DNA , RNA structures & biological functions

1. DNA, RNA, Proteins.
The molecules of life

2. ‫النواة‬ ‫داخل‬ ‫النووية‬ ‫االحماض‬ ‫من‬ ‫نوعان‬ ‫يوجد‬:
.1‫رايبوزي‬ ‫ديوكسي‬ ‫حمض‬Deoxyribonucleic acid
.2‫ريبوزي‬ ‫حمض‬Ribonucleic acid
‫وال‬ ‫النيوكليوتيدات‬ ‫تسمى‬ ‫وحدات‬ ‫من‬ ‫النووية‬ ‫االحماض‬ ‫تتركب‬‫تي‬
‫فوسفات‬ ‫ومجموعة‬ ‫خماسي‬ ‫وسكر‬ ‫نيتروجينية‬ ‫قواعد‬ ‫من‬ ‫تتكون‬

3.  Nucleotides
◦ A, G, T, C
 Sugar and
phosphate form the
backbone
 Bases lie between
the backbone
 Held together by
H-bonds between
the bases
◦ A-T – 2 H bonds
◦ G-C – 3 H bonds

4. Basic chemical units
 A 5 carbon sugar - deoxyribose
 phosphate - link between sugars
 bases: purines = adenine and guanine
pyrimidines = thymine and cytosine

5.  Base-pairing rules
◦ AT only (AU if DNA-
RNA hybrid)
◦ GC only
 DNA strand has
directionality – one end
is different from the
other end
 2 strands are anti-
parallel, run in opposite
directions
◦ Complementarity results
◦ Important to replication

7. ‫العالمان‬ ‫تمكن‬‫وكريك‬ ‫واطسن‬‫وضع‬ ‫من‬‫ا‬ ‫ن‬ ‫د‬ ‫للـ‬ ‫نموذج‬.
‫النيتروجي‬ ‫القواعد‬ ‫يمثل‬ ‫حيث‬ ‫شريطين‬ ‫من‬ ‫يتركب‬ ‫النموذج‬ ‫هذا‬‫ني‬‫ة‬
‫الدرج‬ ‫وهذا‬ ‫السلم‬ ‫هذا‬ ‫درجات‬(‫النيتروجينية‬ ‫القواعد‬)
‫هيدروجي‬ ‫برابطة‬ ‫بالثايمين‬ ‫يرتبط‬ ‫الذي‬ ‫االدنين‬ ‫من‬ ‫آما‬ ‫يتكون‬‫أو‬ ‫ثنائية‬ ‫نية‬
‫ثال‬ ‫هيدروجينية‬ ‫برابطة‬ ‫بالسيتوزين‬ ‫يرتبط‬ ‫الذي‬ ‫الجوانين‬ ‫من‬‫ثية‬
‫ويلتف‬DNA‫ك‬ ‫في‬ ‫نيوكليوتيدات‬ ‫عشر‬ ‫يوجد‬ ‫بحيث‬ ‫نفسه‬ ‫حول‬‫لفة‬ ‫ل‬
‫ليتكون‬DNA‫نموذج‬ ‫وضع‬ ‫فبمجرد‬ ‫المزدوج‬ ‫الحلزوني‬DNA‫بدأ‬
‫سلوك‬ ‫دراسة‬ ‫في‬ ‫التفكير‬DNA‫ثابت‬ ‫سلوكه‬ ‫وهل‬ ‫نفسه‬ ‫يضاعف‬ ‫وكيف‬
‫؟‬ ‫الكائنات‬ ‫جميع‬ ‫في‬

10.  We must start to think of the nucleotides – A,
G, C and T as part of a special language – the
language of genes that we will see translated
to the language of amino acids in proteins

11.  A gene is the sequence of nucleotides
within a portion of DNA that codes for a
peptide or a functional RNA
 Sum of all genes = genome

