Bio Study Guide for Protein Synthesis/Gene Expression Test
Suppose you are analyzing a strand of DNA that contains 400 cytosines. If the strand contains a total of 1,000 bases, how many adenines does it contain? Why do you know this to be true?
100 adenines would be present. 400 cytosines + 400 guanines would leave 200 bases of thymine and adenine.
If a strand of DNA is found to contain 250 adenine bases, how many thymine bases does it have?
250 because adenine and thymine are complementary
How many nitrogen bases compose a single codon?
3
How many codons, when expressed, will stop the translation process?
3 (UGA, UAA, UAG)
Considering the 5' and 3' ends, in which direction is a molecule of RNA synthesized?
5' → 3'
Explain why the term 'gene expression' is utilized when describing the process of generating protein from DNA.
A gene is a segment of DNA that codes for a protein. Through the process of protein synthesis, your cells are 'expressing' genes in the form of proteins for which they code.
Define the term mutation and give an example of a substitution mutation and an example of a frameshift mutation in a DNA strand.
A mutation is an unintended change in the sequence of DNA bases. Substitution: AUG CCC UAG → AUG CAC UAG Frameshift: AUG CCC UAG → AUG CCU AG
In what way is a tRNA molecule that has taken part in translation different before and after the process?
A tRNA molecule that has taken part in translation will lack an amino acid as it has already deposited the amino acid at the ribosome.
What is a 'template/"non-sense' strand in terms of DNA replication?
A template strand is the strand that is used to make a new strand of DNA. The new strand will match the bases currently in existence on the template strand, and the two strands, one old, one new, will be complementary.
If an mRNA codon reads UGC, what is the anticodon on the tRNA molecule with which it will bind? What amino acid will this tRNA molecule carry?
ACG, Cytosine
What amino acid will you find in the beginning of all sequences that create proteins?
AUG
Match the strand of DNA below with its appropriate mRNA sequence: TAC-GGT-CAT-TGA
AUG-CCA-GUA-ACU
What three letters will begin all mRNA sequences that code for proteins? Explain your answer.
AUG. AUG is the 'start' codon, it codes for the amino acid methionine, and every translation sequence will begin with this codon.
Match the strand of DNA below with its appropriate mRNA sequence: TACTGGTTCAGC
AUGACCAAGUCG
Match the single strand of DNA below with its complementary strand: TACCGCATC
AUGGCGAAUCAGUAA; UACCGCUUAGUCAUU; Met-Ala-Asn-Gln
If you were to sequence the DNA of a housefly, what bases would you find in its genome?
Adenine, thymine, cytosine and guanine. All living organisms possess DNA that is basically the same in structure, and contains these 4 bases.
What DNA and RNA bases would you find in the DNA of a blue whale?
Adenine, thymine, guanine, cytosine, uracil. These bases are the same regardless of the organism.
Why are DNA, RNA and their codons referred to as the universal code of life?
All life on Earth uses this form of genetic material to live, grow and reproduce. These molecules exist in the same form and basic function in all living organisms.
What is the relationship between codons and anti-codons in the translation process?
Anti-codons from tRNA bind to codons to form amino acids of a protein.
Explain what the term 'antiparallel' means in terms of DNA replication.
Antiparallel means that one strand of a DNA molecules runs from the 5' end to the 3' end, while the matching strand runs from 3' to 5'.
Why is the term 'translation' appropriate for the last step of gene expression?
Because you translate the amino acid from the mRNA code to protein.
How are chromosomes related to chromatin?
Chromatin are tightly packed chromosomes wrapped around histone proteins.
What is the relationship between codons and proteins?
Codons are used to create proteins. Each codon represents an amino acid, which are the monomers of proteins.
Explain why it is necessary to be able to replicate DNA in order to sustain life.
DNA needs to replicate to process, reproduce and grow as an organism, hence (hi Tina), life would only be sustainable through the replication of DNA
How does the 'packing' of DNA impact the process of gene expression in cells?
DNA packed can not be reached by RNA polymerase and can not be transcribed.
What is the 'central dogma' of biology? Explain why this saying is used to describe the biological concept.
