Macromolecules

Universal genetic code

- All organisms use the same 4 bases in their DNA. - All species use the same 20 amino acids to build proteins. - The 'code' uses 3 bases at a time to direct protein assembly. - The same mRNA codon codes for the same specific amino acid. - The same tRNA molecules carry the same amino acid.

Carbohydrates

- Contain the elements carbon, hydrogen and oxygen. - Called polysaccharides (many sugars). - Energy storage includes glycogen in animals and starch in plants. - The subunits are monosaccharides (simple sugars) like Glucose, which is used as a ready source of energy for both plants and animals.

Lipids

- Contain the elements carbon, hydrogen and oxygen. - Solid at room temperature = fat. - Liquid at room temperature = oil. - Subunits are 3 fatty acids and 1 molecule of glycerol. - Excellent insulators and are used for long term energy storage as lipids contain twice the energy per gram as carbohydrates or proteins.

Protein synthesis

- DNA begins the process. DNA is found inside the nucleus, and does not leave the nucleus. Proteins, however, are made in the cytoplasm of the cell by ribosomes. The DNA code must be copied and taken to the cytoplasm. - In the cytoplasm, this code must be read so amino acids can be assembled to make polypeptides (proteins). This process is called protein synthesis. For protein synthesis to work, DNA and RNA are involved. There are 3 types of RNA used by they all use the same nucleotides.

DNA vs RNA

- DNA is a double helix, whereas RNA is single stranded. - RNA is smaller than DNA. - DNA is composed of deoxyribose sugar, whereas RNA is composed of ribose sugar. - The bases in DNA are A, T, C and G, whereas the bases in RNA are A, U, C and G.

Structure of DNA

- DNA is an extremely large molecule in a double helix shape. - The repeating units are nucleotides. Each nucleotide consists of 3 parts: a sugar (deoxyribose), a phosphate group and a nitrogenous base. - There are 4 different bases - Adenine (A), Guanine (G), Cytosine (C) and Thymine (T). Thus, there are 4 different nucleotides. - Each DNA molecule contains thousands of nucleotides. - The order of the nucleotides in the DNA molecule is the code for making proteins.

DNA fingerprinting

- Individuals have unique DNA sequences, allowing everyone to be identified through DNA fingerprinting. 99% of human DNA is identical between individuals, but the 1% that differs enables scientists to distinguish identity. 1. Receive a sample of DNA (blood, semen, hair, saliva etc). 2. RE'S cut the DNA into smaller pieces. 3. Gel electrophoresis separates the DNA fragments based on size. The smaller fragments move farther across the gel than the larger ones. 4. A DNA/RNA probe is complementary to the DNA sample. As the probes are radioactively labelled, they leave marks from where they attach to the DNA sample. - These markings allow researchers to analyse the DNA fingerprint. The DNA fragments will be unique to every individual.This is how a distinctive fingerprint occurs.

Proteins

- Made up of C, H, O, N and sometimes S. - Subunits are called amino acids, to which there are 20. - A polypeptide is a chain of amino acids in a specific sequence. This sequence can be up to any length. - Polypeptides then form different shapes for different functions. - The 20 amino acids can be in different combinations and orders. - The difference in sequence of amino acids will change also depending on how many (length) of amino acids are in the polypeptide chain.

Macromolecules

- Made up of organic compounds. - Contain carbon and are complex. - Are produced by or associated with living things. - There are 4 major types: carbohydrates, lipids, proteins and nucleic acids. - Relatively large and are made of smaller molecules called subunits, which join together in long chains. - Involved in structures and chemical reactions.

Codons

- Protein synthesis relies on the genetic code. Each triplet of bases on DNA codes for 1 amino acid. A copy of this code made of RNA is called a codon. - The 20 amino acids are coded for by 1 or more codon. - An individual codon only codes for 1 amino acid. - There are codons for 'start' (AUG) and 'stop' (UAA, UAG, UGA) to make the amino acid chain. - This code is universal - present in all living organisms.

Functions of polysaccharides

- Starch (energy storage for plants). - Cellulose (lends strength to cell walls of plants). - Chitin (forms the exoskeleton of many animals). - Glycogen (energy storage in the muscles and liver).

Nucleic Acids

- The chemical unit of genetic information in most organisms is DNA. - DNA stores information to control the activities of the cell and transmits this from generation to generation. - The subunit of nucleic acids is a nucleotide. This is composed of a deoxyribose sugar, a phosphate group and a nitrogenous base. There are 4 bases (A, T, C, G). - RNA is the other nucleic acid which is also made up of nucleotides but the sugar is ribose, the bases are A, U, C, G and it is single stranded, not double.

Time

- The more time you have, the more changes (mutations in the DNA) can occur. Closely related groups of organisms have had little tine to make changes, so the DNA sequence has not changed much. - When DNA changes, so does the nucleotide sequence, so does the codon, so does the amino acid sequence and so does the protein.

Functions of proteins

- Transport - haemoglobin in blood and proteins in membranes. - Defense - antibodies are proteins that fight disease by binding to foreign particles. - Membrane receptors - act as receptor sites. - Structural - nails, feathers, horns, quils.

