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IB Categories Archives: Topic 7: Nucleic acids

7.6 – Enzymes

7.6 – Enzymes

7.6.1 – State that metabolic pathways consist of chains and cycles of enzyme catalysed reactions

Metabolic pathways form a series of reactions that regulate the concentration of substances within cells by enzyme-mediated linear and circular sequences. Respiration and photosynthesis are examples of a metabolic pathway (see below). All these reactions may be classified into two types.

Catabolic Reactions

This is the breaking down of larger molecules, releasing energy. This is exergonic. Enzymes in these reactions will break apart the chemical bonds, and two molecules are formed. These reactions include digestion and cellular respiration.

Anabolic Reactions

This is when smaller molecules form bonds and become larger molecules. This process requires energy, therefore it is endergonic. Enzymes will draw the smaller molecules in and help the new bonds to form. Examples include protein synthesis (build up of polypeptides from peptides) and cellular respiration.

 

Chain Pathways move from one reaction to the next. Each substrate has its own enzyme. The final product is called the end product.

Cyclic Pathways are when the initial substrate is fed into the cycle. The final product is reacted with the initial substrate. From here, the products are converted. The only difference in this pathway is the regeneration of the final intermediate. Examples of this type of pathway include Krebs cycle and the Calvin cycle.

7.6.2 – Describe the induced fit model

In the more accurate, induced fit model, there is modification. Enzymes are fairly flexible, and will reshape the active site by interactions with the substrate. Hence, the substrate does simply bind to a rigid active site, but the amino acid side chains will mould into positions for the enzyme to perform its function.

This change in shape is critical to momentarily raise the substrate molecule to the transitional state, when it can react. This model also accounts for the range of substrates that some enzymes can bind to.

7.6.3 – Explain that enzymes lower the activation energy of the chemical reactions that they catalyse

The activation energy is the minimum amount of energy required to raise substrate molecules to their transition state. The reaction cannot happen until this energy barrier has been overcome. The use of an enzyme reduces the amount of this energy that is needed.

The transition state is when the bonds in the reactant molecules break and begin to form the bonds of the products. Since breaking bonds is an endothermic process, the reactants require some energy to be added before they can start making the new bonds and begin the reaction. This amount of energy is the activation energy.

Enzymes work by providing an alternative reaction pathway that requires a lower activation energy. The frequency of collision between molecules increases, speeding up the reaction.

7.6.4 – Explain the difference between competitive and non-competitive inhibition, with reference to one example of each

Enzyme inhibitors deactivate enzymes. They come in two types:

Reversible Inhibitors are used to control enzyme activity.

Competitive inhibition is when the inhibitor and substrate must compete for the active site. The inhibitor is structurally similar to the substrate, and it prevents the substrate from binding. Examples are:

  • O₂ competing with CO₂ for the active site of RuBisCo
  • Malonate competing with succinate for the active site of succinate dehydrgenase

Non-competitive inhibitors slow down the rate of reaction because they distort the shape of the active site. When there is a build-up of the end product or lack of substrate, the enzyme may become deactivated. Examples are:

 

  • Cyanide ions blocking cytochrome oxidase in terminal oxidation in cell aerobic respiration
  • Nerve gas Sarin blocking acetyl cholinesterase in synapse transmission

Irreversible Inhibitors bind to the enzyme permanently and destroy their catalytic activity. These will covalently modify the enzyme.

Many drug molecules are enzyme inhibitors.

 

7.6.5 – Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sites

Allosteric inhibition is a process when metabolic pathways are switched off. Allosteric enzymes have two sites – the active site and the site where an additional substance can lock in. When this additional substance locks in, the entire enzyme is altered, and the active site is deactivated.

This process regulates and adjusts individual pathways in metabolism. In end product inhibition, as the product molecules accumulate, the steps in their production are switched off. This is because the final product inhibits the enzyme that catalyses the first step in the pathway. However, these products become substrates in subsequent reactions. They are used up, and production of more molecules with recommence.