DNA→ RNA→ Protein Central dogma means 'major theme' or 'underlying idea.' Scientists use this term to describe gene expression, because gene expression is the underlying theme behind all biological activities. Without this process, life as we know it cannot exist, and so it is the 'fundamental belief' around which the rest of life revolves
The fact that a single amino acid may be coded for by multiple codons may help to diminish the negative effects of a DNA mutation. Explain why this may be true.
Different codons can code for the same amino acid, so DNA mutations may not occur with some codons.
How is it possible that even though all the cells of a multicellular organism contain the same DNA, there are many different types of cells that differ in structure and function?
Different segments of DNA can be activated or deactivated, leading to specialization and differentiation of cells, depending on what segment of DNA is activated, the cell will develop and perform differently.
Compare the process of translation to the process of writing a sentence. What does each letter represent? What does the completed sentence represent? What would happen if the words or letters were in the incorrect order?
Each letter represents an amino acid, the completed sentence is a completed protein. If the words or letters were rearranged, the sentence would mean something totally different, or would not make any sense. If the amino acids in a protein were rearranged, the protein would have a totally different function, or no function at all.
In which step (initiation, elongation, termination) are new amino acids added during translation?
Elongation
If an mRNA codon reads CCU, what will its complementary anticodon be?
GGA
What is the appropriate scientific term used to describe 'a series of bases that code for a protein?'
Gene
Sometimes the term 'protein synthesis' is used to describe gene expression. Explain the relevance of this term to this process.
Gene expression is the process of coding proteins.
In a newly replicated molecule of DNA, how much of the molecule has just been synthesized, and how much was pre-existing?
Half is newly synthesized and the other half was pre-existing.
What role do histones play in the packing of DNA?
Histones are proteins that organize and package strands of DNA in the nucleus (think of story of Suro packing climbing rope)
How is 'translation' in terms of biology similar to 'translation' in terms of linguistics?
In linguistics, one language is converted to a different language, in biology, the language of RNA (or ultimately DNA) is converted to the language of proteins.
How could a change in the DNA sequence of a gene have an impact on the translation process?
In many cases, changing just one nitrogen base in a sequence of DNA will alter the sequence of amino acids in the translation process. In some cases, adding or removing a base may alter every amino acid in the protein after the location of the mutation. In either case, the protein may be drastically altered in structure and function.
How are the termination steps of transcription and translation different?
In transcription, a termination sequence of DNA signals the RNA polymerase to cease and detach, whereas in translation, one of three codons does not correspond with an amino acid, and cause the translation process to end.
Does RNA polymerase bind to the template strand or non-template strand of DNA? Explain why this makes sense for creating RNA that contains the needed information contained in the DNA molecule.
It binds to the template strand. This makes sense because the non-template strand actually contains the bases that build the gene that can be translated into a protein. By creating an mRNA strand from the template strand, the enzyme is creating the same sequence as the non-template strand, which contains the valuable information.
Supposed you are analyzing a strand of DNA that contains 375 thymines. If the strand has 900 bases, how many guanines does it have?
It would have 75 guanine bases
What amino acid is specified by the codon AUG?
Methionine (START)
Discuss how a mutation affects the processes associated to the Central Dogma.
Mutations actually do not affect the processes, as the Central Dogma of DNA will continue to function by itself and uninterrupted.
Discuss how a mutation in DNA can affect the function of a resultant protein.
Mutations can result in different codes which result in different proteins (amino acid sequences) that perform different functions which can either make no difference or be very harmful to the organism.
Can you accurately predict the number of cytosine bases found in a DNA strand if provided with only the number of thymine bases in that strand?
No because cytosine binds with guanine. If there was a total number of bases, then you could.
Suppose an error occurs in the translation phase of gene expression. Will this error affect the DNA sequence of the gene? Why or why not?
No, DNA is not affected by translation.
Does the process of DNA replication involve uracil? Why or why not?
No, because DNA replication only involves DNA itself so uracil is not included in this process
Is the process of gene expression the same in prokaryotes as it is in eukaryotes? Explain your answer.