DNA replication

1. DNA is untwisted and unzipped. The weak hydrogen bonds between the bases are broken. 2. Each new DNA strand then acts as a template for the construction of a new DNA strand. Free nucleotides from the cytoplasm migrate to the nucleus and are attached to their complementary nucleotides on the original DNA strand. DNA polymerase enzyme does the attaching and DNA ligase attaches the backbone molecules. 3. When the DNA nucleotides are attached the new DNA molecules then retwist into new daughter molecules. Thus, 2 identical DNA molecules are produced, each consisting of 1 old and 1 new strand of DNA. This is why replication is called semi-conservative replication.

Gene

A segment of DNA on the chromosome that contains the complete sequence of bases required to direct the manufacture of a polypeptide or an RNA molecule. Each gene sits at a specific locus on a chromosome.

Active site

A specific shape on the region of an enzymes surface. It is where the substrate binds to.

Competitive inhibitors

Are so similar to the substrate that they bind to the active site of the enzyme and prevent it from bonding.

Primary structure

Basic order of amino acids in the polypeptide protein chain. This is before there is any folding or bonding between amino acids. Proteins are not usually functional on this level. Order of amino acids.

Non-competitive inhibitors

Bind to an enzyme, but not its active site. It changes the shape of the enzyme so the active site changes and the substrate no longer fits.

Enzymes

Biological catalysts. They work within cells (intracellular) and outside of cells (extracellular). They are proteins that always remain unaltered so they can be used again and again. In a reaction the substrate fits in an active site and forms an enzyme-substrate complex. Within this complex, the reaction occurs to convert substrate to product.The products, which are no longer attached to the active site, are released. The substrate becomes the product.

DNA Sequencing

Compare the base sequence of sections of DNA from different organisms. Organisms which are closely related will have less differences in their DNA sequence compared to organisms which are distantly related.

Transcription

Copying the DNA code (in the nucleus). - The part of the DNA molecule (the gene) that the cell wants the information from to make a protein unwinds to expose the bases. The rest stays closed. - Free RNA nucleotides in the nucleus base pair with one strand (the sense strand) of the unwound DNA molecule. A copy of the DNA is called messenger RNA (mRNA). - This mRNA strand is a complimentary copy of the gene in the DNA. The DNA triplets are copied to become mRNA codons. The mRNA is made fresh each time - it does not pre-exist. - When the whole gene has been copied the mRNA molecule peels away from the DNA and leaves the nucleus via the nuclear pores and goes to the ribosomes for translation. The DNA closes up and rewinds. - This process is called transcription (transcribe = to copy).

Necessity of protein synthesis

DNA contains genes, sequences of nucleotide bases. These genes code for polypeptides (proteins). Proteins are used to build cells and do much of the work inside cells. Without the right proteins, nothing happens.

DNA-DNA Hybridisation

DNA from 1 species is heated to separate the strands. Single stranded DNA from another species is added and the mixture is cooled. The strands bind. Closely matched strands will bind more tightly than those not well matched. The mixture is reheated: closely matched strands (closer species) are more stable and split at higher temperatures. Poorly matched strands (distantly related species) split at lower temperatures.

pH

Enzymes are most active at an optimum pH. Enzymes lose activity in low or high pH as the structure is disrupted.

Temperature

Enzymes are most active at the optimum temperature (37 degrees). Enzymes lose activity at high temperatures as denaturation occurs. This is due to the bonds within the enzyme breaking, so the shape of the enzyme and active site is changed. As a result, the substrate can no longer bind to the active site and a reaction cannot take place. Enzymes show little activity at low temperatures, due to there being less movement and fewer collisions, so reactions are insufficient.

Comparison of proteins

Haemoglobin and cytochrome c. The seems better suited to studying less closely related species.

Induced-fit model

In this model: - The active site is flexible, not rigid. - The shapes of the enzyme, active site and substrate adjust to maximise the fit, which improves catalysis.

Chromosome

Long thread like strands of DNA in the nucleus. Not visible unless the cell is dividing, and then appears as short, thick rods. Chromosomes are made up of DNA wrapped around proteins. They contain DNA and protein and each chromosome has genes specific to it, therefore it is identifiable.

Inhibitors

Molecules that cause a loss of catalytic activity. They prevent substances from fitting into the active site.

Microinjection

Multiple copies of the desired gene are injected into a recently fertilised egg. The gene (if successfully incorporated into the DNA of the cell) will be present in every cell. However, this is a very inefficient process.

DNA in evolution

Nucleic acids (DNA and RNA) are the only known molecules that are able to store genetic information and transmit genetic information (copy it and pass it on). They are found in all living things on Earth. Therefore, DNA us universal. This leads to the conclusion that life as we know it today has the same origin.

Summary of translation

Occurs in the cytoplasm. RNA ---> Protein. - mRNA attaches to ribosomes. - tRNA molecules bring specific amino acids to the ribosome, according to the codon on the mRNA. - The complementary triplets on the tRNA are called anticodons. - The polypeptide chain grows as the amino acids are joined. - The completed polypeptide breaks away from the ribosome and folds to form a 3D protein.

