1. Nucleic Acids and Protein Synthesis
Dr. Mamoun Ahram
Biochemistry for Nursing
First semester

2. Terms DNA: deoxyribonucleic acid RNA: ribonucleic acid
Chromosomes: a long strand of DNA (in eukaryotes, when it is complexed with proteins, it is called chromatin)

4. Gene
Gene

5. Chromosome vs. chromatin
Chromatin is not condensed (uncoiled) and cannot be distinguished from each other before cell division.
Chromosomes: condensed (coiled) DNA molecules that can be distinguished from other chromosomes at cell division.

7. DNA and RNA are polymers
DNA and RNA are known as nucleic acids
They are linear polymers composed of monomers called nucleotides

8. Chemical composition and bonds
All nucleotides have a common structure:
a phosphate group linked by a phosphoester bond to a pentose
The pentose is linked to a nitrogenous base via a glycosidic bond

9. Glycosidic bond

10. DNA vs. RNA In RNA, the pentose is a ribose
In DNA, it is a deoxyribose

11. Nitrogenous bases
DNA and RNA each consists of only four different nucleotides of two classes: purines and pyrimidines
Purines are adenine and guanine
Pyrimidines are cytosine, thymine, and uracil
The bases adenine, guanine, and cytosine are found in both DNA and RNA
Thymine is found only in DNA
Uracil is found only in RNA
The bases are often abbreviated A, G, C, T, and U, respectively

12. The bases

13. How bases are connected to ribose?
In nucleotides, the 1 carbon atom of the sugar (ribose or deoxyribose) is attached to the nitrogen at
position 9 of a purine (N9) or
position 1 of a pyrimidine (N1)

14. Nucleotides are acidic
Due to the presence of phosphate, which dissociates at the physiological pH inside cells, freeing hydrogen ions and leaving the phosphate negatively charged

15. Nucleotides vs. Nucleosides
Nucleosides are combinations of a base and a sugar without a phosphate
Nucleotides are nucleosides that have one, two, or three phosphate groups esterified at the 5’ hydroxyl
Nucleoside monophosphates have a single esterified phosphate
diphosphates contain a two phosphate group
triphosphates have three phosphates

16. Nucleotides vs. Nucleosides

18. Nucleic acid polymer
When nucleotides polymerize to form nucleic acids, the hydroxyl group attached to the 3’ carbon of a sugar of one nucleotide forms a bond to the phosphate of another nucleotide
A single nucleic acid strand is a phosphate-pentose polymer (a polyester) with purine and pyrimidine bases as side groups
The links between the nucleotides are called phosphodiester bonds

19. Directionality
A nucleic acid strand has an end-to-end chemical orientation:
The 5’ end has a free hydroxyl or phosphate group on the 5’ carbon of its terminal sugar
The 3’ end has a free hydroxyl group on the 3’ carbon of its terminal sugar
This directionality has made polynucleotide sequences written and read in the 5'3' direction (from left to right)
Example: the sequence AUG is assumed to be (5')AUG(3')

20. DNA structure
DNA consists of two associated polynucleotide strands that wind together through space to form a structure often described as a double helix.

21. DNA structure
The sugar-phosphate groups are on the outside of the double helix, and the bases project into the interior.

22. DNA structure The sugar-phosphate groups are termed backbone.
The orientation of the two strands is antiparallel.

23. RNA structure
Note: RNA is single-stranded and does not have a specific structure

24. Base pairing
In DNA, the larger purine (A or G) must pair with a smaller pyrimidine (C or T)
A almost always hydrogen bonds with T and G with C, forming A·T and G·C base pairs
A is paired with T through two hydrogen bonds; G is paired with C through three hydrogen bonds

25. Chargaff's rules
In addition, Erwin Chargaff established certain rules about the amounts of each component of DNA:
Pyrimidines (T + C) always equals purines (A + G).
T always equals A.
C always equals G.
A + T is not necessarily equal to G + C.

