Key questions: Whew!! All finally done. Way to keep at it!
1.What is the difference between “DNA”, “chromosome”, and “gene”? DONE
DNA holds the genetic code of an organism. DNA stands for deoxyribonucleic acid. It consists of a string of nucleotides, each made from a Phosphate group, a five carbon sugar (Deoxyribose), and a nitrogenous base. The nitrogenous base always consists of either Adenine paired with an opposing nitrogenous base of thymine, or Cytocine paired with Guanine. These four bases make up the Genetic code. Similar to the binary code on a computer using a 0 or 1, these four N-bases depending on their combination control and tell the body how to function by determining which proteins to create. This is commonly referred to as the genome. DNA is not one long molecule; it is comprised of sections called chromosomes. Within each Chromosome are 100s or 1000s of genes. These genes are sections of genetic code that determine a particular trait. If these genes are different or ordered wrong then a mutation can occur.
2.Why would it be appropriate to call tRNA an “interpreter” molecule? DONE
It is appropriate to call tRNA an “interpreter” because in order for translation to work, a molecule needs to recognize the language in mRNA and convert it to something else (an amino acid sequence). In this case, the RNA molecule, tRNA, is converting the codons of nucleic acids from the mRNA into amino acids of proteins. The tRNA molecule has to do this because the amino acids themselves cannot recognize the codons in the mRNA (GOOD SENTENCE :)). The tRNA matches the amino acids to the appropriate codons in order to form a new polypeptide by picking the right amino acids and recognizing the right codons on the mRNA.
3.How does the genetic code ultimately dictate the shape of the proteins that are synthesized? DONE
The genetic code ultimately dictates the shape of the proteins that are synthesized through a long series of steps. First is DNA replication, this is the process of copying the sense strand and anti-sense strand from the DNA and combining it into a new DNA strand. This is pretty much just a copy of both sides of the DNA so that DNA multiplication and replication can take place. This new DNA strand is read by RNA polymerase and the new mRNA travels to a ribosome in the cytoplasm, translation takes place. This is where the ribosomes 'read' the nitrogen-base codes on the mRNA and assemble the corresponding amino acid into a chain called a polypeptide. Depending on the charge, bulkiness or shape of the amino acid, the protein then changes shape. So, the sequence of the DNA ultimately is transferred down into the sequence of amino acids in the protein, which then according to their charges and sizes determines the shape of the protein.
4.Refer back to previous units, and give at least 3 examples where the shape of a protein is key to its function. DONE
First of all the shape of a protein is important for transport proteins. Transport proteins only allow certain molecules that are, needed by the cell, to pass through the cell membrane. Things that are harmful to the cell are not able to get in because they are not the same size and shape that the protein is, therefore it won't be able to get in. It is like a child’s shape sorter toy; only the right shape will pass. Secondly, the shape of the protein is important in the sodium potassium pump because in order to get only sodium ions and potassium ions the protein has to be in a certain shape. The shape allows only sodium and potassium ions to be transported, nothing else. Lastly, the shape of the receptor proteins involved in signal transduction are important because the shape of the protein only allows the specified molecule to react with it and send the right message within a cell.
5.Why are some point mutations serious and others no problem at all? DONE
Point mutations refer to differences of just a few nucleotides in a DNA sense strand. Since DNA polymerase is copying DNA to make new DNA at 50 bases/second during DNA replication there are sometimes going to be mistakes in the new DNA that is synthesized. However, point mutations might not be that serious if the substitution that occurs might not change the charge on the amino acid or size of the R group. For example a silent mutation along a DNA strand like AAC mutated into GAC causes RNA polymerase to code for the same amino acid, leucine. This would mean that there would be no change in the protein created in the process of translation. However, if a DNA strand were to be AGC and mutated into ATC, the mRNA would create a stop codon instead of serine. If this were to occur, the stop codon would appear in a different position along the mRNA strand possibly causing only half protein to be created, or no protein to be created at all if the stop codon is near the start codon. However, there would be a small change if the mutated stop codon appeared right before the actual stop codon of the mRNA. So, this would mean fewer amino acids would be bonded together and a smaller protein would be synthesized. If a mutation is in an intron, there is no consequence for the mutation. The intron containing the mutation is disassembled and the pieces are later used for assembling more mRNA chains.