In the pathway above, isoleucine is the end product, which inhibits the enzyme threonine deaminase. This occurs at the inhibition site. Thus, excess isoleucine switches off the production of more isoleucine. When it is used up, production will start again. This is very similar to non-competitive inhibition. This mechanism allows for self-regulation of production.

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7.5 – Proteins

7.5 – Proteins

7.5.1 – Explain the four levels of protein structure, indicating the significance of each level

Primary Structure (1 degree)

This is the number and sequence of the amino acids in a polypeptide, attached by peptide bonds. This structure is determined by the base sequence of the gene that codes the polypeptides. The shape of the protein is defined by the chemical interaction of each amino acid. The structure is read from the NH₂ terminal to the COOH terminal. Each amino acid is identified by its R group. Most polypeptides are between 50-1000’s amino acids long.

Interestingly, there is very little diversity in the polypeptides of cells in many organisms, as only a small fraction of these polypeptides can be found in living things.

Secondary Structure (2 degree)

This is the shape of the polypeptide chain, which takes place immediately after formation at the ribosome. Parts of the chain will become folded, twisted, or both in various ways. This may happen as a result of hydrogen bond interaction between neighbouring CO and NH groups. Not all the parts of the polypeptides form secondary structures. α helix – This is a coil formed from hydrogen bonds with a regular

α helix – This is a coil formed from hydrogen bonds with a regular helix shape. These helices often form the basis for fibrous polymers. There are 3.6 amino acids per turn.

β sheets – These are pleated sheets. They are called this because of the folds that can be seen from the side. The polypeptide chain is more stretched than the alpha helix. These sheets often have twists to increase the strength and rigidity of the structure. Each amino acid forms two hydrogen bonds.

Open Loops – These connect alpha helices and beta-pleated sheets. They are short chains of amino acids which form neither of these structures, but simply link sections together. Often these form important regions of proteins (such as the active sites of enzymes)

Tertiary Structure (3o)

This is the way the proteins are folded and held in a particular, complex shape; also known as the conformation of the polypeptide. The folds are formed as a result of interaction between the R groups, or side chains of the amino acids. The molecule is folded around a heme group, which binds oxygen. There are four types of bonding that occur to make this happen.

Disulfide Bonding (or Bridges)

These are bridges that help maintain the structure of the molecule. They are strong, covalent bonds formed by the oxidation of SH groups of two cysteine side chains on amino acids Ionic Bonding

Ionic Bonding

This is simply electrostatic interaction between oppositely charged ions, which can be easily broken if the pH changes. Also called salt bridges.

Hydrophobic Forces

These happen between atoms that are very close. This may also be called hydrophobic interactions.

Hydrogen Bonds

This is when a hydrogen atom is shared by two other atoms. They are weak, but common, and help to stabilise the protein molecule

Quaternary Structure (4 degree)

This is the linking together of two or more polypeptides to form a single protein. Sometimes, these may contain a non-polypeptide structure called a prosthetic group. A prosthetic group is an inorganic group. The polypeptides in the case of haemoglobin are connected to a heme group (not made of amino acids – it is here that iron is found). Any proteins with a prosthetic group are called conjugated proteins.

7.5.2 – Outline the difference between fibrous and globular proteins, with references to two examples of each protein type

Fibrous Proteins

Fibrous proteins are generally long, narrow and insoluble in water. They are physically tough and may be supple or stretchy. Their tertiary structure is a much-coiled chain. Their function is often to provide strength and support to tissues.

Collagen is the basis of connective tissue and has a triple helix shape. This is the most common protein in animals, and is a component of bone, skin and tendons. When collagen does not form links to the mineral components of the bone, this leads to brittle cone disease. It strengthens the tissue.

Keratin is a common protein in animals. It is composed of seven helices and is the main protein in hair and nail structure.

Myosin causes contraction of muscle fibres, which causes movement in animals. It acts with another protein called actin.

