1. Protein Synthesis
The genetic code – the sequence of nucleotides in DNA – is ultimately translated into the sequence of amino acids in proteins – gene expression
in general, one gene encodes information for one protein (can be structural or enzymatic) – one-gene, one-protein hypothesis
DNA does not directly synthesize proteins
RNA acts as an intermediary between DNA and protein – polymer of nucleotides but has several important differences:
RNA DNA
sugar ribose deoxyribose
bases A,U,C,G A,T,C,G
strands single double

2. transcription – a molecule of mRNA is made using DNA as a template
Protein synthesis occurs in two major steps – transcription and translation
transcription – a molecule of mRNA is made using DNA as a template
translation – the molecule of mRNA is used to make the protein

3. Overview of Protein Synthesis
During transcription, one DNA strand, (template strand), provides a template for making an RNA molecule.
Complementary RNA molecule is made using base-pairing rules, except uracil pairs with adenine.
During translation, blocks of three nucleotides (codons) are decoded into a sequence of amino acids.

4. Three types of RNA
1. messenger RNA (mRNA) – the “copy” of the DNA that is used to specify the sequence of amino acids in the protein
mRNA nucleotides are read in groups of three called codons
each codon codes for a specific amino acid

5. 2. transfer RNA (tRNA) – bring amino acids to the ribosome during protein synthesis
each tRNA carries a specific type of amino acid
each tRNA can recognize a specific mRNA codon because it has a complementary anticodon (sequence of three bases that associates with the codon by base pairing)

6. Each amino acid is joined to the correct tRNA by aminoacyl-tRNA synthetase
Aminoacyl tRNA – tRNA with it’s amino acid attached

7. 3. ribosomal RNA (rRNA) – forms part of the ribosome

8. Transcription
synthesis of RNA using DNA as a template
most RNA is synthesized by DNA-dependent RNA polymerases
enzymes that require DNA as a template
similar to DNA polymerases
synthesize RNA in a 5’ to 3’ direction
use nucleotides with three phosphate groups as substrates (nucleoside triphosphates), removing two of the phosphates as the subunits are linked together (just like DNA synthesis)
the transcibed strand of DNA and the complementary RNA strand are antiparallel

10. Transcription begins with an RNA polymerase attaching to a DNA sequence called the promoter (promoter is not transcribed) – marks the beginning of the gene
RNA polymerase unwinds the DNA strand
only one of the strands of DNA is transcribed – called the transcribed strand, template strand, or antisense strand
The strand that is NOT transcribed is the sense strand
RNA polymerase continues down the gene synthesizing a single strand of mRNA through base-pairing (A matches with U) until it reaches a termination signal

12. Translation – protein synthesis
In the process of translation, a cell interprets a series of codons along a mRNA molecule.
Transfer RNA (tRNA) transfers amino acids from the cytoplasm’s pool to a ribosome.
The ribosome adds each amino acid carried by tRNA to the growing end of the polypeptide chain.

13. Each ribosome has a large and a small subunit
Ribosome Structure
Each ribosome has a large and a small subunit
These are composed of proteins and ribosomal RNA (rRNA)
Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.
The P site holds the tRNA carrying the growing polypeptide chain.
The A site carries the tRNA with the next amino acid.
Discharged tRNAs leave the ribosome at the E site.

14. Translation occurs in steps called: initiation, elongation, and termination
Step1. Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits.
First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, which carries methionine and attaches to the start codon.
in all organisms, protein synthesis begins with the codon AUG (codes for methionine)
Initiation factors bring in the large subunit which closes in a way that the initiator tRNA occupies the P site.

15. Step 2. Elongation – the addition of amino acids to the growing polypeptide chain
initiator tRNA is bound to the P site of the ribosome
A site is filled with the next tRNA -specified by the codon (tRNA anticodon matches with codon by base-pairing)
the amino acids are linked together (peptide bond)
the tRNA in the P site moves to E site to be released and the ribosome moves down freeing up the A site
the ribosome moves in a 5’ to 3’ direction as the mRNA is translated

16. The genetic code is series of codons; read one triplet at a time
genetic code is redundant – certain amino acids are specified by more than one codon – 64 possible codons but only 20 amino acids
61 codons specify amino acids – three do not (UAA, UGA, and UAG are all stop codons – code for nothing)

17. Step 3. Termination – ribosome reaches the termination codon (stop codon) at the end of the sequence – stop codon does not code for an amino acid

19. Transcription and Translation in Eukaryotes
prokaryotic mRNAs are used immediately after transcription
prokaryotes can transcribe and translate the same gene simultaneously.

20. eukaroytic mRNAs must go through further processing – posttranscriptional modification and processing:
At the 5’ end of the pre-mRNA molecule, a modified form of guanine is added, the 5’ cap.
This helps protect mRNA from hydrolytic enzymes.
It also functions as an “attach here” signal for ribosomes.
At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides, the poly(A) tail.

21. eukaryotic genes have interrupted coding sequences – they contain long sequences of bases within the protein-coding sequences that do not code for amino acids in the final protein
noncoding regions within the genes are called introns (intervening sequences)
protein-coding sequences are called exons (expressed sequences)
a eukaryotic gene may have multiple introns and exons

22. the entire gene that is transcribed as a large mRNA molecule is called a precusor mRNA or pre-mRNA – contains both introns and exons
a functional mRNA may be 1/3 the length of the pre-mRNA

23. In order for a pre-mRNA to become a function message, it must be capped, have a poly-A tail added, have the introns removed, and have the exons spliced together
excision of introns and splicing of exons catalyzed by snRNPs (small nuclear ribonucleoprotein complexes)