Chapter 3 HELP chemistry of life BIO HL!

[dandoon96]

DNA, anyone?

Transcription?

Translation?

DNA replication

5'3. Carbon?

DNA structure?

Proteins?

HL aspects of topic?

Anyone with knowledge on this chapter! Please helpp! As I missed lessons and my teachers travelling so must self study! Please help! I hate this whole chapter! And I'm very lost what's a 5' carbon? What's the enzymes involved? And any other processess?

Thanks

[Sandwich]

Have you actually got a textbook? Because people here would only be paraphrasing the textbook. In a textbook (or indeed on Wikipedia!) you can find these things already written out and explained for you without people on IBS having to spend hours typing it up for you.

Why don't you try reading the textbook and then, if you're still stuck or confused with something, ask us. You might find this thread useful as some of the harder stuff (transcription, translation) is already explained in here Biology SL/HL help

5' and 3' (5 prime and 3 prime) carbons are explained very well on the Wikipedia entry: http://en.wikipedia....lecular_biology) but in short they refer to a particular carbon atom within the deoxyribose sugar that forms DNA. If you look at the diagrams in the Wiki entry, you'll see that DNA is comprised of a series of nucleotides all added together. An individual nucleotide is shown in the first image - it consists of the deoxyribose sugar (the central numbered ring), a phosphate group up on the left and a 'base'. As you can see, the carbons within the deoxyribose sugar are numbered, 1-5. 3' and 5' refer to carbons 3 and 5 (which is out on that 'stalk', attaching to the phosphate).

Look at the second diagram and you can see that the 5th carbon of the top nucleotide is attached to an -OH group, rather than a phosphate. As it's effectively "free", it's called the 5' end of that section of DNA. The opposite end (called the 3' end) has no nucleotide coming after it and so has an -OH group at carbon 3. So at one end of any stretch of DNA, you have a free carbon 5 and at the other end you have a free carbon 3. The 5 prime and 3 prime ends. This is significant because DNA can only be synthesised in one direction (5' to 3'). If you consider that DNA forms a double-stranded arrangement, where the strands pair up and look roughly like so:

5' ----------- 3'

3' ----------- 5'

You can see that this presents a dilemma, because if you make new DNA in a 5' - 3' direction on one strand, the other strand goes in the opposite direction, so effectively you can only synthesise one of the two strands OR you need to transcribe both strands simultaneously in opposite directions which would be almost impossible to coordinate - so what happens?? Well, read your textbook

Anyway - if you have specific questions, please ask. However, you will need to do some work yourself beforehand. Read the textbook (because biology is really pretty self-explanatory...) and ask about things which confuse you, rather than asking about absolutely every aspect of everything! In life, if you miss lessons, it's up to you to catch up and then take the responsibility for clarifying what's still confusing for you. Nobody spoon-feeds you after the first time. Self-directed learning is part of the IB and definitely pretty much all you do at Uni!

[kim luffy]

Hey i agree with what Sandwich said, if you have any particular questions, we can answer them Because the whole DNA replication process and every other bit of it is really long to explain. And also the 'base' of DNA is actually a nitrogenous base compromised of Thymine, adenine, guanine and cytosine. The bases are complimentary based paired i.e. they only pair up with a specific base which is thymine bonds with adenine and guanine bonds to cytosine. The bonds between the two bases are hydrogen bonds. Then there's this whole business to do with purines and pyrimidines. Anyway, if you still have confusion after reading, then feel free to ask good luck!

[Award Winning Boss]

Concise questions get concise answers.

Do a some research and 1 of 2 things will happen:

1. you don't need any extra help

2. you'll come back for help with some specific questions and you'll get better help.

have fun

[Kirimin]

Hopefully some of this is helpful to you, or to anyone else. And before people say I haven't just paraphrased my textbook, its my own work.

I don't know what you want to know on proteins but here are the four levels of structure as it helps with some of the DNA stuff:

Primary - many amino acids condense to form a polypeptide chain

- order of amino acids determines this structure

- peptide bonds hold it together

Secondary - hydrogen bonds can form between amino acids

- if the primary structure is repeating this can lead to formation of an alpha helix or beta pleated (folded) sheet.

Tertiary - further folding gives the protein a complex 3D shape

- held by : hydrogen bonds, ionic bonds and strong covalent bonds, eg disulphide bridges.

Quaternary - when two or more polypeptide chains join together to form a protein

- e.g. haemoglobin has 4 polypeptide chains

For DNA structure this site gives quite a good basic outline: http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html

Transcription - This is the process by which a sequence of DNA is copied to messenger RNA (mRNA)

Basic outline - Gene uncoils -> Combines with free RNA nucleotides - mRNA (with RNA polymerase) -> mRNA -> mRNA + ribosome -> mRNA + ribosome + transfer RNA (tRNA) + amino acid -> polypeptide chain.

^Hopefully that will make sense in a minute!!!

It involves the sense and antisense strand, the sense strand runs in the 5' to 3' direction and the antisense in the 3' to 5'. The sense strand is basically the code being replicated and the antisense strand is complementary, so this is what the mRNA nucleotides attach to. Firstly, the promoter is a short section of DNA that allows the RNA polymerase to join on and break hydrogen bonds between the DNA bases. The RNA polymerase unwinds the two strands in this way and allows the mRNA bases to attach. The mRNA strand formed will be the same as the sense strand but with one important difference, anywhere there was a Thymine base on the sense strand, there is Uracil. The DNA recoils again and the hydrogen bonds reform. The RNA polymerase continues until it reaches the terminator sequence, which is a section of DNA that tells it to detach.

Editing - This comes in between transcription and translation, basically for some reason DNA contains introns, which is non-coding DNA. This is no use when replicating DNA so it is edited before translation to remove any introns, so that it all codes for amino acids.

Translation - This involves a ribosome - formed of a large ribosomal unit on one side of the mRNA and a small ribosomal unit on the other. There are three sites on the ribosome, the P site, the E site and the A site. tRNA attaches to the P site and it has an amino acid attached (tRNA is kind of like a taxi for amino acids) and each 3 bases (a codon) codes for a specific tRNA + amino acid. After the first tRNA has attached the mRNA moves along one codon, the original tRNA is now in the E site and detaches. The A site is where the incoming tRNA attaches. The amino acid then attaches to the one brought in by the next tRNA. This movement and formation of bonds continues until the stop codon is reached, when everything detaches and you have a chain of amino acids (polypeptide chain) which is the primary structure of a protein.

Ummmm that one probably didn't make much sense so here is a diagram http://biology.about.com/library/bltranslation.htm and here is a video: http://www.youtube.com/watch?v=983lhh20rGY

DNA replication - Firstly DNA Helicase moves along the DNA strand and unwinds it by breaking the hydrogen bonds between the bases. RNA primase moves along the two single strands and attaches small sections of complementary RNA (RNA primer), which then allows the DNA polymerase III to attach. On the leading strand this is able to follow the helicase and attach complementary bases in the 5' to 3' direction (use the website in the earlier post to read up on these). However on the lagging strand the polymerase III has to work backwards in a way and so can only attach a small number of bases at a time, which leads to the formation of Okazaki fragments. Then DNA polymerase I goes along the strands, removing the RNA primer and replacing it with DNA bases. Finally DNA ligase joins up the okazaki fragments on both strands and the DNA has finished replicating.

Red text = enzymes used

Hope this is helpful