Syllabus Statements Topic 7 [HL]

Terms in this set (28)

The first stage of DNA replication in prokaryotes is the uncoiling of the DNA double helix by the enzyme helicase. Helicase separates the DNA into two template strands. RNA primase then adds a short sequence of RNA to the template strands. This short sequence of RNA is a primer which allows DNA polymerase III to bind to the strands and start the replication process. Once this is done, DNA polymerase III adds nucleotides to each template strand in a 5'→3' direction. The nucleotides have 3 phosphate groups and are called deoxyribonucleoside triphosphates. Two of these phosphate groups break off during the replication process to release energy. Since the strands are anti-parallel (the two strands have their 5' end and 3' end in opposite sides) and replication can only occur in a 5'→3' direction, one of the strands will be replicated in the same direction as the replication fork and the other will be replicated in the opposite direction of the replication fork. This means that one of the strands is synthesised in a continuous manner (named the leading strand) while the other one is synthesised in fragments (named the lagging strand). The leading strand only needs one primer while the lagging strand needs quite a few as it is formed in fragments. These fragments are called Okazaki fragments. DNA polymerase I will remove the RNA primers and replace these with DNA. The enzyme DNA ligase then joins the Okazaki fragments together to form a continuous strand.

Summary:
Helicase uncoils the DNA
RNA primase adds short sequences of RNA to both strands (the primer)
The primer allows DNA polymerase III to bind and start replication
DNA polymerase III adds nucleotides to each template strand in a 5'→3' direction
These nucleotides are initially deoxyribonucleoside triphosphates but they lose two phosphate groups during the replication process to release energy
One strand is replicated in a continuous manner in the same direction as the replication fork (leading strand)
The other strand is replicated in fragments (Okazaki fragments) in the opposite direction (lagging strand)
DNA polymerase I removes the RNA primers and replaces them with DNA
DNA ligase then joins the Okazaki fragments together to form a continuous strand
mRNA is produced during transcription. In prokaryotes, RNA polymerase recognises a specific sequence of DNA called the promoter. The promoter basically "tells" the RNA polymerase where to start the transcription process. Transcription is initiated with the binding of RNA polymerase to the promoter site. The RNA polymerase then uncoils the DNA and separates the two strands. One of the strands is used as the template strand for transcription. The RNA polymerase will then use free nucleoside triphosphates to build the mRNA in a 5'→3' direction. These nucleoside triphosphates bond to their complementary base pairs on the template strand. As they bind they become nucleotides by losing two phosphate groups to release energy. Since RNA does not contain thymine, uracil pairs up with adenine instead. RNA polymerase forms covalent bonds between these nucleotides. It moves along the DNA to keep elongating the sequence of mRNA until it reaches a sequence of DNA called the terminator. This sequence of DNA "tells" the RNA polymerase to stop transcription. The RNA polymerase is then released from the DNA and the newly created mRNA separates from the template DNA strand. Finally, the DNA rewinds back to its original double helical structure.

Summary:
RNA polymerase binds to the promoter region
This initiates transcription
RNA polymerase uncoils the DNA
Only one strand is used, the template strand
Free nucleoside triphosphates bond to their complementary bases on the template strand
Adenine binds to uracil instead of thymine
As the nucleoside triphosphates bind they become nucleotides and release energy by losing two phosphate groups
The mRNA is built in a 5'→3' direction
RNA polymerase forms covalent bonds between the nucleotides and keeps moving along the DNA until it reaches the terminator
The terminator signals the RNA polymerase to stop transcription
RNA polymerase is released and mRNA separates from the DNA
The DNA rewinds
There are many different types of tRNA and each tRNA is recognised by a tRNA-activating enzyme. This enzyme binds a specific amino acid to the tRNA by using ATP as an energy source. The tRNA molecule has a specific structure. It contains double stranded sections (due to base pairing via hydrogen bonds) and loops. It has an anticodon loop which contains the anticodon and two other loops. The nucleotide sequence CCA is found at the 3' end of the tRNA and allows attachment for an amino acid. Each type of tRNA has slightly different chemical properties and three dimensional structure which allows the tRNA-activating enzyme to attach the correct amino acid to the 3' end of the tRNA. There are 20 different tRNA-activating enzymes as there are 20 different amino acids. Each enzyme will attach a specific amino acid to the tRNA which has the matching anticodon for that amino acid. When the amino acid binds to the tRNA molecule a high energy bond is created. The energy from this bond is used later on to bind the amino acids to the growing polypeptide chain during translation.

