Protein Synthesis =)

3.5.1: Compare the structure of RNA and DNA
RNA
-single stranded
-found in nucleus and ribosomes
-contains uracil
-OH present making it ribonucleic acid

DNA
-Double stranded
-No OH present at the 2' end making it deoxyribonucleic acid
-found in nucleus
-contains thymine
external image RNA-comparedto-DNA_thymineAndUracilCorrected.png


external image Sugars%20in%20RNA%20DNA%20fig3.jpg
3.5.5 - Discuss the relationship between one gene and one polypeptide.

Genes store the information needed to make amino acids that make up polypeptides in a coded form.

The sequence of bases in a gene codes for the sequence of amino acids in a polypeptide.

7.3.4 - State the Eukaryotic RNA needs the removal of introns to form mature mRNA

Eukaryotic RNA needs the removal of introns to form mature mRNA. This is because the introns are Repetitive Sequences, or non-coding sequences.
After introns are removed after transcription and before translation, the exons are joined. This process is called splicing.

7.4.4 - State that translation occurs in a 5' -3' direction
Translation occurs in a 5' - 3' direction. This is because the 5' to 3' direction is faster and a lot easier than the other way. Although the other way doesnt use 3' to 5' it uses the lagging strand which is slower. It isnt posssible to translate from the 3' to the 5'.
7.1.5 - State the eukaryotic genes can contain exons and introns
Eukaryotic genes can contain exons and introns. The introns are cut off and the exons are joined together to be used. Refer to the vidoe for more help.

3.5.2 - Outline DNA transcription in terms of the formation of the RNA strand complementary to the DNA strand by RNA polymerase
RNA polymerase is basically the facilitator of the DNA transcription process, as it is what forms the RNA strand that is complementary to the DNA strand to carry out protein synthesis.RNA polymerase is an enzyme that moves along the DNA strand, and copies it as it does. This copy is a strand of RNA, now referred to as mRNA, or messenger RNA. This transcription is complementary, as it i copying using complementary base pairing. This complementary base pairing ensures that the mRNA strand has the nucleotides complementary to the strand of DNA, such as Guanine to Cytosine.

7.3.1 - state that transcription is carried out in a 5 prime to 3 prime direction
Transcription is carried out in a five prime to three prime direction, as it is the most efficient way for a DNA strand to be read by enzymes in the body. This direction is the same direction that is used in DNA replication, showing that it is indeed efficient for the body. In DNA replication, the strands are replicated by DNA polymerase, but the leading strand goes much faster then the lagging strand because the leading strand is read in a five to three direction. The lagging strand is going in the opposite direction than the leading strand, so in order for the body to read it in a 5 to 3 direction it has to compensate and basically read it backwards. The body will always want to read DNA in a 5 to 3 direction, so the process of transcription is no exception.

7.4.1 - Explain that each tRNA molecule is recognized by a t RNA activating enzyme that binds a specific amino acid to the tRNA
Each tRNA molecule in the body has specific amino acids bonded to it, but only after they have received them from a tRNA enzyme. tRNA is also know as transport RNA and its function is to transport these amino acids to the mRNA strand bonded to the ribosomes so protein synthesis can be carried out. The tRNA activating enzyme bond the tRNA to an amino acid, and after the anti codon on the tRNA is read by the codon on the mRNA strand, this amino acid become part of a polypeptide forming on the ribosome to be used in the body. This would not occur without the tRNA activating enzyme however.

