translation
Protein

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

16. Structure of genes in prokaryotes
Adjacent genes of the same orientation in prokaryotes can be transcribed simultaneously, forming a structure, called an operon.
A typical operon contains the following elements:
Open reading frames;
Upstream regulatory elements
A downstream transcriptional terminator
Promoter
region
Ribsome binding site
FT binding
site
Terminator
TSS
-300
-35
-10 +1
Upstream regulatory region
Prediction of genes (ORFs) in prokaryotes has reached a high accuracy using machine learning algorithms.

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

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

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

20. Transcription
Transcription is controlled by the interaction of tran-acting elements called transcription factors (TFs) and cis-acting elements of DNA.
Prediction of cis-acting elements or TF binding sites is a challenging problem in computational biology.
Regulation of transcription in prokaryotes
FT binding
site
Promoter
region
Ribosome
binding site
Terminator
TSS a b
TF1
TF2 s
-300
-35
-10 +1
Transcription
3’ UTR
RNA

21. RNA processing in eukaryotes
A “cap” is added to the 5’ end, consisting of a methylated guanosine and cap-binding proteins
A string of bout 200 adenosines are added to the 3’ end. This poly-A tail is bound by poly-A binding proteins.
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
Translation starts by the association of ribosome with the ribosome binding site in the mRNA molecule, and the following components are involved :
Ribosome: consisting of a small and a large subunit, each is composed of a few rRNA and hundreds of protein molecules.
tRNA: carrying a specific amino acid, and recognizing a codon using its anti-codon through base paring.
Amino acyl-tRNA synthetase: attaching an amino acid to its tRNA.

23. Transcription and translation are two highly coupled process
FT binding
site
Promoter
region
Ribosome
binding site
Terminator
TSS a b
TF1
TF2 s
-300
-35
-10 +1
Transcription
Ribosome
binding site
3’ UTR
RNA
Translation
5’ UTR
Proteins

24. Standard genetic codons
There are 61 sense codons and 3 non-sense (stop) codons;
Degeneracy of codons;
Some codons for the same amino acid are more frequently used than the others, a phenomenon called codon bias;
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.