12. Denaturation.1‫الطبيعي‬ ‫التركيب‬ ‫تغير‬
‫سلسلتي‬ ‫بين‬ ‫الهيدروجينية‬ ‫الروابط‬ ‫فك‬ ‫على‬ ‫يعمل‬ ‫التسخين‬‫مما‬ ‫الحلزون‬
‫الضو‬ ‫االمتصاص‬ ‫ويزيد‬ ‫اللزوجة‬ ‫تزيد‬ ‫وبذلك‬ ‫فصلهما‬ ‫إلى‬ ‫يؤدي‬‫ئي‬
‫البنفسجية‬ ‫فوق‬ ‫لألشعة‬.
‫بدرجة‬ ‫الطبيعي‬ ‫التغير‬ ‫عندها‬ ‫يحدث‬ ‫التي‬ ‫الحرارة‬ ‫درجة‬ ‫تعرف‬
‫اإلنصهار‬Tm
‫التبريد‬ ‫عند‬ ‫أخرى‬ ‫مرة‬ ‫السلسلتان‬ ‫تتحد‬

13. 2-‫الكثافة‬
‫المزد‬ ‫الحلزون‬ ‫في‬ ‫والسايتوسين‬ ‫الجوانين‬ ‫بزيادة‬ ‫الكثافة‬ ‫تزداد‬‫وج‬(‫لماذا؟‬)
‫الشريط‬ ‫كثافة‬ ‫من‬ ‫أعلى‬ ‫المزدوج‬ ‫الحلزون‬ ‫كثافة‬(‫لماذا؟‬)
3-‫والشكل‬ ‫الحجم‬
‫الب‬ ‫في‬ ‫وحلقى‬ ‫الراقية‬ ‫الكائنات‬ ‫في‬ ‫خيطي‬ ‫متفرع‬ ‫غير‬ ‫مستقيم‬‫كتريا‬.

14.  On your paper, complete the missing DNA
strand by adding the complementary bases.
 A T C G T G C C A T C
 T A G C A A C G G T A G
 Make the complementary RNA strand for the
single strand of DNA below:
 A A T C A T C A C G T T
 U U A G U A G U G C A A

15.  What is the Main Job of DNA?
 It contains the code for the proteins an
organism may produce.
 What are the basic units or monomers of
DNA?
 Nucleotides make up DNA.
 Where is DNA found?
 It is found mostly in the nucleus of a cell
making up its chromosomes.

16. ‫رايبوزي‬ ‫حمض‬
RiboNucliec
Acide
‫عن‬ ‫يختلف‬DNA‫في‬:
‫واحد‬ ‫شريط‬.
‫خماسي‬ ‫سكر‬
‫الرايبوز‬Ribose
‫يوراسيل‬Uracile‫بدل‬
‫الثيامين‬Thyamine.

17.  RNA is typically a single-
stranded molecule.
 Q: What base does RNA
have that DNA doesn’t
have?
 Q: What base does DNA
contain that RNA Doesn’t
have?
Image: RNA, Biology CornerFrom the Virtual Microbiology Classroom on ScienceProfOnline.com

18.  What is the Main Job of RNA?
 It retrieves the protein code from DNA and
carry out the processes needed to produce
proteins.
 What are the basic units or monomers of
RNA?
 Nucleotides
 Where is RNA found?
 It is found both inside and outside of the
nucleus.

19.  Messenger RNA (mRNA) - Long strands of
RNA nucleotides that are formed
complementary to one strand of DNA. They
travel from the nucleus to the ribosome to
direct the synthesis of a specific protein.
 Ribosomal RNA (rRNA) - Associates with
proteins to form ribosomes in the
cytoplasm.
 Transfer RNA (tRNA) - Smaller segments of
RNA nucleotides that transport amino acids
to the ribosome.

