Biological Molecules Flashcards
What are the characteristics of water that pertain to its biological role and what causes these characteristics?
- High boiling-point, specific heat capacity and thermal stability caused by strong hydrogen bonding network
- High surface tension caused by hydrogen bonding network
- Water can act as a solvent for polar or charged substances as a result of its polarity
- Less dense in solid form than liquid form; this is caused by the rigid and open tetrahedral network of water molecules formed when water freezes
- Water has cohesive (sticking to itself) and adhesive (sticking to other materials) properties due to its polarity causing it to form intermolecular bonds with itself and other polar substances
What biological roles do water’s characteristics allow it to perform?
- Main constituent of cytosol - Its ability to act as a solvent means substances can dissolve within the cytosol and react with one another.
- Transport medium - Its ability to act as a solvent and its ability to travel via capillary action mean dissolved substances can readily travel within it around organisms. This is observed in mammalian blood vessels and in xylem.
- Coolant and thermal regulator - Its high specific heat capacity allows it to provide thermal stability to the surrounding environment, which is essential for enzyme function. This occurs within and outside organisms.
- Main constituent of certain habitats - Its thermal stability provides a constant temperature for aquatic organisms. Its high surface tension allows certain organisms, e.g. pond skaters to live on it. Ice’s lower density means an insulating layer forms on top of bodies of water at low temperatures, allowing aquatic live to thrive beneath it.
What are the chemical elements that make up the biological molecules carbohydrates, lipids, proteins and nucleic acids?
- Carbohydrates - carbon, hydrogen and oxygen
- Proteins - carbon, hydrogen, oxygen, nitrogen and sometimes sulfur
- Lipids - carbon, hydrogen, oxygen
- Nucleic acids - carbon, hydrogen, oxygen, nitrogen and phosphorus
Lipids can contain elements such as phosphorus, nitrogen and sulfur, but for the sake of this qualification, assume they only contain carbon, hydrogen and oxygen (unless phospholipids are clearly involved)
What is the structure of alpha-glucose?
What is the structure of beta-glucose?
As both types of glucose monomers have six carbons, it is referred to as a hexose monosaccharide
What is the structure of ribose?
As ribose has five carbons, it is referred to as a pentose monosaccharide
What are the properties of glucose?
- Small
- Polar
- Soluble in polar solvents like water
These properties extend to all monosaccharides
How are polysaccharides formed?
General explanation
- Polymerisation reaction involving monosaccharides as monomers
- The reaction is a condensation reaction as a molecule of water is produced with the formation of every bond
- The same processes occur in the dimerisation reaction to form disaccharides from monosaccharides
- Disaccharides can react with one another or with monosaccharides to form polysaccharides
How exactly is a maltose molecule formed and what is the bond that forms called?
- Two alpha glucose molecules react
- The hydroxyl group on carbon one of a glucose molecule and the hydrogen on the hydroxyl group on carbon four of another glucose molecule are cleaved, releasing a molecule of water
- A bond forms between the carbon one and the oxygen on the carbon four
- The bond formed is called a 1,4 glycosidic bond
It is possible for the whole hydroxyl group to break from carbon four and only hydrogen to break from carbon one instead
How are polysaccharides broken apart?
- One or more molecules of water are introduced
- A molecule of water will react with a glycosidic bond, reforming both hydroxyl groups and cleaving the two monomers
- This process is known as hydrolysis, and consumes water
What monosaccharides do the disaccharides maltose, sucrose and lactose consist of?
- Maltose - two glucose molecules
- Sucrose - a glucose and a fructose molecule
- Lactose - a glucose and a galactose molecule
Fructose and galactose are hexose monosaccharides
What are the two types of starch?
- Amylose - makes up around 20% of natural starch
- Amylopectin - makes up around 80% of natural starch
What is the structure of amylose?
- Consists of alpha glucose molecules joined together by 1,4 glycosidic bonds, forming a linear, unbranched chain
- The angle of these bonds causes the chain to twist, forming a helix stabilised by internal hydrogen bonding
What is the structure of amylopectin?