Globular Proteins

Globular proteins are tightly folded and are usually soluble in water. They have more compact and rounded shapes. Their functions include pigment and transport proteins, and the immune system.

Examples include haemoglobin, which is a transport protein, and immunoglobin, an antibody in the immune system. Enzymes such as catalase are also globular structures, as
well as hormones, like insulin.

Haemoglobin bind to oxygen in the lungs and transport it to respiring tissues. Immunoglobin act as antibodies. Part of the molecule can be varied, so that an almost endless variety of antibodies can be produced.

Some proteins have both fibrous and globular properties.

 

7.5.3 – Explain the significance of polar and non-polar amino acids

The distribution of polar and non-polar amino acids in a protein molecule influence where the protein is located and its functions.

Polar Amino Acids
Polar amino acids have hydrophilic properties due to the chemical characteristics of their R groups. When these are built into protein in prominent positions, they may influence the properties and functioning of the protein in cells. Polar amino acids on the surface of proteins make them water soluble. Polar amino acids in the active site of an enzyme allow chemical interaction between

Polar amino acids in the active site of an enzyme allow chemical interaction between the substrate and enzyme to form an activated complex. This transitional state allows the weakening of internal molecular structure and therefore the reduction of the activation energy. In cell membrane proteins, the sections of the molecule that contain polar amino acids

In cell membrane proteins, the sections of the molecule that contain polar amino acids are hydrophilic, and can be in contact with water. These allow for the positioning of proteins on the external and internal surface. Both the cytoplasm and the tissue fluid are water-based regions. Polar amino acids also create channels thorough which hydrophilic substances can diffuse. Positively charged R groups allow negatively charged ions through, and vice versa.

Non-Polar Amino Acids

These have hydrophobic R groups. These amino acids in the centre of water soluble proteins stabilize their structure. The non-polar amino acids cause proteins to remain embedded in the membrane.

In the enzyme superoxide dismutase, a ring of amino acids with negatively charged R groups repel the negatively charged superoxide ions to helps direct them to the active site. The active site contains amino acids with positively charged R groups. These attract the negatively charged superoxide ions to the active site.

In the enzyme lipase, the active site contains amino acids with non-polar R groups. These bind to non-polar triglycerides. Part of the enzyme acts as a hinged lid which can cover the active site when not in use, hiding the non-polar R groups.

 

7.5.4 – State four functions of proteins, giving a named example of each

Hormones – Chemical Messengers

Hormones are chemical messengers produced and secreted by cells of endocrine glands. These can be polypeptides or proteins. Other hormones are steroids, which are lipids.

An example of this is insulin. It is produced in the pancreas and its target tissues are muscle cells and liver cells. It brings about the uptake of glucose across the cell membrane and the storage of it as the insoluble polymer glycogen.

Antibodies – Defence against disease

Antibodies secreted by a type of white cell (B-lymphocytes) in response to non-self substances (antigens) that may invade the body. These antibody proteins are known as immunoglobins. Great variation exists in the heavy chains which allow a response to virtually any possible antigen surface. Due to their high specificity in identifying antigen, they are used in a wide variety of biotechnologies.

Enzymes – Biological Catalysts

These alter the speed of chemical reactions, making biochemical changes possible under the normal conditions of life. They reduce the energy of activation. These are large globular proteins, often with prosthetic groups. Catalase is a very large molecule. Liver catalase has a turnover rate of 4 x 107 s-1, which

Catalase is a very large molecule. Liver catalase has a turnover rate of 4 x 107 s-1, which is the maximum number of substrate molecules that can be converted per second.

Transport of Respiratory Gases

Haemoglobin in red cells is a conjugated protein, which means that it has the non-protein heme part attached to the globin protein. This combines with oxygen in the lungs and frees it in respiring tissues (dissociation). Each heme group can carry an oxygen atom. Its formula is C3032H4816O872N780S8Fe4

Other roles include muscle movement, structure and support.

