My Biology Thread

[alchemy]

             

Please keep this thread limited to only questions and free from any extraneous discussion.

Question: Transcription takes place from the 5’ to the 3’ end of the m-RNA. Why?

My answer: Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3’ end. This means the corresponding mRNA will have to assemble starting from the 5’ end. That is my initial thought, but can someone expand on it? Is this explained by why replication is performed in the 5' to 3' direction as suggested by this link: http://biology.stackexchange.com/q/477/5085
Also, is the DNA template strand same as the sense strand?

EDIT: Its seems as though the nomenclature for DNA sense and template strand can be same or differentiable as suggested by this: http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/temp-strand.html

[DJA]

Could you explain in simple terms the difference between a gene, a genome, chromosomes, DNA and RNA.

Thanks!

[Yacoubb]

Could you explain in simple terms the difference between a gene, a genome, chromosomes, DNA and RNA.

Thanks!

DNA (Deoxyribose Nucleic Acid) is the hereditary information and genetic instructions that determines how an organism functions, ultimately. Genes are units of DNA thar code for specific proteins. Genome refers to the complete array of genes present in a living organism or cell, including nuclear, mitochondrial & chloroplastal DNA, etc. RNA = Ribose Nucleic Acid. There are 3 types of RNA: tRNA, mRNA and rRNA.
tRNA = transfer RNA; this tRNA carries a specific amino acid to the ribosome.
mRNA = messenger RNA; this mRNA carries the transcribed set of genetic instructions to the ribosome.
rRNA = ribosomal RNA; together with other proteins, constitutes the make-up of the ribosome organelle, where protein synthesis occurs.

A chromosome is a structure made up if tightly coiled DNA. In eukaryotes, chromosomes are linear, rod-shaped, and in prokaryotes, chromosomes are circular.

[psyxwar]

Question: Transcription takes place from the 5’ to the 3’ end of the m-RNA. Why?

I have a feeling you've been reading the TSFX notes for this topic; completely disregard them for this, they are wrong.

I will be using the term "pre-mRNA" in my response; to prevent any confusion (in case you haven't covered this yet), the pre-mRNA strand is the product of transcription. It then undergoes post-transcriptional modification to yield your mRNA strand which is read by the ribosomes during protein synthesis.

Transcription involves RNA polymerase (RNApol), which is responsible for both locally unwinding the double helix and for the actual process of assembling the pre-mRNA transcript. RNApol runs along the antisense strand (aka. template strand) 3' to 5', creating the new pre-mRNA strand 5' to 3'.

A few things: the DNA sense strand is the "coding strand", and the pre-mRNA strand is the same as it (with the exception of T->U) because the pre-mRNA strand is transcribed off the antisense strand, which itself is complementary to the sense strand. For the purposes of VCE Biology, it is probably a waste of time to learn it as "sense" and "antisense"; "coding" and "template" is much more intuitive and it's what VCAA writes in their model answers.

If you are curious as to why the new pre-mRNA strand is built 5' to 3': all nucleic acids are built 5' to 3' because on the 3' end of the pentose sugar of nucleotides there is a hydroxyl (OH-) functional group.



In order to join the nucleotides together you need this hydroxyl group (due to the nature of the phosphodiester bonds that link the nucleotides together). Thus, the only way to build the strand is to add new nucleotides to the 3' end of an existing one (where the OH group lies), and hence the new strand must be build 5' to 3' (as you are adding stuff to the 3' end).

Also, just an interesting fact while I'm at it: deoxyribonucleic acid is so called because it is a ribonucleic acid with one less oxygen (de-oxy).



Now think about the significance of a di-deoxyribonucleic acid. What do you think this would do if used in transcription?

[alchemy]

Could you explain in simple terms the difference between a gene, a genome, chromosomes, DNA and RNA.

Thanks!

Pretty sure you could have Googled those definitions, but I will provide them for the sake of simplicity.

DNA is abbreviated for Deoxyribonucleic acid. It consists of two polynucleotide strands together, forming a helix shape, terming it a Bio macromolecule. The two strands of DNA are termed ‘anti-parallel’ meaning one runs in opposite direction to the other, hence the 3’ and 5’ notation. It is important to note the structure of DNA consisting of a Pentose sugar (Deoxyribose), a phosphate group and a nitrogenous base. DNA consists of 4 nucleotides, namely, Adenine, Thymine, Guanine and Cytosine. The primary purpose of DNA is for biological information storage.

