and passed to subsequent generations of cells or passed between organisms,
Chromosomes: are cellular structures that physically carry hereditary information. The chromosomes contain the genes.
Genes: are segments of DNA (except in some viruses, in which they are made of RNA) that code for functional products.
Genotype: Is collection of genes
Genotype of an organism is its genetic makeup. The information that codes for all the particular characteristics of the organism.
Phenotype: Is collection of proteins
Refers to actual, expressed properties such as the organism’s ability to perform a particular chemical reaction.
As one of four macromolecules (carbohydrates, lipids, proteins, NA) in the cell, is classified as one type of NA. The other type of NA is RNA.
A very large, long molecule is made up of smaller “subunits” called Nucleotides .
Are made up of three components:
One of four nitrogenous bases (cyclic compounds made up of C, H, O, N): Adenine (A), Thymine (T), Cytosine C, guanine G.
a) Purines : A and G (double-ring structure)
b) Pyrimidines : T, C, and U (single-ring structure)
A 5-carbon sugar (deoxyribose)
A phosphate group
one base + deoxyribose +phosphate=nucleotide
Bases are held together by hydrogen bond
G = C
Combination of a purine or pyrimidines plus a pentose sugar.
purine+ sugar No phosphate pyrimidine+ sugar group
N-glycosidic linkage - refers to the type of bond between the sugar and base
Is a double helical molecule consists of two “strands” that form a “right-handed” spiral
The two strands are aligned antiparallel to each other (one seems to pointing downward and other upward)
The two strands are held together by hydrogen bonds.
THE GENETIC MATERIAL
DNA = deoxyribonucleic acid. The sugars in DNA contain a 2' hydrogen
DNA is chemically stable
DNA functions as the carrier of genetic information (usually)
DNA contains the bases A, G, C, and T
RNA = ribonucleic acid. The sugars in RNA contain a 2' hydroxyl group
Due to the presence of the 2' hydroxyl group, RNA is less stable than DNA
RNA usually functions as the carrier of genetic information
RNA contains the bases A, G, C and U
Oligonucleotide growth occurs in the 5' to 3' direction via an attack by 3' hydroxyl groups upon the 5' alpha phosphate of nucleotide triphosphates
The resulting linkage is a phosphodiester
Current Model for DNA Replication
The replication of DNA is accomplished by a multienzyme DNA replicase system.
There are four stages in the replication process
Prepriming (preparation for replication)
Priming (synthesis of DNA primers)
Elongation (addition of DNA sequences to the 3’-termini of primers)
Termination (removal of RNA primers & their replacement w/DNA sequences & the subsequent covalent joining of the DNA fragments).
Cont1. Replication / 1. Prepriming
The continuous unwinding of DNA at the replication fork is performed by a number of proteins known as helicases:
Helicase II or III binds to the lagging strand
The Rep protein also a helicase binds to the leading strands.
The subsequent stabilization of the unwound DNA, & prevention of reanealing of the two seperated strands is provided by tetrameric aggregates of SS DNA-binding proteins (SSB).
During the progression of replication, the SSB proteins are recycled & bind to new single stranded sites along DNA.
Cont2. Replication / 2. Priming
Involves the synthesis of the 5’-3’ RNA primers (length 10 nucleotides)
Priming is catalyzed by the enzyme primase
Six proteins dnaB, c, I, n, n’, n’’, perform specific functions & together they form an aggregate known as primosome
Cont3. Replication / 3. Elongation
Involves the addition of DNA sequences to the 3’-termini of the RNA primers synthesized during priming.
The chain elongation process is catalyzed by DNA polymerase III holoenzyme. The complete synthesis of an intact DNA strand is performed with two additional enzymes, DNA polymerase I & DNA Ligase.
Cont4. Replication / 4. Termination
During termination degradation of RNA, & elongation of DNA are catalyzed concurrently by two distinct active sites in DNA Polymerase I.
DNA Poly. I removes RNA primers (5’-3’ exonuclease activity).
DNA poly. I extends the DNA sequence on the 3’-terminus of one of the phosphate group at the 5’-terminus of the other.
DNA Ligase catalyzes the formation of a phosphodiester bond bet. two fragments by joining the 3’-OH terminus of one of the phosphate group at the 5’-terminus of the other.
Cont5. Replication / 4. Termination
In animal cells and bacteriophage the energy required is provided by ATP hydrolysis. ATP
The synthesis of a single stranded RNA
Depends on a DNA template
Occurs in the 5’-3’ direction
Produces an antiparallel complementary copy of one of the two strands of the DNA
Requires ribonucleoside triphosphates as substrates
Is catalyzed by RNA polymerase
Advances by pyrophosphate cleavage, & the subsequent hydrolysis of the pyrophosphate to inorganic phosphate.
Cont1 . Transcription
The holoenzyme ( 2 ’ ) is required for the synthesis of all three RNAs (mRNA, rRNA, tRNA) in E.coli.