No, because Prokaryotes do not have a nucleus. Transcription takes place in the cytoplasm instead.
Why is it important that the nucleus of a cell contains nuclear pores?
Nuclear Pores allow for mRNA and ribosomes to leave the nucleus after production.
Why are new DNA strands only created in a 5'-3' direction?
Nucleotides can only be added to the 3' end of the template strand, and since the new strand is antiparallel to the template, the new strand is made from 5' to 3'.
Explain how the termination segment of translation occurs.
One of the three stop codons is reached on the mRNA. No amino acids correspond to this codon, so no tRNA molecule binds to the mRNA. The ribosome subunits disassemble and the process ends.
Explain how the meaning of the terms prokaryote and eukaryote help explain the structure of the cell.
Prokaryote has no nucleus. Eukaryote does.
What is the difference between prokaryotic and eukaryotic DNA?
Prokaryotic DNA is circular. Eukaryotic is linear.
Which amino acid will the tRNA (GGA) carry?
Proline
What is the final product of the translation process?
Proteins
What is the role of rRNA in the process of protein synthesis?
RNA composes the ribosome, the organelle on which the process of translation occurs.
What enzyme conducts the process of transcription in cells?
RNA polymerase
Where does the process of translation occur in the cell?
Ribosome
What occurs in the translation process when the codon UGA is reached?
STOP
What amino acid is specified by the codon UCG?
Serine (STOP, hammer time.)
What does the comprehensive gene expression process throughout living organisms suggest about the origins of life?
Suggests that all life shares the same ancestry.
What end of the DNA strand has a phosphate group attached? The 5', or the 3'?
The 5' end of the DNA strand has the phosphate group
What is the physical difference between a 5' end and 3' end of a DNA molecule?
The 5' end starts with a phosphate as the nucleotide and the 3' end starts with deoxyribose, or the sugar as the nucleotide.
Why do we often describe a DNA molecule as an 'archive' of information?
The DNA molecule is able to hold and keep track of the information that composes and determines the organism's functions
What is the role of the 'P' site in translation?
The P site is the location from where the new protein will emerge from the ribosome
What part of a tRNA molecule specifies the amino acid to which it will bind?
The anti-codon.
How does the codon sequence of mRNA specify which tRNA molecules will bind to the mRNA?
The codons of mRNA are complementary to the anticodons of tRNA. The tRNA with the anticodon that matches the mRNA will bind and the appropriate amino acid will be deposited. A tRNA molecule without the appropriate anticodon cannot bind to the mRNA.
Describe the relationship between genes and proteins.
The information stored in genes in DNA form is used to create proteins through the assembly of amino acids in a specific order
In what way is the 'A' site on the ribosome similar to a loading dock at a warehouse?
The mRNA enters through the A site during the elongation stage of translation and the parts of the protein are added to the mRNA at the A site. It enters, loads, and then leaves.
The area of a DNA molecule where the replication process takes place is often referred to as a 'replication fork.' Explain why you think this term is used to describe this location.
The molecule stems out into two separate strands, hence the fork name is applied to describe the resulting shape
Why are both the non-template DNA strand and mRNA both 5'→3' in orientation?
The non-template DNA strand and the mRNA are identical (except for the thymine/uracil), because they are both complementary to the template strand of DNA.
How are the codons that specify a protein similar to the words that make up a sentence? What would happen if you were to change the sequence of the words?
The order and composition of the words determine the perceived meaning and intention of the sentence. Changing the sequence can cause a result in a sentence that may not make sense or create a completely different perceived meaning.
Why it is important for the efficient production of proteins that the cell has many tRNA molecules available?
The process of translation occurs extremely quickly, and the tRNA molecules with their corresponding amino acids must be available to keep the process moving productively.
What role does the promoter region of a DNA sequence play in the transcription process?
The promoter region can be recognized by RNA polymerase, and cause the RNA polymerase to bind to the DNA and begin transcription.
Compare the promoter and termination sequences of DNA to a traffic light.
The promoter region of a DNA sequence is like a green light, signaling the transcription process to begin, while the termination sequence stops the entire process, similar to a red light.