- Amylopectin also consists of glucose molecules joined by 1,4 glycosidic bonds that form linear chains
- However, approximately every 25 glucose molecules (subunits), two glucose molecules will be joined by a 1,6 glycosidic bond
- This gives amylopectin a branched structure with many linear chains
- Each individual chain of amylopectin is able to coil
- A 1,6 glycosidic bond involves bonding between carbon one on one glucose monomer and carbon six on another; everything else is the same
What is the structure of glycogen?
- It has the same structure as amylopectin, except it has 1,6 glycosidic bonds every 10 subunits instead of every 25 subunits
- This provides it with a highly branched structure
Each individual chain of glycogen is able to coil
What is the structure of cellulose?
- Cellulose consists of chains of beta glucose molecules, with every other beta glucose molecules being flipped upsidedown to allow the hydroxyl groups to interact
- There is no coiling or branching - it is just a straight, linear chain
- These chains form hydrogen bonds between one another, forming microfibrils
- These microfibrils combine to make macrofibrils, which combine to form cellulose fibres
What are the properties of amylose, and how do these properties link to its function?
- It is very compact
- It is insoluble and unreactive (not readily reduced or digested)
- These properties allow it to store a large amount of glucose (which is used as energy) in a small area while not reacting or dissolving
What are the properties of amylopectin, and how do these properties link to its function?
- Its many terminal ends make it able to readily release and accept glucose molecules
- This is optimal for respiration and energy storage on demand in plants
- It is mostly insoluble, though a little more soluble than amylose, so it can be stored without dissolving
- Its branched structure means it has many glucose monomers per grain, though a single molecule of amylopectin is less compact than a molecule of amylose
- Overall, it is very compact, which is an ideal characteristic for an energy storage molecule
What are the properties of glycogen, and how do these properties link to its function?
- Its many terminal ends make it able to readily release or accept, facilitating the rapid respiration and energy storage animals require for movement
- Its branching makes it more compact than both types of starch; this is essential for animals that move around
- It is insoluble, so can be stored without dissolving
What are the properties of cellulose, and how do these properties link to its function?
- High tensile strength (ability to resist breaking under tension) due to covalent and hydrogen bonding
- Permeable
- Very insoluble and difficult to break down (indigestible)
- These properties make it suitable for plant cell walls, as it means cell walls can maintain the rigidity of cells, withstand turgor pressure and allow substances through without being dissolved
What is the difference between fats and oils?
- Fats are lipids that are solid at room temperature
- Oils are lipids that are liquid at room temperature
There are some lipids that are not fats or oils, however
What is the structure of fatty acids?
- They are carboxylic acids with long hydrocarbon chains
- They can be saturated (no double bonds) or unsaturated (double bonds)
- A fatty acid with one double bond is monounsaturated, while one with multiple is polyunsaturated
- The hydrocarbon chain can have heteroatoms attached to it
- Cis-trans isomerism is exhibited across the double bond(s), resulting in what we call ‘trans-fats’
- Double bonds lead to kinks, reducing the ability for unsaturated lipids to pack closely together, making them more likely to be oils
What is the structure of glycerol?
- Glyercol is a type of alcohol called a triol (three hydroxyl groups)
- It consists of three carbons, each with a hydroxyl group bonded to them
What is the structure of a triglyceride and what are its properties?
- Three fatty acids bonded to glycerol
- It is considered a macromolecule in its own right, though it is not a polymer
- It is non-polar due to the long fatty acid chains; the head is slightly polar but this is not enough to counteract the non-polarity of the fatty acids or to make the head hydrophilic
- This makes it highly insoluble in water and hydrophobic
- It is soluble in non-polar solvents, or solvents that are mostly non-polar like ethanol
Glycerol is polar when isolated, but its polarity is muted after the hydroxyl groups are removed
How does a triglyceride form?
- Through an esterification reaction, which is a type of condensation reaction
- An ester bond forms between the glycerol and each of the three fatty acids (the carboxylic acid group interacts with the hydroxyl group)
- Three molecules of water are produced per triglyceride formed
Like polysaccharides, triglycerides can be broken down by hydrolysis after water molecules are introduced, reforming the hydroxyl and carboxylic acid groups on their respective molecules
What is the structure of a phospholipid and what are its properties?
- It is a triglyceride, except an entire fatty acid (including the COO) has been replaced by a phosphate ion (PO₄³⁻)
- Since the phosphate ion is negatively charged, it makes the head of a phospholipid hydrophilic
- However, the remaining two fatty acid chains remained unchanged, so are still non-polar and hydrophobic
- This makes phospholipids amphipathic - containing both hydrophilic and hydrophobic parts
What is cholesterol and what are its properties?
