DNA contains the genetic material of organisms and is made up of nucleotides with a sugar-phosphate backbone. DNA is organized into chromosomes within the nucleus of eukaryotic cells. Genetic information flows from DNA to protein through two main processes - transcription of DNA to mRNA and translation of mRNA to protein using transfer RNA and ribosomes.

1. DNA, GENES
and
CHROMOSOMES
Ahmed Osman, Ph.D.
Professor of Biochemistry, Faculty of Science,
Ain Shams University

2. DNA is the genetic materials

3. 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)

4. 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

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

6. 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.

7. 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.

11. Structural Elements of Chromosomes

12. RNA & the
Transcriptome

13. 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.
Ribose
DNA DNA DNA DNA
Adenine (A) Guanine (G) Cytosine (C) Uracil (U)
Purines (Pu) Pyrimidines (Py)

14. End modification,
Processing Processing
Splicing & Editing

15. Proteins & the
Proteome

17. R1 R2
Amino acid 1 Amino acid 2

Dipeptide
Peptide bond

18. The Flow of Information in the Cell: DNA
From DNA to RNA through Transcription
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. RNA
Translation
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 Protein
the mRNA and the amino acid sequence of the encoded
protein.

19. 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.

20. The Genetic Code, cont.:
 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).

22. 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 strand).
strand
 The transcription process takes place, by complementary
base pairing, from the strand that is complementary to the coding
strand (called template strand), in order to create an
strand 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 frame”.
frame

23. 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 Frame; ORF”), where other frames
Frame ORF 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”).

24. DNA sequence and translation / reading frames

25. DNA sequence and translation / reading frames
. . . . . .
1 GGCTCCGCGGCCGCCTTGTTTAACTTTAAGAAGGAGCCCTTCACTCGAGTTAACGACAAG 60
180 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 120
120 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