Summary:
Each tRNA activating enzyme recognises a specific tRNA molecule
The tRNA molecule is made up of double stranded sections and loops
At the 3' end of the tRNA there is the nucleotide sequence CCA to which the amino acid attaches to
The different chemical properties and three dimensional structure of each tRNA allows the tRNA-activating enzymes to recognise their specific tRNA
Each tRNA enzyme binds a specific amino acid to the tRNA molecule
The tRNA-activating enzyme will bind the amino acid to the tRNA with the matching anticodon
Energy from ATP is needed during this process
Translation occurs in the cytoplasm. It starts off with the tRNA containing the matching anticodon for the start codon AUG binding to the small subunit of the ribosome. This tRNA carries the amino acid methionine and is always the first tRNA to bind to the P site. The small subunit of the ribosome then binds to the 5' end of the mRNA. This is because translation occurs in a 5'→3' direction. The small subunit will move along the mRNA until it reaches the start codon AUG. The large subunit of the ribosome can then binds to the small subunit. The next tRNA with the matching anticodon to the second codon on the mRNA binds to the A site of small subunit of the ribosome. The amino acids on the two tRNA molecules then form a peptide bond. Once this is done, the large subunit of the ribosome moves forward over the smaller one.The smaller subunit moves forward to join the larger subunit and as it does so the ribosome moves 3 nucleotides along the mRNA and the first tRNA is moved to the E site to be released. The second tRNA is now at the P site so that another tRNA with the matching anticodon can then bind to the A site. As this process continues the polypeptide is elongated. Once the ribosome reaches the stop codon on the mRNA translation will end as no tRNA will have a matching anticodon to the stop codon. The polypeptide is then released. Many ribosomes can translate the same mRNA at the same time. They will all move along the mRNA in a 5'→3' direction. These groups of ribosomes on a single mRNA are called polysomes.

Summary:
The tRNA containing the matching anticodon to the start codon binds to P site of the small subunit of the ribosome
The small subunit binds to the 5' end of the mRNA and moves along in a 5'→3' direction until it reaches the start codon
The large subunit then binds to the smaller one
The next tRNA with the matching anticodon to the next codon on the mRNA binds to the A site
The amino acids on the two tRNA molecules form a peptide bond
The larger subunit moves forward over the smaller one
The smaller subunit rejoins the larger one, this moves the ribosome 3 nucleotides along the mRNA and moves the first tRNA to the E site to be released
The second tRNA is now at the P site so that another tRNA with the matching anticodon to the codon on the mRNA can bind to the A site
As this process continues, the polypeptide is elongated
Once the ribosome reaches the stop codon on the mRNA translation ends and the polypeptide is released
Many ribosomes can translate a single mRNA at the same time, these groups of ribosomes are called polysomes
Enzyme inhibitors are substances which inhibit enzyme activity. There are competitive enzyme inhibitors and non-competitive inhibitors.
Competitive Inhibitors:
These are structurally similar to the substrate of the enzyme and bind to the active site. This means that when a competitive inhibitor binds to the active site of an enzyme, it prevents the substrate from binding to the active site. Only once the inhibitor has been released from the active site can the substrate bind. The inhibitor is called a competitive inhibitor as it competes with the substrate for the active site.
The effects of a competitive inhibitor can be reduced by increasing the substrate concentration. More substrate would successfully bind to the active site than inhibitor and therefore reducing the effect of the inhibition. The maximum rate of reaction or a level very close to the maximum rate of reaction can be reached.
An example of a competitive inhibitor is malonate. Malonate is structurally similar to the substrate succinate. Succinate is found in the Krebs cycle of aerobic respiration and binds to the active site of the dehydrogenase enzyme. Malonate can compete with succinate for the active site and in doing so it can prevent succinate from binding.

Non-Competitive Inhibitors:
These are not similar to the substrate and they do not bind to the active site of the enzyme. Instead they bind to a different site on the enzyme and change the conformation of the active site. The substrate may still be able to bind to the active site however the enzyme is not able to catalyse the reaction or can only do so at a slower rate.
In the presence of a non-competitive inhibitor, increasing the substrate concentration cannot prevent the inhibitor from binding to the enzyme as the two bind to different sites. Therefore, no matter how high the concentration of substrate is, some of the enzymes will still be inhibited. The maximum rate of reaction will always be lower in the presence of a non-competitive inhibitor.
An example of a non-competitive inhibitor is ATP. When ATP accumulates it binds to a site other than the active site on the enzyme phosphofructokinase. In doing so it changes the enzyme conformation and lowers the rate of reaction so that less ATP is produced.
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