21.  Nucleic acids are polymers
◦ Monomers are called nucleotides
◦ Nucleotides = base + sugar + phosphate
 Base = purine or pyrimidine
 Purines = adenine, guanine
 Pyrimidines = thymine, cytosine, uracil
 Sugar = deoxyribose or ribose
 Phosphate, a single phosphate in DNA
◦ Sugar of nt 1 is linked to the phosphate of nt 2 by
a phosphodiester bond

22. From the Virtual Microbiology Classroom on ScienceProfOnline.com
Made of monomer building blocks called
__________________.
Image: Nucleotide Structure, Wikipedia

24. ‫ع‬ ‫كريك‬ ‫فرانسز‬ ‫العالم‬ ‫تمكن‬‫ام‬
1956‫نظرية‬ ‫وضع‬ ‫من‬ ‫م‬
‫توضح‬ ‫والتي‬ ‫المركزي‬ ‫المبدأ‬
‫البيو‬ ‫األحداث‬ ‫تدفق‬ ‫كيفية‬‫لوجية‬
‫خالل‬ ‫من‬ ‫تحدث‬ ‫التي‬ ‫الهامة‬
‫ال‬ ‫جزئ‬DNA.

25. Process of duplication of the entire genome prior to cell
division
Biological significance
 extreme accuracy of DNA replication is necessary in
order to preserve the integrity of the genome in
successive generations
 In eukaryotes , replication only occurs during the S
phase of the interphase of the cell cycle.
 Replication rate in eukaryotes is slower resulting in a
higher fidelity/accuracy of replication in eukaryotes

26. 26
 S phase during interphase of the
cell cycle
 Nucleus of eukaryotes
Mitosis
-prophase
-metaphase
-anaphase
-telophase
G1 G2
S
phase
interphase
DNA replication takes
place in the S phase.
copyright cmassengale

27. ◦ Initiation
 Proteins bind to DNA and open up double helix
 Prepare DNA for complementary base pairing
◦ Elongation
 Proteins connect the correct sequences of nucleotides into a
continuous new strand of DNA
◦ Termination
 Proteins release the replication complex

28. 28
 Begins at Origins of Replication
 Two strands open forming Replication
Forks (Y-shaped region)
 New strands grow at the forks
Replication
Fork
Parental DNA Molecule
3’
5’
3’
5’copyright cmassengale

29. 29
 As the 2 DNA strands open at
the origin, Replication Bubbles
form
 Prokaryotes (bacteria) have a
single bubble
 Eukaryotic chromosomes have
MANY bubbles
Bubbles Bubbles
copyright cmassengale

30. 30
 Enzyme Helicase unwinds
and separates the 2 DNA
strands by breaking the
weak hydrogen bonds
 Single-Strand Binding
Proteins attach and keep
the 2 DNA strands
separated and untwisted
copyright cmassengale

31. 31
 Enzyme Topoisomerase attaches to the
2 forks of the bubble to relieve stress
on the DNA molecule as it separates
Enzyme
DNA
Enzyme
copyright cmassengale

32. 32
 Before new DNA strands can form,
there must be RNA primers present
to start the addition of new
nucleotides
 Primase is the enzyme that
synthesizes the RNA Primer
 DNA polymerase can then add the
new nucleotides
copyright cmassengale

33. 33
 DNA polymerase can only add nucleotides
to the 3’ end of the DNA
 This causes the NEW strand to be built
in a 5’ to 3’ direction
RNA
PrimerDNA Polymerase
Nucleotide
5’
5’ 3’
Direction of Replication
copyright cmassengale

34. 34
O
O=P-O
O
Phosphate
Group
N
Nitrogenous base
(A, G, C, or T)
CH2
O
C1
C4
C3 C2
5
Sugar
(deoxyribose)
copyright cmassengale

35. 35
P
P
P
O
O
O
1
2
3
4
5
5
3
3
5
P
P
P
O
O
O
1
2 3
4
5
5
3
5
3
G C
T A
copyright cmassengale

36. 36
 The Leading Strand is synthesized as
a single strand from the point of
origin toward the opening replication
fork
RNA
PrimerDNA PolymeraseNucleotides
3’5’
5’
copyright cmassengale