Another form of point mutation is a deletion or insertion. This causes a frameshift mutation as long non-multiple of three nucleotides were deleted or an extra non-mulitple of three was added into the DNA sense sequence. As a result, the entire remaining nucleotides would shift over causing an alteration in the amount and grouping of the codons. This change in grouping changes the amino acids the codons code for, thereby changing the shapes of the proteins and finally altering a process in the body. In dogs, a Bully Whippet is a very popular deletion mutation.
6.What causes mutations? DONE
Mutations are caused by spontaneous mistakes or by mutagens. One form of mistake is made during the copying of DNA during DNA replication. At such a fast rate, it is easy for the DNA polymerase to make a mistake and mismatch the DNA to the new DNA. The other cause of mutation is mutagens. Mutagens are environmental agents that generate mutations (thus, the word mutagen). Examples of these environmental agents are ionizing particles like beta particles, x rays or gamma rays; ultraviolet light (from the sun or UV light source) or certain chemicals. During the Vietnam War, "Agent Orange" was a popular chemical used to extract enemy hiding in the forest and is now blamed for many mutations in veterans and in Vietnamese children.
Vocabulary exercise: Explain why the following words make sense (why their names help tell what they do)
7.“polymerase” DONE
A "polymerase" is a "polymer-maker" enzyme that forms polymers of DNA and RNA. Based on the nucleotide on the DNA sense strand, for example, the enzyme knows which ones to attach to it (the base pairing rule). It links nucleotides to form a new DNA strand or a new RNA strand.
8.“transcription” DONE
Since this involves the process of transferring genetic information from DNA into RNA, "transcription" it is good to call this process transcription because nucleic acids are being rewritten, or "transcribed" as a new sequence of bases on an RNA strand. A copy of the DNA is made because proteins are not made in the nucleus, they are made in ribosomes in the cytoplasm.
9.“translation” DONE
In this step of protein synthesis, ribosomes read the nitrogen base code on the mRNA and turn it into a completely new "language" - proteins. Prior to this step, transcription was the converting of DNA nitrogenous bases into RNA nitrogenous bases, keeping the "language" of nitrogenous bases consistent.
10.“antiparallel” DONE
Antiparallel makes sense because the DNA is not exactly parallel because the phosphate group on the sense strand and the anti-sese strand are on opposite sides of the DNA. One is at the top and the other is at the bottom, this is why they are not exactly parallel.
11.“messenger” RNA DONE
Messenger RNA makes sense for what it does because it carries a copy of the DNA to the ribosome in the cytoplasm so that the ribosomes can assemble the correct protein. So it is a messenger because it carries and relays the information contained in the DNA, it would not make sense if it was called a "greeter" RNA or "reader" RNA.
12.“transfer” RNA DONE
The tRNA is moving the amino acids from being single to the ribosome where the amino acids from other tRNA molecules connect by peptide bonds and form a polypeptide. The tRNA is transferring the amino acids to ribosomes.
13.“sense” strand DONE TWICE
(1) The sense strand of the two strands that make up DNA is the one transcribed. It makes sense because during the process of translation, it is the nitrogenous-base code on the mRNA that the ribOsomes "sense" or "read" in order to assemble the correct protein.
(2) This is the side of the DNA that is used during transcription, or the side that is being transcribed. It is called the “sense” strand because it only makes sense for one side to be transcribed by the cell because when it reaches translation the mRNA senses or reads the codon to give it the right protein. The antisense strand does not carry the information for making a "sensible" protein.
14.“anti-sense” strand DONE
The anti-sense strand is the unread side of the DNA and its nitrogenous bases are complimentary to the "sense" strand's nitrogenous bases (i.e. if the sense strand had a C, then the anti-sense strand has a G). It is called the anti-sense strand because it is the side of the DNA that is not used to create new mRNA. If it were used, the anti-sense strand would not make sense to the polymerase when creating the new mRNA, everything would be "backwards".
15.“promoter” DONE
A promoter site is a sequence of N bases where RNA Polymerase bonds with DNA. It is correctly named a promoter site because it promotes the beginning of transcription so that DNA can be copied into mRNA.