What is the final product of a strand of DNA that has undergone a mutation?
The protein is unaffected if the mutation is silent, while all other mutations will cause misfolded proteins.
How does the ribosome link individual amino acids together during the process of translation?
The ribosome catalyzes the formation of a covalent bond between the amino acid in the A site with the adjacent amino acid in the P site.
How does the sequence of bases impact the physical structure of RNA differently than DNA?
The sequence of bases can affect the way in which an RNA molecule folds and interacts with itself, changing the overall shape/function as a result.
How does the sequence of nitrogenous bases affect the appearance of a molecule of RNA?
The sequence of bases determines the shape of the RNA molecule due to hydrogen bonding between base pairs.
How does a strand of mRNA compare to the non-template strand of DNA from which it was created?
The strand of mRNA will be identical to the non-template strand of DNA, with the exception of uracil replacing thymine
DNA strands are considered to be antiparallel. How would the molecule appear differently if they were 'parallel' instead?
The strands would run in the same direction, so the 5' and 3' ends would be on the same side, instead of on opposite ends as in antiparallel.
In what way are codons similar to airport codes? (ex. PHL = Philadelphia)
The three letter codons match an abbreviation of an amino acid, just like a three letter code for an airport.
If there are only 20 amino acids used in the process of translation, explain the existence of thousands of different types of proteins in living organisms.
There are infinite combinations of amino acids that can be used to create what is essentially an infinite number of proteins. A single protein can consist of thousands of amino acids, and changing just one of these amino acids may create an entirely different protein.
Why are the two strands of a molecule of DNA referred to as 'Complementary?'
They compliment each other to create a specific set that works in unison.
Why is the process of transcription essential to the utilization of DNA?
Transcription allows the information coded in DNA to be transferred to a molecule of RNA, which can then be interpreted and used to create proteins. Without it, DNA just ends up being similar to a book in a foreign language
How is the presence of transcription factors related to the characteristics that define living organisms?
Transcription factors are necessary to only certain living organisms. E coli has operators so they don't need transcription factors, but humans do not have operators so they need the transcription factors to activate the RNA Polymerase.
How does the presence of transcription factors influence the process of gene expression?
Transcription factors determine which segments of DNA are transcribed and which aren't.
How is the process of transcription related to the process of translation in the cell?
Transcription makes mRNA which allows for translation.
Create a flowchart using words and arrows to show the entire process of gene expression. (You should use 5 words)
Transcriptional control→ RNA splicing/editing (processing control) → RNA Transport control→ Translational control→ Post translational (Protein assembly) control
What does the 't' in tRNA represent? Why is this an appropriate name when considering the role of this molecule in the translation process?
Transfer. The tRNA molecules carry (transfer) amino acids from the cell's interior to the ribosome and the growing amino acid chain.
What will occur in the ribosome when the codon UAG is reached on the mRNA?
Two subunits of the ribosome will disassemble and translation will terminate.
What is the anticodon on the first tRNA molecule that will begin every translation process? How can you predict this accurately?
UAC, because the codon for every mRNA start is AUG.
Which nitrogen base is involved in transcription but not DNA replication? Why is this the case?
Uracil. Uracil replaces thymine in RNA, but since RNA is not involved in DNA replication, uracil does not appear in this process.
What amino acid is specified by the codon UCA?
Valine
Below is a template strand of a gene that codes for a protein. Provide the related mRNA, tRNA and amino acid sequences: TAC-GGT-CTA-CCG-ACT
mRNA: AUG-CCA-GAU-GGC-UGA tRNA: UAC-GGU-CUA-CCG-ACU
Below is a template strand of a gene that codes for a protein. Provide the related mRNA, tRNA and amino acid sequences: TAC-CGC-TTA-GTC-ATT
mRNA: AUG-GCG-AAU-CAG-UAA tRNA: UAC-CGC-TTA-GUC-AUU
What is the role of tRNA in the process of translation?
tRNA goes into the ribosome with the anticodon. It carries the appropriate amino acid to the growing amino acid chain.