26. Genetic heredity
It is the transfer of genetic material (DNA) from parents to offspring.
When a sperm fertilizes an egg, it combines a full set of DNA (one set of DNA molecule comes from father and one set DNA molecule from mother).
Cells divides and every time a cell divides, DNA must be copied.
When a “mother” cell divides, the information is passed along to the daughter cells, which ultimately pass this genetic information to their daughter cells.
Within cells, the genetic information is encoded in the DNA and it directs the synthesis of proteins, a process known as the expression of DNA.

27. Genetic processes
The genetic information occur as the result of three fundamental processes:
Replication is the process by which an identical copy of DNA is made when a cell divides.
Transcription is the process by which the genetic messages contained in DNA are read and copied into RNA, which carry the instructions stored in DNA out of the nucleus to the sites of protein synthesis.
Translation is the process by which the genetic messages carried by RNA are used to build proteins.

28. DNA replication

29. Semiconservative model
The process of replication follows the semiconservative model.
It means that the new DNA molecule is made of an old strand and a new strand each time a cell replicates its DNA.

30. DNA template
The process of DNA templating involves the recognition of each nucleotide in the DNA template strand by a free complementary nucleotide; that is A for T, C for G, T for A, and G for C

31. Enzyme and substrate
The nucleotide polymerizing enzyme is called DNA polymerase.
The free nucleotides that serve as substrates for this enzyme are deoxyribonucleoside triphosphates.

32. Origin of replication
DNA replication begins in the nucleus with partial unwinding of the double helix.
This process involves enzymes known as helicases that use unwind DNA.
The unwinding occurs in many specific locations known as origins of replication.
“Bubbles” are formed and each bubble is composed of replication forks.

33. The replication fork and types of new strands
Within a bubble, replication moves progressively along the parental DNA double helix bidirectionally.
Because of its Y-shaped structure, this active region is called a replication fork.

34. Direction of replication
DNA polymerase catalyzes the reaction between the phosphate on an incoming nucleotide and the free 3’-OH on the growing polynucleotide.
Therefore, the template strand can only be read in the 3’ –to-5’ direction, and the new DNA strand can grow only in the 5’ to 3’ direction.

35. New DNA (long vs short)
During replication, there is a long strand and shorter pieces of DNA at the growing replication fork
The small DNA fragments are known as Okazaki fragments
The Okazaki fragments polymerize in the 5-to-3 direction and join together after their synthesis to create long DNA chains

36. Leading vs. lagging strand
The DNA daughter strand that is synthesized continuously (the long strand) is known as the leading strand
On the other hand, the daughter strand synthesized discontinuously is known as the lagging strand
its synthesis is delayed waiting for the leading strand to expose the template strand.

37. DNA ligase
To form the lagging strand from the Okazaki fragments, these short fragments are joined by the action of an enzyme known as DNA ligase.

38. RNA: structure and function

39. DNA vs. RNA

40. Major types of RNA
Ribosomal RNAs: they are part of ribosomes, which are small granular organelles where protein synthesis takes place.
Each ribosome is a complex consisting of about 60% ribosomal RNA (rRNA) and 40% protein
Messenger RNAs (mRNA) carry information transcribed from DNA. They are formed in the cell nucleus and transported out to the ribosomes.
Transfer RNAs (tRNA) are smaller RNAs that deliver amino acids one by one to protein chains growing at ribosomes.

41. Transcription-the mechanism

42. General description
Transcription is the process of making RNA from DNA
One of the two strands of the DNA double helix acts as a template for the synthesis of an RNA molecule

43. Complementary sequences
As in DNA replication, the nucleotide sequence of the RNA chain is determined by the complementary base-pairing between incoming nucleotides and the DNA template
The RNA chain produced by transcription is also known as the transcript.

44. Enzyme and substrate
The enzymes that perform transcription are called RNA polymerases.
Like the DNA polymerase, RNA polymerases catalyze the formation of the phosphodiester bonds between two nucleotides.
The growing RNA chain is extended in the 5-to-3 direction.
The substrates are nucleoside triphosphates (ATP, CTP, UTP, and GTP).