7.4.5 Draw and label a diagram showing the structure of a peptide bond between two amino acids

Ok so I cheated a bit and it isnt hand drawn, but I'm sure I will be forgiven!400px-Peptidformationball.svg.png



3.5.3- Describe the genetic code in terms of codons composed of triplets of bases.
A codon is a combination of three nitrogenous bases from 3 nucleotides, each codon coding for one amino acid. There are 4 different bases; adenine, thymine/uracil, guanine, and cytosine; so there are 64 possible combinations since 4 cubed is 64. ​Because there are only 20 amino acids, there about 3 different codons that code for each amino acid. But there have to be 3 bases in a codon, and therefore extra combinations, because 4 to the first power is only 4 and 4 to the second power is only 16, both of which are less than 20. 4 to the third power is the only option.
The genetic code is just the sequence of nitrogenous bases that makes up a particular gene, so it is really the sequence of codons that make up a gene. This isn't quite the same as the codons that make up the mRNA the gene codes for because of the thymine/uracil difference and because in eukaryotic cells there are introns that are in the genes but not in the mRNA.
7.3.2- Distinguish between the sense and antisense strands of DNA.
The sense strand of DNA is the strand that coes for the mRNA, while the antisense strand is the strand that does not. The sense strand is also known as the template strand. Note that on a single DNA, there are genes on both strands so the sense and antisense strands don't apply to an entire DNA at once, but rather are particular to each gene.
7.4.2- Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, 3 tRNA binding sites, and mRNA binding sites.
Ribosomes are composed of RNA and proteins. The smaller subunit is composed of one rRNA (ribosomal RNA) molecule and 21 different proteins. The bigger subunit is composed of 2 rRNA molecules and 31 proteins, hence it being bigger. The rRNA in the smaller subunit is called 16S, and is made up of 1,542 nucleotides. The 2 in the bigger subunit are called 23S and 5S and are made up of 2,904 and 120 nucleotides, respectively.
Funful chart:


RNA function and turnover in the cell

Type
Function
Different Kinds
Nucleotides
% of Synthesis
% of Total RNA
Stability
mRNA
Messenger
Thousands
500-6000
40-50
3
T1/2 = 1-3 min
rRNA
Ribosome
3 (23S, 16S, 5S)
2904, 1542, 120
50
90
Stable
tRNA
Adapter
~50
73-93
3
7
Stable

There are 3 tRNA binding sites, on the smaller subunit technically but mostly inside the larger one. They are the A site, where the tRNA's anticodon is tested to see if it is a match for the mRNA's codon and bonds to it if it is, the P site where the tRNA's amino acid detaches and joins the growing polypeptide, and the E site where the tRNA detaches from the mRNA.
There is just 1 mRNA binding site, also on the smaller subunit of the ribosome. There is just 1 because it is huge, stretching across the entire smaller subunit so that the mRNA can lie on it lengthwise.
7.4.6- Explain the process of translation, including ribosomes, polysomes, start codons and stop codons.
Once an mRNA leaves the nucleous, the process of translation begins. First, 2 ribosome subunits, the large and small, bind together. Then, the mRNA comes and binds to the mRNA binding site. It starts to move through the ribosome like a conveyor belt, synthesizes a polypeptide as it goes. To do this, it must start with the aptly named start codon, which is AUG. This codes for the methionine, or Met, amino acid in eukaryotic cells, though this is sometimes taken out later if it is not needed or desired for the protein. In order to get that Met amino acid to the right place, a tRNA bearing the amino acid on one end and the anticodon that is the complement to the codon which codes for that amino acid on the other end, arrives at the ribosome at the A tRNA binding site. Here, the anticodon is tested as a match to the codon which is currently at that site, AUG in this case, and then if it is a match bonds to it. Then the mRNA moves, and the tRNA with it, so that the tRNA is at the P site where the Met amino acid detaches to start forming the polypeptide. The mRNa moves again, so the tRNA is at the E site where it detaches. This process continues for the rest of the codons on the mRNA, adding a particular amino acid to the growing polypeptide chain for each, until the stop codon is reached. There are actually 3 different stop codons: UAG, UGA, and UAA. These have been given the names amber, opal, and ochre, respectively. These are also called nonsense codons or termination codons. When these stop/nonsense/termination codons are read, the polypeptide is released from the ribosome so that it can form itself into a protein and go off to be used somewhere.