37. 37
 The Lagging Strand is synthesized
discontinuously against overall direction of
replication
 This strand is made in MANY short segments
It is replicated from the replication fork
toward the origin
RNA Primer
Leading Strand
DNA Polymerase
5’
5’
3’
3’
Lagging Strand
5’
5’
3’
3’
copyright cmassengale

38. 38
 Okazaki Fragments - series of short
segments on the lagging strand
 Must be joined together by ligase
enzyme
Lagging Strand
RNA
Primer
DNA
Polymerase
3’
3’
5’
5’
Okazaki Fragment
copyright cmassengale

39. 39
 The enzyme Ligase joins the Okazaki
fragments together to make one
strand
Lagging Strand
Okazaki Fragment 2
DNA ligase
Okazaki Fragment 1
5’
5’
3’
3’
copyright cmassengale

40. 40
Replication
Fork
Point of Origin
copyright cmassengale

41.  Helicase opens double helix and helps it
uncoil
 Single-strand binding proteins (SSBP)
keep strands separated – large amount of
this protein required
 Sliding clamp
◦ Subunit of polymerase
◦ Helps polymerase slide along strand
 All are coordinated with one another to
produce the growing DNA strand (protein
machine)

42. 42
 DNA polymerase initially makes about 1
in 10,000 base pairing errors
 Enzymes proofread and correct these
mistakes
 The new error rate for DNA that has
been proofread is 1 in 1 billion base
pairing errors
copyright cmassengale

43. 43
 What would be the
complementary DNA
strand for the following
DNA sequence?
DNA 5’-CGTATG-3’
copyright cmassengale

44. 44
DNA 5’-CGTATG-3’
DNA 3’-GCATAC-5’
copyright cmassengale

45. 45
 Chemicals & ultraviolet radiation
damage the DNA in our body cells
 Cells must continuously repair
DAMAGED DNA
 Excision repair occurs when any of
over 50 repair enzymes remove
damaged parts of DNA
 DNA polymerase and DNA ligase
replace and bond the new nucleotides
together
copyright cmassengale

46.  A permanent change that occurs in a cell’s
DNA is called a mutation.
 Types of Mutations
◦ Point mutation
◦ Insertion
◦ Deletion

48. Normal hemoglobin DNA
‫الطبيعي‬ ‫الهيموجلوبين‬ ‫دنا‬
Mutant hemoglobin DNA
‫الطافر‬ ‫الهيموجلوبين‬ ‫دنا‬
Sickle-cell hemoglobin
‫المنجلية‬ ‫الخلية‬ ‫هيموجلوبين‬
Normal hemoglobin
‫الطبيعي‬ ‫الهيموجلوبين‬
mRNAmRNA
ValGlu
*
*
The molecular basis of Sickle-cell disease
‫المنجلية‬ ‫الخلية‬ ‫لمرض‬ ‫الجزيئي‬ ‫األساس‬

49. Normal gene
‫الطبيعي‬ ‫الجين‬
Protein
‫بروتين‬
Base substitution
‫القاعدية‬ ‫االستعاضة‬
Base deletion
‫القاعدي‬ ‫الحذف‬
Missing
‫حذف‬
mRNA
Met Lys Phe Ser Ala
Met Lys Phe Gly Ala
Met Lys Leu Ala His
Types of
mutations and
their effects
‫وتأثيراتها‬ ‫الطفرات‬ ‫أنواع‬
‫المختلفة‬

51.  Through transcription, the DNA code is
transferred to mRNA in the nucleus.
 DNA is unzipped in the nucleus and RNA
polymerase binds to a specific section where
an mRNA will be synthesized.

52.  As the DNA strand unwinds, the RNA polymerase
initiates mRNA synthesis and moves along one of the
DNA strands in the 3’ to 5’ direction.
 Template strand – read by RNA polymerase, and
mRNA is synthesized by a complement to the DNA
nucleotides.
 Nontemplate strand – not read by RNA Polymerase
 The mRNA transcript is manufactured in a 5’ to 3’
direction, adding each new RNA nucleotide to the 3’
end.
 Uracil is incorporated instead of thymine as the
mRNA molecule is made.
 Eventually, the mRNA is released, and the RNA
polymerase detaches from the DNA.
 The new mRNA then moves out of the nucleus
through the nuclear pore into the cytoplasm.