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7.4 – Translation

7.4 – Translation

7.4.1 – Explain that each tRNA molecule is recognised by a tRNA-activating enzyme that binds a specific amino acid to the tRNA, using ATP for energy

Each amino acid has a specific tRNA-activating enzyme. Before they are used in translation,
amino acids are attached to a matching tRNA molecule.

On the 3i end of the molecules, the base sequence CCA appears, which binds to the amino acid with the aid of the activating enzyme. The tRNA molecules recognise the correct amino acid due the variation in their shape. They will match to a certain enzyme.

The attachment of the amino acid requires ATP for the enzyme to induce the reaction.

The anticodon is three bases long, and uses complementary base pairing to match to the code on the mRNA molecule. Note that the DNA code is degenerate, since a single amino acid may bind to multiple tRNA molecules.

 

7.4.2 – Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three tRNA binding sites and mRNA binding sites

Ribosomes are primarily made up of two parts – the small subunit and the large subunit. The small subunit has the binding site for the mRNA molecule, whilst the large subunit has three binding sites for tRNA molecules. These three binding sites are called the E, P and A sites.

Ribosomes are enzymes for the translation of mRNA into a polypeptide. One ribosome may catalyse the translation of many different mRNA molecules.

 

7.4.3 – State that translation consists of initiation, elongation, translocation and termination

Initiation

During this stage, the mRNA molecule and the tRNA molecule both bind to the ribosome for translation to begin. The first tRNA molecule to bind to the small subunit carries the anticodon for the start codon. The small subunit then attaches to the mRNA molecule at the 5i end. The small subunit then slides along towards the 3i end until it reaches the start codon, and translation begins.

Elongation

The tRNA molecules will attach to the complementary bases on the mRNA, using codon to anticodon recognition. As this happens, the amino acids are brought together so that they can bond and form polypeptides. Once the amino acids form peptide bonds, they are detached from the tRNA by the large subunit. Throughout translation, the polypeptide will be held in position by a single tRNA molecule.

Translocation

Within the ribosome, there are three areas called the E, P and A sites. During translation, the tRNA will move through this, depending on which stage of translation it is at. The tRNA first enters at the A site. Then, as the peptide bonds form, the molecule will move to the P site. Finally, it will move to the E site to be release.

Termination

Eventually, the ribosome will reach the stop codon on the 3i end of the mRNA. Since there are no tRNA molecules with an anticodon for it, translation will stop. The mRNA and the newly synthesised polypeptide are released from the ribosome. The tRNA is also released, which will be reused and attach to another amino acid.

By this point, the polypeptide will have started to fold into the shape of the final protein. The subunits of the ribosome will also separate.

 

7.4.4 – State that translation occurs in a 5′ → 3′ direction

The small subunit of the ribosome moves along the large subunit and moves the three nucleotides along the mRNA. This always takes place in a 5i to 3i direction, meaning that it starts at the 5i end of the mRNA molecule and moves towards the 3i end. The genetic code is therefore translated in this direction. The start codon will always be near the 5i end.

7.4.5 – Draw and label a diagram showing the structure of a peptide bond between two amino acids

Peptide bonds form in a condensation reaction between amino acids, releasing a water molecule as a by-product. This forms the primary structure of the protein.

7.4.6 – Explain the process of translation, including ribosomes, polysomes, start codons and stop codons

As discussed before, translation begins at the stage of initiation. The mRNA molecule binds to the small subunit of the ribosome at the 3i end. The tRNA carrying Methionine binds as well, and will attach to the start codon (AUG). The large subunit will sit over it, with the tRNA in the A site until it binds and is in position.

The tRNA moves to the P site to add to the polypeptide chain. At the E site, the tRNA is then released without the amino acid. It will be activated and reused later. The anticodon specificity of the tRNA ensures that the right amino acids are added to the chain.