16.“terminator” DONE
A terminator site is a sequence of N bases which tell the enzyme RNA Polymerase to stop creating mRNA from DNA. It is correctly named because it terminates transcription of a strand of DNA.
Write a sentence (or 2) to show a relationship between the following sets of terms.
17.phosphate group, nucleic acid, nucleotide DONE
One nucleotide consists of a sugar, a nitrogenous base (Thymine, Adenine, Cytosine, Guanine, & Uracil), and a phosphate group. The nucleotide bonds with other nucleotides to form a nucleic acid. The way they are put together is the sugar in one nucleotide bonds with the phosphate group of another through dehydration synthesis. The sugar and the phosphate group form the wall of the nucleic acid, while the nitrogenous bases face inward.
18.thymine, uracil, DNA DONE
Both thymine and Uracil are nitrogenous bases that bond to adenine with a hydrogen bond. Although thymine is only used in the double helix structured DNA. Uracil is only present in RNA.
19.DNA replication, DNA transcription DONE
During DNA replication, the two strands of DNA untwist and nucleotides will be linked together using DNA polymerase to form the other half of the DNA. This happens on both halves, creating two identical copies of the original DNA molecule. A similar process occurs in DNA transcription. The two strands of DNA will untwist, but this time one half of the DNA (the sense strand) is copied into mRNA, linked together using RNA polymerase.
20.gene, chromosome, DNA DONE
DNA, or deoxyribonucleic acid, is divided into 46 chromosomes for humans. These chromosomes contain hundreds of genes, or sections of DNA that code for a specific trait on the human, such as eye color, hair color, or even personality traits. We, as humans, have approximately 22,000 genes in our DNA, all of which are divided among our 46 chromosomes.
21.promoter, start codon, transcription, translation DONE, BUT WHAT I WAS HOPING YOU'D CONTRAST WAS HOW TRANSCRIPTION BEGINS AT THE PROMOTER SITE ON DNA AND TRANSLATION BEGINS AT A START CODON ON mRNA.
In the process of transcription, RNA polymerase bonds at the promoter site on the DNA, and once bonded, begins copying DNA at the start codon. Once transcription is finished, the new mRNA leaves the nucleus through a nuclear pore and goes to a ribosome in the rough endoplasmic reticulum for translation.
22.nuclear pore, transcription, ribosome DONE
After the process of transcription is completed, the mRNA leaves the nucleus via a nuclear pore. After this the mRNA now in the cytoplasm is read by the ribosome so the correct amino acids can be matched with the certain nitrogenous bases.
23.anticodon, amino acid, tRNA DONE
The anticodon of a tRNA determines what amino acid is bonded for translation. The amino acids attached to tRNA in the P site form a peptide bond with the amino acid with the tRNA in the A site. This elongates a polypeptide chain during translation.
24.polypeptide, peptide bond, stop codon DONE
A polypeptide is held by the tRNA at the ribosome’s P site. At the A site, an amino acid bonds to the amino acid at the P site. The bonding of the two amino acids is a peptide bond and when a stop codon is reached the process is signaled to end.
25.rough ER, smooth ER, proteins DONE
The rough ER is where the polypeptide chain or protein travels to if it is needed to exit the cell later on. In the rough ER, the polypeptide chain is packaged in a transport vesicle and is then shipped to the Golgi apparatus where it gets modifies and finished. In the smooth ER, is where the synthesize of lipids takes place.
26.substitution, frameshift mutation, deletion DONE
A deletion mutation to the sense strand, for example when one nucleotide is left out or is missing from the DNA causes a frameshift mutation, when the entire transcript is shifted over resulting in the complete change of all the remaining codons. Say for example you take the phrase, "THE FAT CAT ATE THE BIG RAT" and take out or delete the letters c and a in cat, it results in a shift of the remaining letters (or codons) creating new words so the phrase now reads, "THE FAT TAT ETH EBI GRA T." The Frameshift happens when one or two of the nucleotides is missing so the grouping of three nucleotides is switched and altered and there are new groupings. This changes the amino acids that will later be read off of the mRNA. A substitution mutation, or replacing one nucleotide with another, to the sense strand changes one codon and as a result, one amino acid, but does not affect the rest of the transcript.
