DNA, GENES and

CHROMOSOMES

Ahmed Ahmed OsmanOsman, , Ph.D.Ph.D.

Professor of Biochemistry, Faculty of Science, Professor of Biochemistry, Faculty of Science, Ain Shams UniversityAin Shams University

DNA is the genetic materials

DNA consists of sugar, phosphate and 4 types of N-containing bases

DNA DNA DNA DNA

Adenine (A) Guanine (G) Cytosine (C) Thymine (T)

Purines (Pu) Pyrimidines (Py)

The 2 polynucleotide chains (strands) are held together by hydrogen bonding between the bases of different nucleotides on each strand forming what is called complementary base-pairing

The sugars and phosphates of different nucleotides are attached covalently forming the DNA backbone

Energetically, the most favorable arrangement is packing the base pairs in the interior of the double stranded structure, thus holding the sugar-phosphate backbones at an equal distance along the DNA molecule.

DNA and chromosomes:

In eukaryotes, almost all DNA is sequestered in the nucleus, where most biological processes dealing with DNA take place. The DNA is divided between a set of different chromosomes, e.g. the human genome contains 3.2 X 10E9 nucleotide pairs distributed over 24 different chromosomes. Each chromosome consists of a single, enormously long linear DNA molecule associated with proteins that fold and pack the fine DNA thread into a more compact structure.

Structural Elements of Chromosomes

RNA & theTranscriptome

Similar to DNA, RNA consists of pentose sugar, phosphate and one of 4 different N-containing bases; However, unlike DNA, they are mostly arranged in a single chain.

The sugar is ribose;The 4 bases are two 2-ring bases called purines and

two 1-ring bases called pyrimidines.

DNA DNA DNA DNA

Adenine (A) Guanine (G) Cytosine (C) Uracil (U)

Purines (Pu) Pyrimidines (Py)

Ribose

End modification,Splicing & Editing

Processing Processing

Proteins & theProteome

Peptide bond

R1R2

Amino acid 1 Amino acid 2

Dipeptide

DNA

RNA

Protein

The Flow of Information in the Cell:

From DNA to RNA through Transcription process;

It involves copying the stored genetic information in the gene through the synthesis of a complementary strand to one of the 2 DNA strands of the gene (the template strand) using a DNA-dependent RNA polymerase that produces the mRNA.

From RNA to protein through Translation process;

It involves the translation of the genetic message carried by the mRNA into a specific amino acid sequence (the Genetic Code), utilizing adaptor molecules (tRNAs)

that form bridges between the nucleotide sequence of the mRNA and the amino acid sequence of the encoded protein.

Tran

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The Genetic Code: A, G, T and C nucleotides are found in DNA of all organisms that

have DNA carries their genetic information. Each 3 nucleotides form a genetic word that called “Codon”, 43 =

64 codons (to cover all the 20 different amino acids). A specific codon will incorporate only one specific amino acid. However, with few exceptions, a specific amino acid could be represented by more than one codon, a phenomenon called “degeneracy”. ATG (or AUG in mRNA) is a codon that is recognized by amino-

methionyl tRNA (encoding methionine; Met; M). This codon is also present in the beginning of the coding sequence of most genes. When present in this position, it is called a “Initiation codon; Start Met; Start ATG/AUG”. The codons, to which no corresponding tRNAs are present, (UAA; UAG & UGA)induce termination of protein translation process and thus they are called stop (termination) codons.

The process of codon recognition by tRNA takes place by complementary base pairing between the codon carried by the mRNA and a complementary triplet nucleotides (in anti- parallel orientation) in the tRNA molecule. This is called the “anti-codon”. The tRNAs are activated by forming amino-acyl tRNA intermediates. This activation reaction is catalyzed by a class of enzymes that is called aminoacyl-tRNA synthetases. At least one species of tRNA exists for each of the 20 amino

acids in each cell (one species of tRNA for each codon except the stop codons).

The Genetic Code, cont.:

Genetic information flow; from DNA to proteins:

The genetic information is specified by the nucleotide sequence of one of the 2 strands of the DNA molecule that is representing the gene (called coding strandcoding strand). The transcription process takes place, by complementary base pairing, from the strand that is complementary to the coding strand (called template strandtemplate strand), in order to create an mRNA molecule that is an identical copy to the coding strand (with the exception of the replacement of “Ts” in DNA by “Us” in RNA). Since the amino acid sequence is determined by the sequence

of the 3-nucleotide codons, then the gene sequence should have 3 reading possibilities for each strand, based on which nucleotide of the 3-letter codon to start with. Each reading possibility is called a “reading framereading frame”.

Genetic information flow; from DNA to proteins, cont.:

Thus, each DNA molecule that represents a certain gene should have 6 reading frames, or 3 from each strand (frames 1-3). The reading frames from the coding strand designated “+” frames, while those from template strand are “-” frames. Only one frame represents the genetic information of the gene. In most cases, this frame is the only opened frame (called “Open Reading FrameOpen Reading Frame; ORFORF”), where other frames are frequently interrupted by stop codons. The amino acid-coding frame may have non-coding sequence in the beginning and at the end (called “5’- and 3’- un- translated regions; UTRs”).

DNA sequence and translation / reading framesDNA sequence and translation / reading frames

DNA sequence and translation / reading framesDNA sequence and translation / reading frames . . . . . . 1 GGCTCCGCGGCCGCCTTGTTTAACTTTAAGAAGGAGCCCTTCACTCGAGTTAACGACAAG 60180 CCGAGGCGCCGGCGGAACAAATTGAAATTCTTCCTCGGGAAGTGAGCTCAATTGCTGTTC 121 G S A A A L F N F K K E P F T R V N D K A P R P P C L T L R R S P S L E L T T S L R G R L V * L * E G A L H S S * R Q   A G R G G Q K V K L L L G E S S N V V L P E A A A K N L K L F S G K V R T L S L S R P R R T * S * S P A R * E L * R C  . . . . . . 61 CACAACTTTCTACAACCATATCTTCATAAACTCTTAATACAACATCTCCATTTTGACTAT 120120 GTGTTGAAAGATGTTGGTATAGAAGTATTTGAGAATTATGTTGTAGAGGTAAAACTGATA 61 H N F L Q P Y L H K L L I Q H L H F D Y T T F Y N H I F I N S * Y N I S I L T Q L S T T I S S * T L N T T S P F * L   V V K * L W I K M F E * Y L M E M K V I L K R C G Y R * L S K I C C R W K S * C S E V V M D E Y V R L V V D G N Q S  . . . . . . 121 GATATAATAATGATTGTGATGATAATTGATGTGGTACACAACACGGACCAGAAATTCTAG 180 60 CTATATTATTACTAACACTACTATTAACTACACCATGTGTTGTGCCTGGTCTTTAAGATC 1 D I I M I V M I I D V V H N T D Q K F * I * * * L * * * L M W Y T T R T R N S Y N N D C D D N * C G T Q H G P E I L   I Y Y H N H H Y N I H Y V V R V L F E L S I I I I T I I I S T T C L V S W F N * Y L L S Q S S L Q H P V C C P G S I R