46. Stages of transcription
Initiation: it starts when RNA polymerase recognizes a control segment (called promoter) in DNA that precedes the first nucleotides that is transcribed.
Elongation: RNA polymerase moves down the DNA segment.
Termination: Transcription ends when the RNA polymerase reaches a stop sequences.

47. Gene
The part of DNA that is transcribed into RNA.

48. Introns and exons Not the whole of mRNA is used to make a protein.
The part that is used to make a protein is called an exon.
Exons are interrupted by sequences known as introns, which are removed.

49. RNA splicing
The intron sequences are removed from the newly synthesized RNA through the process of RNA splicing.

50. Alternative splicing These are known as protein isoforms.
The transcripts are spliced in different ways to produce different mRNAs and different proteins.
These are known as protein isoforms.
The process is known as alternative splicing.

51. The genetic code

52. What is a codon?
An mRNA chain is like a coded sentence that spells out the order in which amino acid residues that form a protein.
Each word consists of a triplet of ribonucleotides, or codon, in the mRNA sentence, which in turn corresponds to a specific amino acid.
Since there are four ribonucleotides, the possible number of codons = 4 x 4 x 4 = 64 codons.

53. The genetic code Of the 64 codons, 61 specify an amino acid.
The remaining three (UAA, UAG, and UGA) are stop codons that signal the termination of protein synthesis
Since there are 20 amino acids, some amino acids are specified by more than one codon.

56. Major types of RNA
Protein synthesis involves interactions between three types of RNA molecules:
mRNA templates
tRNAs
rRNAs

57. General process
Once made in the nucleus, mRNA is moved out of nucleus into cytosol where it binds to the ribosome, which are made of rRNA and proteins.
Amino acids are delivered one by one by tRNA molecules to be joined into a specific protein by the ribosomes.

58. Transfer RNA (tRNA)

59. General function
Reading the nucleotide sequence of mRNA and translating it into amino acids is mediated by transfer RNA molecules

60. tRNA structure
tRNAs are short, L-shaped, single RNA chains held together by regions of base pairing.
An amino acid is covalently attached to the ribose of the terminal adenosine
Each tRNA molecule carries one amino acid.

61. Codon vs. anticodon
tRNAs also contain a three-nucleotide sequence known as anticodon that pairs with mRNA molecules.
The anticodon of each tRNA is complementary to an mRNA codon and is specific to the particular amino acid that the tRNA carries.

62. Ribosomes and ribosomal RNA (rRNA)

63. Prokaryotic vs. eukaryotic ribosomes
Ribosomes consist of two subunits: small and large.
The large ribosomal subunit is able to catalyze the formation of peptide bonds (the peptidyl transferase reaction).

64. The general mechanism of translation

65. Directionality
Translation is generally divided into three stages: initiation, elongation, and termination.
The direction of translation is 5’  3’.
Protein synthesis begins at the amino terminus and extends toward the carboxyl terminus.

66. Translation initiation
The mRNA binds to the small ribosomal subunit followed by the first tRNA.
The first tRNA (codon) that bids to the mRNA is AUG, which codes for methionine.
The large ribosomal subunit the associates with the three.

67. tRNA-binding sites in ribosomes
The ribosome has three sites for tRNA binding:
P (peptidyl) site,
A (aminoacyl) site, and
E (exit) site
The first tRNA binds to the P site.

68. Translation elongation I
The next aminoacyl tRNA binds to the A site by pairing the anticodon with the second codon of the mRNA.
A peptide bond links amino acid 1 to amino acid 2.
GTP
Energy

69. Translation elongation II
The ribosome moves three nucleotides along the mRNA, positioning the next codon in an empty A site
The empty tRNA moves from the A site to the E site, and the tRNA with two amino acids moves to the P site.
A new aminoacyl tRNA binds to the A site.

70. and so on

71. Translation termination
When a stop codon (UAA, UAG, or UGA) is reached, an enzyme, called the releasing factor, binds to a termination codon and releases the complex of mRNA, tRNA, and the ribosomal subunits.

72. Polyribosomes
Each messenger RNA can be translated by several ribosomes at the same time.
The group of ribosomes bound to an mRNA molecule is called a polyribosome.