As the tRNA brings amino acids to the ribosome, these will form peptide bonds, making a polypeptide chain. This is the process of elongation.

Following this, the tRNA will be released from the amino acid, releasing energy in the process. The large subunit moves along the mRNA by three bases, or one codon, in the direction of the 3i end.

The tRNA in the E site is released into the cytoplasm of the cell. A new tRNA molecule is in the A site, ready to bind to the mRNA and add to the polypeptide chain. As the polypeptide chain grows, it will begin to fold and shape into the primary structure of the protein.

Once the stop codon is reached, no more tRNA molecules will bind to the mRNA, and translation stops. The process enters the termination stage, releasing the mRNA and new polypeptide chain, and the subunits will separate.

The protein is then sent to the Golgi apparatus, the endoplasmic reticulum or is secreted from the cell for use elsewhere.

 

7.4.7 – State that free ribosomes synthesize proteins for use primarily within the cell, and that bound ribosomes synthesise proteins primarily for secretion or for lysosomes

Within a cell, ribosomes can be found in a number of locations. Some are bound to the rough endoplasmic reticulum. These ribosomes will usually synthesise proteins that will be secreted from the cell in vesicles for use elsewhere.

On the other hand, other ribosomes may be found floating freely in the nucleus. These
normally synthesise proteins that will be used within the cell.

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7.3 – Transcription

7.3 – Transcription

7.3.1 – State that transcription is carried out in a 5′ → 3′ direction

The 5’ end of the free RNA nucleotide is added to the 3’ end of the RNA molecule that is already synthesised.

7.3.2 – Distinguish between the sense and antisense strands of DNA

Sense strand – The coding strand that carries the promoter sequence of bases to which RNA polymerase binds and begins transcription. It has the same base sequence as mRNA, except with uracil instead of thymine. It also carries the terminator sequence of bases at the end of each gene, causing RNA polymerase to stop transcription

Antisense strand – The template strand for transcription by complementary base pairing. It has the same base sequence as tRNA with uracil instead of thymine.

7.3.3 – Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleotide triphosphates and the terminator

In prokaryotes, transcription and translation occur together because there is no nucleus and the mRNA molecule is in direct contact with the cytoplasm.

Promoter Region

This acts as the start signal for transcription, and is located immediately before the gene

RNA Polymerase

This is the enzyme that makes the single strand of RNA, using the antisense strand of DNA as a template. It recognises start and stop signals to control the length of the RNA molecule.

Polymerisation occurs in a 5’ to 3’ direction, making covalent bonds between nucleotides. Complementary base pairing is used, although uracil replaces thymine in the RNA strand.

Nucleotide Triphosphates

As in replication, free nucleotides are found as nucleotide triphosphates. The condensation reaction causes two phosphates to be released.

Terminator

This is the base sequence that signals the end of the gene and causes transcription to stop. RNA polymerase and the mRNA strand are freed from the site of the gene.

7.3.4 – State that eukaryotic RNA needs the removal of introns to form mature mRNA

Between the exons, there are introns, which are non-coding sequences. The introns are spliced out and broken down in the nucleus. The remaining, mature mRNA is exported from the nucleus for translation. The process is called post-transcriptional modification

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7.2 – DNA Replication

7.2 – DNA Replication

7.2.1 – State that DNA replication occurs in a 5′ → 3′ direction

The 3’ end of the nucleotide is a free -OH group. The 5’ end of the free DNA nucleotide is added to the 3’ end of the chain of nucleotides that is already synthesised.

 

7.2.2 – Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates

In prokaryotes, the initiation spot on the DNA is called the ori, or origin point. Replications finishes at the ter spot, or termination point.

DNA Helicase

This binds to the double helix to stimulate the separation of the strands. The hydrogen bonds between base pairs break to form replication forks. The helicase is located at these replication forks.