Summary of transcription

Occurs in the nucleus. DNA ---> RNA. - DNA strands separate at the site of the gene. - One strand of the DNA is used as a template for mRNA synthesis (complementary base pairing of free mRNA nucleotides to the DNA template strand. U is used instead of T). - mRNA breaks away from DNA and travels through nuclear pores to ribosomes in the cytoplasm. The DNA strands rejoin.

Mutation

Occurs when the base sequence in part of the DNA molecule is changed. The base sequence of DNA can be altered by bases being deleted, added or substituted. These produce changes in the codons, hence the order of amino acids, hence the proteins made.

Plasmid

Removed from bacteria and is cut with the same RE used to cut the gene of interest. This produces the same sticky ends. The DNA of interest is added to the plasmid DNA and the plasmid is reinserted back into the bacterium. The bacteria can infect desired cells for transfer of gene.

Selecting DNA

Step 1: DNA extraction from cells. - Break up the cell. - Centrifuge (spin) to extract the nucleus. - Remove the nuclear membrane. - Isolate the DNA from the proteins.

Restriction Enzymes

Step 2: Cut the DNA using Restriction Enzymes. - RE's are used by bacteria to cut up the DNA of invading viruses and foreign bacteria (it is not present in humans). - These RE's are extremely specific and work by recognising short nucleotide sequences in DNA molecules. - The first RE worked out is called EcoRI. - RE's cut at a specific sequence in the DNA, resulting in the production of short sequences of DNA with 'sticky ends'.

DNA Probe

Step 3: Part A. Once the DNA is in pieces, the gene of interest can be selected, by using a probe. - Using DNA/RNA probes to select/identify the gene of interest. - DNA/RNA probes are short sequences which are single stranded and are complementary to part of the gene of interest. - The probe is labelled fluorescently or radioactively. - The probe is mixed with the DNA pieces that have been cut by the RE'S. The solution is heated so the double stranded DNA pieces can separate and thus become single stranded. - The mixture is then cooled - hopefully the probe will specifically bind to the complementary sequence on the gene of interest rather than the gene recombining with its opposite strand.

Gene Product

Step 3: Part B. A gene product (protein) is injected into an animal so the animal produces antibodies specific to the protein. - The antibodies are collected and labelled fluorescently or radioactively. - The whole DNA library is cut up into fragments using RE's, and these DNA fragments are incorporated into a large number of bacteria. - The labelled antibodies are mixed with the bacteria. They will only bind to bacteria that are producing the original protein (from the gene of interest). - These bacteria must contain the gene of interest.

PCR

Step 4: Making multiple copies of the gene of interest. This is referred to as the Polymerase Chain Reaction (PCR). - PCR requires primers, heat tolerant DNA polymerase, free nucleotides and the original DNA template (from the gene of interest). - The mixture is alternatively heated and cooled. Heating breaks the bonds of the template DNA. Primers attach to DNA strands upon cooling so that the strands do not rejoin. - DNA polymerase brings in the required nucleotides in the correct sequence to make new daughter DNA molecules. - The process is repeated over and over.

Transferring the gene of interest

Step 5: Transferring the gene of interest. Gene transfers involve the following elements: Plasmids, using viruses as vectors and microinjection.

Translation

The language of DNA (base sequences) is translated into the language of proteins (amino acids). This stage is involved in the ribosomes. - In this process, the mRNA molecule firstly attaches to the ribosome. The ribosome is made of rRNA and can only attach to 6 bases on the mRNA at a time. - The next step involves bringing amino acids to the ribosome and the mRNA, as mRNA codes for amino acids. - This is achieved by another kind of RNA called transfer RNA (tRNA). - The 3 bases of an anticodon on tRNA are complementary to the 3 bases of a codon on mRNA. tRNA attaches amino acids. - The amino acid it picks up is coded for by its codons. It will only carry one amino acid and no other.

Substrate

The reactants of an enzyme, which fit to the active site. This is because the active site is complementary to the substrate. Although the substrate and enzyme are complementary, they do not make a perfect fit. The enzyme has to change its shape to do this.

Substitution

The same amino acid may still result since several codons can code for the same amino acid. There will be a problem if a different amino acid results from a substitution.

Using viruses as vectors

The virus is genetically modified to add the gene of interest and can purposely infect host cells, so the gene is spread.

Tertiary structure

This is the complex, 3D protein shape resulting from the folding of the polypeptide chain. This 3D structure is critical to the proteins function as it facilitates recognition and binding of specific molecules.

Secondary structure

This is the repeated, regular protein chain due to hydrogen bonding between amino acids. The 2 forms include the b-pleated sheet or the alpha helix. Coiling of amino acid chain.

Gel electrophoresis

When DNA is cut by RE's, it is loaded onto a gel to undergo the process of gel electrophoresis which separates the DNA based on its size. Smaller segments can move further and larger segments are not able to move as far in the time given.

Quaternary structure

When one or more polypeptide chains have bonded together. This is the functional form of many proteins.

Additions/Deletions

Worst type of mutation since every codon will change, hence it is likely to have completely different amino acid sequences resulting, which can produce different proteins.