RNA is abbreviated for Ribonucleic acid. Unlike DNA, it consists of a single polynucleotide strand. Nucleotides in RNA are Adenine, Uracil, Guanine and Cytosine. The primary role of RNA is to take part in cell reactions as it is more reactive than DNA. It carries genetic info in certain viruses (i.e. HIV).

Genes, termed molecular heredity units, are the information in a very long DNA segment. Genes are a locatable region (locus) on a DNA helix. They consist of many nitrogenous bases and serve to specify all proteins, RNA chains and many other enzymes.

A chromosome is a single organised DNA, RNA or protein structure. There are 46 chromosomes in humans (23 pairs). Chromosomes, being DNA structures, consist of many genes (~1000) and are consequently very long.

The genome is a complete array of an organism’s hereditary information (genes and non-coding sequences in DNA/RNA) .

[DJA]

Pretty sure you could have Googled those definitions, but I will provide them for the sake of simplicity.

DNA is abbreviated for Deoxyribonucleic acid. It consists of two polynucleotide strands together, forming a helix shape, terming it a Bio macromolecule. The two strands of DNA are termed ‘anti-parallel’ meaning one runs in opposite direction to the other, hence the 3’ and 5’ notation. It is important to note the structure of DNA consisting of a Pentose sugar (Deoxyribose), a phosphate group and a nitrogenous base. DNA consists of 4 nucleotides, namely, Adenine, Thymine, Guanine and Cytosine. The primary purpose of DNA is for biological information storage.

RNA is abbreviated for Ribonucleic acid. Unlike DNA, it consists of a single polynucleotide strand. Nucleotides in RNA are Adenine, Uracil, Guanine and Cytosine. The primary role of RNA is to take part in cell reactions as it is more reactive than DNA. It carries genetic info in certain viruses (i.e. HIV).

Genes, termed molecular heredity units, are the information in a very long DNA segment. Genes are a locatable region (locus) on a DNA helix. They consist of many nitrogenous bases and serve to specify all proteins, RNA chains and many other enzymes.

A chromosome is a single organised DNA, RNA or protein structure. There are 46 chromosomes in humans (23 pairs). Chromosomes, being DNA structures, consist of many genes (~1000) and are consequently very long.

The genome is a complete array of an organism’s hereditary information (genes and non-coding sequences in DNA/RNA) .

Thank you!

[alchemy]

Thank you!

No worries, but next time, please don't quote the whole text just to say thanks. If anything a +1 would be nice .

Question:
A student recorded the events of a reaction using an enzyme at 37oC in his lab book. Into test tube 1, he put 10 mL of a boiled egg-white solution. This was cloudy in appearance. Then he added 2mL of an enzyme solution and stirred the solution. Ten minutes later, the solution had turned clear.
The suspension might have become clear more quickly if:
A. More egg protein had been used.
B. The mixture had not been stirred.
C. The pH of the mixture had been changed.
D. The temperature had been raised to 75°C.
E. Iodine had been added to the test tube.

My answer: D. The temperature raise. Why isn't this correct? Isn't heat a contributing factor of protein denaturation?
Answer: C. The pH of the mixture has been changed. I suspected this too, but it didn't specify if the pH was increased or decreased. Would an increase or decrease in pH mean a greater rate of denaturation?

Source: NQE Biology 2007.

[psyxwar]

<snip>
My answer: D. The temperature raise. Why isn't this correct? Isn't heat a contributing factor of protein denaturation?
Answer: C. The pH of the mixture has been changed. I suspected this too, but it didn't specify if the pH was increased or decreased. Would an increase or decrease in pH mean a greater rate of denaturation?

Source: NQE Biology 2007.

Heat is a contributing factor towards protein denaturation, which is why your answer is wrong? The proteins in egg white (eg. albumin) are broken down by the enzymes, resulting in it going from cloudy to clear. It becoming clear more quickly implies a faster rate of reaction -> conditions for enzymatic action were more optimal. Out of all the options C is the best, because it's very likely at such a high temperature the enzymes would have denatured.

[alchemy]

Heat is a contributing factor towards protein denaturation, which is why your answer is wrong? The proteins in egg white (eg. albumin) are broken down by the enzymes, resulting in it going from cloudy to clear. It becoming clear more quickly implies a faster rate of reaction -> conditions for enzymatic action were more optimal. Out of all the options C is the best, because it's very likely at such a high temperature the enzymes would have denatured.

