B8 Nucleic Acids

B.8.1 Describe the structure of nucleotides and their condensation polymers (nucleic acids or polynucleotides).
Nucleic acids are polymers made up of nucleotides. A nucleotide contains a phosphate group, a pentose sugar and an organic nitrogenous base. Nucleic acids are joined by covalent bonds between the phosphate of one nucleotide and the sugar of the next, resulting in  a backbone with a repeating pattern of sugar-phosphate-sugar-phosphate. Nitrogenous bases are attached to the sugar of the backbone.
Recognise the structures of the five bases: adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U).

Includes DNA and RNA, acidic molecules found in cell nuclei (but RNA found elsewhere). Both are polymers (polynucleotide), built from nucleotide monomers.

DNA
- responsible for genetic information, and passing it onto the next generation
needs:
- to be stable, to retain precise chemical structures in cell conditions
- to contain some 'code' that stores genetic information
- to be able to be replicated - must be able to produce an exact copy of itself

RNA
- expresses genetic information
- by controlling primary structures of proteins synthesised.

Structure

Nucleotides
- building blocks of nucleic acids
- made of 3 components:

Pentose (C5) sugar: C5H10O5

DNA - deoxyribose, RNA - ribose
Difference: C2, deoxyribose lacks an -OH

Phosphate group PO4 3-, phosphoric acid H3PO4

Organic nitrogenous base

- two types: purines and pyrimidines
Purines: larger, 2 fused rings
Pyrimidines: smaller, single ring

Both have: A, G, C
Thymine is exclusively in DNA and Uracil is exclusively in RNA.
Nucleotides formed as pentose, phosphate and base are joined together by condensation reactions (water released).
Base always condensed to C1 of sugar, and phosphate to C5 (also known as 'five prime', 5', position)

DNA: a) full structure, b) shorthand form
Source: IB Chemistry Textbook

Condensation

Nucleotides --> Polynucleotides
- involves phosphate at 5' of on nucleotide and -OH group at 3' on the next nucleotide
- builds chain held together by covalent bonds between alternating sugar and phosphate residues
- bonds: phosphodiester link
- nitrogenous bases do not take part in the polymerisation, remains attached at C1

a) part of a nucleotide b) shorthand form
Source: IB Chemistry Textbook

B.8.2 Distinguish between the structures of DNA and RNA.
RNA has a single strand nucleic acid.
DNA has deoxyribose. Deoxyribose lacks an oxygen atom on C2. DNA is a double-strand nucleic acid.

Ribonucleotides in RNA
- ribose sugar
- A, G, C or U

Deoxyribonucleotides in DNA
- deoxyribose sugar
- A, G, C or T

a) ribonucleotide, b) deoxyribonucleotide
Source: IB Chemistry Textbook

B.8.3 Explain the double helix structure of DNA
The structure has two nucleic acid strands that spiral around an axis. Hydrogen bonding between specific pairs of nucleotide bases.
DNA
- double helix of 2 polynucleotides
- sugar-phosphate backbone on the outside and nitrogenous bases on the inside
- strands held together by h-bonds formed between bases
- certain base-pairings: one purine, one pyrimidine (A&T, C&G)
- A = T (2 h-bonds), C = G (3 h-bonds)

 

10 nucleotides = 1 complete turn of the helix (length of 3.4mm)
The two strands are anti-parallel, they run in opposite directions (3'-->5' and 5'-->3'). They are upside down relative to each other.
(Refering to B.8.1)
Stability: maximises hydrophobic interactions between bases in the middle of the molecules while polar, charged groups in the sugar-phosphate backbone interacts with aqueous solution
Code: sequence of bases are codes of information in the strand, with infinite varieties.
Exact replication: complementary base pairings allows this.

RNA
- single stranded polynucleotide
- constructed similarly to DNA
- also carries information in base sequence
- less stable than DNA
- usually more short-lived in the cell
- able to cross nuclear membrane (so it can move between the nucleus and cytoplasm)
3 different forms (each with a distinct role):
Messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)
All 3 required in protein synthesis.