53.  The code on the DNA is interrupted
periodically by sequences that are not in the
final mRNA.
 Intervening sequences are called introns.
 Remaining pieces of DNA that serve as the
coding sequences are called exons.
 Other processing includes adding a protective
cap on the 5’ end and adding a tail of many
adenine nucleotides, called the poly-A tail, to
the 3’ end of the mRNA.
 The cap aids in ribosome recognition but
scientists do not understand the full function
of the poly-A tail.
 The mRNA that reaches the ribosome has
been processed.

54. ‫النسخ‬:‫لجزيء‬ ‫معين‬ ‫جين‬ ‫في‬ ‫الوراثية‬ ‫التعليمات‬ ‫كتابة‬ ‫إعادة‬ ‫خاللها‬ ‫من‬ ‫يتم‬ ‫عملية‬RNA.
‫في‬ ‫النسخ‬ ‫يتم‬‫أنوية‬،‫النواة‬ ‫حقيقية‬ ‫الخاليا‬‫و‬‫على‬ ‫تحتوي‬ ‫التي‬ ‫السيتوبالزم‬ ‫منطقة‬ ‫في‬DNA‫النواة‬ ‫بدائية‬ ‫الخاليا‬ ‫في‬.
‫النسخ‬ ‫خطوات‬
1-‫أنزيم‬ ‫يرتبط‬
‫بلمرة‬RNA‫في‬
‫االبتداء‬ ‫موقع‬.
‫هو‬ ‫االبتداء‬ ‫موقع‬
‫من‬ ‫معين‬ ‫تتابع‬
‫نيوكليوتيدات‬DNA،
‫أنزيم‬ ‫يرتبط‬ ‫حيث‬
‫بلمرة‬RNA
‫النسخ‬ ‫يبدأ‬.
‫سلسلتي‬ ‫التفاف‬ ‫ينفك‬
DNA‫تنفصالن‬ ‫و‬.
2-‫بلمرة‬ ‫أنزيم‬ ‫يضيف‬RNA‫نيوكليوتيدات‬RNA‫جانب‬ ‫إلى‬ ‫الحرة‬
‫سلستي‬ ‫إحدى‬ ‫في‬ ‫الموجودة‬ ‫النيوكليوتيدات‬DNA.‫عن‬ ‫تنتج‬ ‫التي‬ ‫السلسلة‬
‫جزيء‬ ‫هي‬ ‫ذلك‬RNA.‫تضاعف‬ ‫في‬ ‫كما‬ ‫و‬DNA‫القواعد‬ ‫ازدواج‬ ‫يحدد‬
‫في‬ ‫النيوكليوتيدات‬ ‫تتابع‬ ‫المتممة‬ ‫النيتروجينية‬RNA‫حديثا‬ ‫أنتج‬ ‫الذي‬
‫فقط‬ ‫معينة‬ ‫منطقة‬ ‫النسخ‬ ‫يستخدم‬(‫جينا‬)‫سلستي‬ ‫إحدى‬ ‫في‬DNA‫كقالب‬.‫و‬
‫بلمرة‬ ‫أنزيم‬ ‫يغادر‬ ‫فيما‬RNA‫سلسلتا‬ ‫تلتف‬ ،‫المنطقة‬ ‫هذه‬DNA‫مجددا‬.
3-‫أنزيم‬ ‫يصل‬RNA،‫انتهاء‬ ‫إشارة‬ ‫إلى‬‫و‬‫تتابع‬ ‫هو‬
‫معين‬ ‫جين‬ ‫نهاية‬ ‫يحدد‬ ‫النيوكليوتيدات‬ ‫من‬ ‫معين‬.
‫بلمرة‬ ‫أنزيم‬ ،‫هذه‬ ‫اإليقاف‬ ‫إشارة‬ ‫بلوغ‬ ‫عند‬RNA‫يحرر‬
RNA‫حديثا‬ ‫الناتج‬‫و‬DNA.‫يمكن‬‫ل‬RNA‫نتج‬ ‫الذي‬
‫يكون‬ ‫أن‬ ‫النسخ‬ ‫أثناء‬mRNA‫أو‬tRNA‫أو‬rRNA