Hmm, that makes sense I guess. However, I never thought of the enzymes being denatured though. What I had in mind was the egg white, although still your answer makes sense to me, because I didn't consider the enzymes.

[alchemy]

Question attached. Source: NQE Biology 2007

These questions are tricking me. I'm usually stuck between choosing two options, one of them which is correct. Here the answer is D. I suspected this because each enzyme has an optimal pH and an optimal temperature. However, option C suggesting substrate concentration seemed equally appealing. I know that more substrate added initially increases the reaction rate if not all of the active sites are occupied. It tampers off when no more enzyme is added, the active sites all becoming occupied. Is it because the question hasn't specified if enzyme has been increased or decreased that means we cannot know whether substrate concentration was an influence to reaction rate?

[psyxwar]

Question attached. Source: NQE Biology 2007

These questions are tricking me. I'm usually stuck between choosing two options, one of them which is correct. Here the answer is D. I suspected this because each enzyme has an optimal pH and an optimal temperature. However, option C suggesting substrate concentration seemed equally appealing. I know that more substrate added initially increases the reaction rate if not all of the active sites are occupied. It tampers off when no more enzyme is added, the active sites all becoming occupied. Is it because the question hasn't specified if enzyme has been increased or decreased that means we cannot know whether substrate concentration was an influence to reaction rate?

It plateaus, meaning the rate of reaction remains CONSTANT, rather than decreases. All the active sites being occupied means the reaction can go no faster. Think of the shape of a square root function; kind of like that, except at a point the reaction rate becomes a straight line.

I recommend going through some of the 3/4 course and building a strong biological foundation before doing the NQE papers

[alchemy]

It plateaus, meaning the rate of reaction remains CONSTANT, rather than decreases. All the active sites being occupied means the reaction can go no faster. Think of the shape of a square root function; kind of like that, except at a point the reaction rate becomes a straight line.

I recommend going through some of the 3/4 course and building a strong biological foundation before doing the NQE papers

Thanks, that's what the diagram in my book shows and now I get it. However, i feel this is helping me build up that foundation rather than testing it. Let's face it, the book questions are dull enough

The next question is attached. Again two answers seem exactly the same to me. What's the difference between B and C? I worked out that the child matches 2/4 (1/2) of fathers DNA in BOTH options B and C. What makes these two options different? The answer is A :Child 1. Doesn't seem like a very biological question, just counting right?

EDIT: The answer is A, not B as mentioned before. Mistake on my behalf, I checked the answers incorrectly.

[Yacoubb]

Thanks, that's what the diagram in my book shows and now I get it. However, i feel this is helping me build up that foundation rather than testing it. Let's face it, the book questions are dull enough

The next question is attached. Again two answers seem exactly the same to me. What's the difference between B and C? I worked out that the child matches 2/4 (1/2) of fathers DNA in BOTH options B and C. What makes these two options different? The answer is B :Child 2. Doesn't seem like a very biological question, just counting right?

The question says which is LEAST likely. That means, has the least banks in common. So, because only child 2 has 2 bands in common, relative to child 3, who has 3 bands in common with either their mother or father. So, the answer is B.

P.S. why are you doing these questions now lol? This is unit 4 stuff, haha, too keen!

[alchemy]

Question is attached. I've already covered this topic at school, so I would assume this is a suitable question.

[alchemy]

Question is attached. I've already covered this topic at school, so I would assume this is a suitable question.

Kudos to Stick for the answer. I'll try to describe it here for future reference and for the benefit of other viewers. Someone please correct me if any of this is biologically inaccurate.

Firstly it is important to note the orientation of the proteins on the main diagram. To describe this in a 'non-scientific' way we could say that the round shaped end faces inward and the squarish shaped end faces outward of the vesicle. In it's secretory pathway through the Golgi Apparatus, the orientation does not change. This now leaves us with option B as the only possible answer. However, in order to confirm this, and the orientation of the proteins after they have fused with the plasma membrane, we must consider the vesicle's interaction with the plasma membrane. Recalling the process of exocytosis  we know that the vesicle's membrane fuses with the plasma membrane in order to release the contents from the cell, meaning the orientation of the proteins be reversed too. This is depicted in option B rendering it to be the answer.