Central dogma of molecular biology
Source: IB Chemistry textbook

B.8.4 Describe the role of DNA as the repository of genetic information, and explain its role in protein synthesis.
DNA
- genetic material that an individual inherits from its parents
- contains all information needed for the development for the individual coded in the base sequences along its length
- expressed through controlling protein synthesis (determining the sequence of amino acids - the primary structure)
- must be translated into code for all 20 amino acids found in protein.
translated into code in 2 main steps: directs mRNA synthesis (transcription) and, through mRNA, directs protein synthesis (translation) using a triplet code.

Transcription (mRNA copies part of the DNA)
- DNA in cell nucleus, protein synthesis on ribosomes in cell cytoplasm
- relevant DNA part is copied, copy is in form of mRNA
- mRNA moves to the ribosome
- synthesis of mRNA from DNA called transcription
- when 2 DNA strands 'unzip', breaks h-bonds between the base pairs
- separate strands are templates for the other complementary strand of mRNA from ribonucleotides
- bc of the specific base pairing, complementary ribonucleotides are aligned in sequence
- DNA is copied EXACTLY
- process all controlled by enzymes
- mRNA then detaches from the DNA template and moves to the ribosome
- DNA stays in the nucleus and reforms a double helix

Transcription produces mRNA
Source: IB Chemistry Textbook

Translation (assembling protein from mRNA code)
- sequences of bases used to determine sequence of amino acids in polypeptide
- involves tRNA, like an adaptor
- one end of the tRNA recognises a specific triplet of bases (a codon) in the mRNA
- other end recognises corresponding amino acid
- codons in mRNA read sequentially, successive tRNA bring appropriate amino acids into position, they link together to form a polypeptide
- base sequence in DNA (then mRNA) determines sequence of amino acids in proteins
- genetic code: specific relationship between bases and amino acids
- triplet code with three bases specifying each amino acid
- universal code, same codon = same amino acid in all organisms
Central dogma: central information flows in one direction in cells, from DNA to RNA to protein

Transcription produces mRNA from DNA --> Translation produces polypeptide from mRNA

Semi-conservative replication of DNA
Source: IB Chemistry Textbook

B.8.5 Outline the steps involved in DNA profiling and state its use.
Include forensic and paternity cases
DNA replication: DNA makes an exact copy of itself
- occurs during cell division
- all cells in the body (except reproductive sex cells) contain an identical set of genetic information
Semi-conservative replication: replication results in new molecules that contain one strand from the parent molecule and one newly synthesised strand.

** Replication is different to transcription**

Both involve separation of DNA strands, and use of single-stranded template

Different processes, controlled by different enzymes

DNA replication: 2 identical daughter DNA molecules

Transcription: produces mRNA

Genome: unique set of DNA (except identical twins)
- identified by DNA profiling
- each cell contains ~ 3 billion base pairs, 99.9% identical in everyone, only 0.1% is unique (0.1% of ~3 billion is ~3 million base pairs, so enough for accurate identification)


DNA profiling
1. DNA extraction (from blood or the subject etc.)
- DNA cut into small pieces using restriction enzymes
- easiest place to detect the unique DNA in places where short sequences of bases are repeated numerous times, called short tandem repeats (STRs)
- test STR in multiple genome places, process is more discriminating

2. Polymerase chain reaction (PCR)
- amplifies region in the DNA by making copies
- uses sequence-specific primers to bind to the DNA that is separated into single strands
- and heat-stable version of enzyme DNA polymerase to polymerise the sections
- works around 70'C
- PCR can add up to a thousand bases per minute (million of copies of STRs)

3. Electrophoresis
- DNA fragments separated and detected
- bc of phosphate groups DNA has a negative charge
- moves towards positive terminal, distance corresponds to molecular size
- shorter fragments move further than longer fragments
- Nitrocellulose sheet used in electrophoresis treated with radiation (32P), and exposed with X-ray film.
- produces autoradiogram, dark bands shows position of fragments
- pattern seen is the DNA profile (compared to others for identification)


Applications
- to identify victims whose bodies are not present at the accident/crime scene
- forensic: to identify the suspect e.g. convicted prisoners have been exonerated (absolve from blame) by DNA evidence
- to confirm biological relationships between individuals e.g. to determine paternity, to determine family relationships for purposes of immigration or inheritance
- to determine relationships between popluations in the study of evolution, migration and ecology.