55.  Scientist knew that 20 amino acids were
used to make proteins, so they knew that
the DNA must provide at least 20 different
codes.
 Experiments during the 1960s
demonstrated that the DNA code was a
three-base code.
 The three-base code in DNA or mRNA is
called a codon.
 Each of the three bases of the codon in the
DNA is transcribed into the mRNA code.

57.  In translation, tRNA molecules act as the
interpreters of the mRNA codon sequence.
 At the middle of the folded strand, there is a
three-base coding sequence called the
anticodon.
 Each anticodon is complementary to a codon
on the mRNA.

58.  When the mRNA leaves the nucleus , the two parts of the
ribosome come together and attach to the mRNA to
complete the ribosome.
 Once the mRNA is associated with the ribosome, tRNA
with the anticodon carrying its respective amino acid will
move in and bind to the mRNA codon at the 5’ end.
 The rRNA in the ribosome now acts as enzyme catalyzing
the formation of a peptide bond between the amino acids
creating the amino acid chain or peptide chain.
 As the amino acids join the tRNA is released.
 This process continues until the ribosome contains a stop
codon and signals the end of protein synthesis.
 Protein release factors cause the mRNA to be released
from the last tRNA and the ribosome disassemble.

59. 1-‫البدء‬:
‫البنائ‬ ‫الوحدتان‬ ‫ترتبط‬‫يتان‬
‫للرايبوسوم‬‫و‬mRNA‫و‬
tRNA‫يحمل‬ ‫الذي‬
‫المثيونين‬.
2-‫االستطالة‬:
‫يرتبط‬tRNA‫يحمل‬ ‫الذي‬
‫الذي‬ ‫األميني‬ ‫الحمض‬
‫المضاد‬ ‫الكودون‬ ‫يحدده‬
‫بالكودون‬‫في‬ ‫التالي‬
mRNA‫رابطة‬ ‫تتكون‬ ‫و‬
‫ببتيدية‬‫األحماض‬ ‫بين‬
‫األمينية‬‫المتجاورة‬
3-‫استمرارية‬
‫االستطالة‬
‫ينفصل‬tRNA
‫األول‬‫و‬‫يترك‬
‫األميني‬ ‫حمضه‬
4-‫اإلنهاء‬
‫العملية‬ ‫تنتهي‬
‫بلوغها‬ ‫عند‬
‫إيقاف‬ ‫كودون‬(
‫له‬ ‫يتوفر‬ ‫ال‬
tRNA)
5-‫الإلنفصال‬
‫الوحدتان‬ ‫تنفصل‬
‫البنائيتان‬
‫للرايبوسوم‬‫يحر‬ ‫و‬‫ر‬
‫عديد‬‫الببتيد‬
‫المتكون‬.

61.  Summary of
transcription
and
translation
Figure 10.15
1Stage mRNA is
transcribed from a
DNA template.
Anticodon
DNA
mRNA
RNA
polymerase
TRANSLATION
Enzyme
Amino acid
tRNA
Initiator
tRNA
Large
ribosomal
subunit
Small
ribosomal
subunit
mRNA
Start
Codon
2Stage Each amino
acid attaches to its
proper tRNA with the
help of a specific
enzyme and ATP.
3Stage Initiation of
polypeptide synthesis
The mRNA, the first
tRNA, and the
ribosomal subunits
come together.
TRANSCRIPTION

62.  Controlling transcription
◦ Transcription factors ensure that a gene is used at
the right time and that proteins are made in the
right amounts
◦ The complex structure of eukaryotic DNA also
regulates transcription.

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