 

DNA Polymerase

Polymerase III replicates DNA in a 5’ to 3’ direction along the leading strand. It starts at the RNA primer, adding nucleotides using complementary base pairing and moving in the direction of the replication fork. On the other hand, along the lagging strand, polymerase III moves away from the replication fork. This results in the formation of Okazaki fragments. Polymerase I replaces the RNA primers with DNA. However, there is still a gap where two nucleotides have not been connected.

It is possible that errors may occur during replication, but the polymerase has mechanisms of back-checking for mutations.

Okazaki Fragments

These are short strands of DNA that are formed on the lagging strand. Each one is initiated at the replication fork, and is later joined to form one continuous length by DNA ligase. The leading strand is replicated in one continuous length

RNA Primase

For replication to occur, a free 3’ hydroxyl group is required. Primase synthesises at the initiation sites.

DNA Ligase

Gaps a made in the DNA from where the primer is removed. Ligase closes the gap by forming a covalent bond between the phosphate groups and the neighbouring fragments are joined.

 

Deoxynucleoside Triphosphates

The free nucleotides have three phosphates. During polymerisation, the condensation reaction, two are removed so that only one remains to form the backbone

7.2.3 – State that DNA replication is initiated at many points in eukaryotic chromosomes

Prokaryotic DNA is replicated in a continuous loop. On the other hand, eukaryotic DNA is replicated at multiple points to speed up the reaction. The DNA is unwound at multiple points along the helix into bubbles that expand, allowing replication to continue in both direction. The bubbles eventually fuse.

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7.1 – DNA Structure

7.1 – DNA Structure

7.1.1 – Describe the structure of DNA, including the antiparallel strands, 3′-5′ linkages and hydrogen bonding between purines and pyrimidines 

DNA has a uniform diameter along its entire length due to complementary base pairing. The two polynucleotide chains are antiparallel, with the polynucleotides formed around the outside of the helix and the bases extending into the centre. The chains held together by hydrogen bonding between the bases on opposite nucleotides.

There is double hydrogen bonding between A and T. On the other hand, there is triple hydrogen bonding between C and G. The purines are the nucleic bases with two rings: adenine and guanine. On the other hand, the single-ringed bases are the pyrimidines, thymine and cytosine.

 

7.1.2 – Outline the structure of nucleosomes

A nucleosome consists of DNA wrapped around eight histone proteins and held together by another histone protein. The DNA double helix has major and minor groves on the outer diameter, exposing chemical groups that can form hydrogen bonds. These groups are bonded to positively-charged proteins called histones, forming two loops around them.

DNA is wound around and bonded to eight histones and secured by the H1 linker protein, holding the DNA in place. This structure allows the long DNA molecules on the nucleus to be condensed into a much smaller space. Together, the histones form ‘beads’. However, there are also other proteins present in the chromosomes, including the enzymes for replication and transcription.

 

7.1.3 – State that nucleosomes help to supercoil chromosomes and help to regulate transcription

During supercoiling, the DNA is condensed by a factor of x15000. The histones are responsible for the packaging of DNA at the different levels. The metaphase chromosome is an adaption for mitosis and meiosis. The fibre must be less condensed for transcription to occur during interphase. Condensing controls if the genes are transcribed or not.

7.1.4 – Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA

Unique or single copy genes form the gene coding region codes for polypeptides, and make up about 3% of the human genome The function of the non-coding region remains unclear. It is often made up of highly repetitive sequences of bases, called satellite regions.

The function of the non-coding region remains unclear. It is often made up of highly repetitive sequences of bases, called satellite regions. These are used in DNA fingerprint technologies.

7.1.5 – State that eukaryotic genes can contain exons and introns

Exon – a coding nucleotide sequence of the DNA of chromosomes

Intron – a non-coding nucleotide sequence of the DNA of chromosomes, present in eukaryotic chromosomes

The highly repetitive sequences of introns, or satellite DNA, constitute 5-45% of the genome, with between 5 and 300 base pairs per repeat. These may be duplicated as many as 105 times per genome.

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