The sigma factor ( ) recognizes a specific binding site on the DNA strand.
The & ’subunits function in the binding of the RNA poly complex to the DNA.
The binding site is called a promoter
The promoter is located about ten bp upstream of the start of the transcription.
Cont2 . Transcription
The consensus sequence (A-T-rich seq of six bps) in the promoter serves as the recognition site for RNA poly binding. This seq is known as pribnow box in procaryotes (6bp).
In eucaryotes this seq is about 20-30 bps before the start of transcription & is called the hogness or the TATA box.
Cont3 Termination of Transcription
Simple termination which is due to stem-&-loop structure in the RNA transcript that was synthesized from an inverted repeat sequence of the gene being transcribed.
Termination requiring an auxillary termination factor, a protein called rho.
rho depletes the substrate for RNA synthesis by hydrolyzing ribonucleoside triphosphates.
Phases in polypeptide synthesis
Amino acid activation
Initiation of polypeptide synthesis
Elongation of a polypeptide chain
Termination of polypeptide synthesis
Polypeptide synthesis occurs on ribosomes (70 S)
The 70 S ribosome of E.coli is composed of a 30 S (small) subunit & a 50 S (large) subunit.
The 30 S subunit is composed of 16 S RNA and 21 proteins.
50 S subunit contains two RNAs (23 S & 5S) and 32 proteins.
Polypeptide synthesis occurs on the head
& platform regions of the
30 S subunit & the upper
half of the 50 S subunit.
Cont2 . Translation
The 30 S subunit is the site of attachment for both mRNAs and tRNAs.
The peptidyl transferase site in the central region of the 50 S subunit.
Cont3 . Translation 1. Amino acid activation
In the Ist step an aminoacyladenylate is synthesized by joining the carboxyl group of an amino acid w/ the alpha phosphate of ATP.
The Rxn is catalyzed by aminoacyl-tRNA synthetase & the required energy is furnished by the cleavage of pyrophosphate of ATP, & the hydrolysis of the pyrophosphate to inorganic phosphate.
Cont4 . Translation 1. Amino acid activation
In the 2 nd step the aa of the adenylate derivative is transferred to a hydroxyl group of the 3’-terminal adenyl nuceotide of a tRNA.
The Rxn is catalyzed by aminoacyl-tRNA synthetase.
AA+ ATP+ tRNA +H 2 0==Aminoacyl-tRNA+ AMP+ 2Pi
11/06/11 enzyme AA ATP
Cont5 . Translation 2. Initiation of Polypeptide Synthesis
An initiation complex consisting of a 30 S subunit, an initiation tRNA carrying N-formylmethionine, & mRNA is formed in the initial step.
3 protein initiation factors (IF1, IF2 & IF3), & GTP are involved in this step. Formylated methionine is the aa that initiates polypeptide synthesis in E.coli .
Cont6 . Translation 2. Initiation of Polypeptide Synthesis
In the 2 nd step of initiation, the 50 S ribosomal subunit combines w/ the 30 S initiation complex to form the 70 S initiation complex.
During this step GTP is hydrolyzed to GDP and Pi, & the three initiation factors are released from the complex .
Cont7 . Translation Elongation of a Polypeptide Chain
Elongation is mRNA directed & proceeds from the N-terminus to the C-terminus of the polypeptide being synthesized.
The ist step of elongation involves the binding of an aminoacyl-tRNA/EFTu-GTP complex to the recognition (R) site of the small (30 S) subunit of a functional ribosome. EFTu is a temperature unstable elongation factor and promotes the hydrolysis of GTP to GDP and Pi.
Cont8 . Translation Elongation of a Polypeptide Chain
The aminoacyl-tRNA is transferred to a second site in the 30 S subunit known as aminoacyl (A) site.
A peptide bond is formed between the two aa residues attached to the tRNAs occupying the P & A sites on the 70 S initiation complex.
Cont9 . Translation Elongation of a Polypeptide Chain
Peptidyl transferase catalyzes the peptide bond formation & transfer of the N-formylmethionyl residue at the P site to the NH 3 group of the aa residue attached to the aminoacyl tRNA at the A site, producing a dipeptidyl-tRNA.
The tRNA w/ out aa at the P site is released, & the peptidyl-tRNA is relocated to the P site by another elongation factor called EFG or transloase.
Cont10 . Translation Termination of a polypeptide bond
The termination of a polypeptide synthesis is signaled by one of the 3 termination codons (UAA, UAG, or UGA) at the end of an mRNA.
The 3-base sequence of a termination codon is recognized by one of the two release factors, RF1 (which recognizes UAA or UAG) of RF2 (which recognizes UAA or UGA).
Both release factors function in combination w/ GTP, which is hydrolyzed to GDP an Pi during termination.
11/06/11 Genetic code: determines how a nucleotide sequence is converted into the sequence of protein.