- A type of lipid belonging to the sterol group
- They are macromolecules with a hydroxyl group
- This hydroxyl group is polar, but most of cholesterol is a hydrocarbon, making cholesterol amphipathic
- Cholesterol is used in the synthesis of vitamin D, steroid hormones and bile
- The function of cholesterol in cell membranes is discussed in another deck
What are the functions of lipids in living organisms?
- Membrane formation
- Long-term energy storage
- Hormone production
- Electrical insulation around neurones
- Thermal insulation
- Waterproofing, cushioning and buoyancy
Lipids have higher energy density than carbohydrates and proteins as they have a higher concentration of C-H bonds and fewer oxygen atoms per molecule. This means they are more reduced, so yield more electrons when oxidised in respiration.
What is the general structure of an amino acid?
- An amino acid consists of a central carbon atom with four bonds
- One bond is to a hydrogen atom
- Another is to an amine group (NH₂)
- Another is to a carboxylic acid group (COOH)
- Another is to an R-group, of which there are 20 different types
How are dipeptides and polypeptides formed?
- Amino acids react with each to form polymers (dipeptides then polypeptides)
- A hydrogen on an amine group of one amino acid and the OH on the carboxylic acid group on another amino acid are lost and a peptide bond forms between the carbon and the nitrogen
- This is a condensation reaction as a molecule of water is produced
- This process is catalysed by peptidyl transferase in ribosomes
- They can be broken down via hydrolysis by introducing water molecules; this process is catalysed by protease enzymes
What is the primary level of protein structure?
The sequence of amino acids in a polypeptide chain, as dictated by the sequence of base pairs in DNA
What is the secondary level of protein structure?
- OH and NH bonds in R-groups and amine groups allow the formation of hydrogen bonds
- Hydrogen bonds therefore form within a polypeptide chain, causing it to conform to different shapes
- The polypeptide chain may coil, forming an alpha helix
- Alternatively, hydrogen bonds can form between straight polypeptide chains that lie parallel to one another, forming a sheet-like structures called beta pleated sheets
The shape that forms depends on the primary structure of the polypeptides
What is the tertiary level of protein structure?
- The folding of a polypeptide chain into its final shape
- A number of different bonds form between R-groups and other parts of the amino acids, including:
-Hydrophobic-hydrophobic interactions and hydrophilic-hydrophilic interactions between polar and non-polar R-groups (fairly weak)
-Hydrogen bonds (weak)
-Ionic bonds between oppositiely charged R-groups (strong)
-Disulfide bonds between sulfuric R-groups (very strong)
What is the quaternary level of protein structure?
- The association of multiple polypeptide chains (which can be considered proteins on their own) to form larger proteins
- The polypeptides in the quaternary structure are called subunits
- These polypeptides interact with one another in a way similar to how a polypeptide chain interacts with itself in its tertiary structure
The subunits can be different or identical
What are the characteristics of globular proteins?
- Compact and spherical
- Water soluble
- Have hydrophobic R-groups on the inside and hydrophilic R-groups on the outside
- Normally have metabolic functions
What are two examples of globular proteins, including a hormone and an enzyme?
- Insulin - Transported in the bloodstream, so must be soluble. Needs a precise shape as it must bind to specific receptors.
- Catalase - Enzyme that breaks down hydrogen peroxide. Must have a specific shape to bind to substrate. Has four haem prosthetic groups with iron (II) ions, so is a conjugated protein.
What are conjugated proteins?
Provide an example and describe its structure
- Globular proteins that contain a non-protein prosthetic group
- Prosthetic groups include lipids, carbohydrates and inorganic ions
- Haemoglobin is a conjugated protein. It consists of two alpha and two beta subunits. Each subunit contains a haem prosthethic group, which consists of iron (II) ions. This means it has four haem groups in total.
What are the characteristics of fibrous proteins?
- Long and linear
- Insoluble as they contain many hydrophobic R-groups
- Consist of a limited range of R-groups, so exhibit much repetition
- Tend not to be folded into complex structures
- Normally have structural functions
What are the properties and functions of keratin?
- It is present in hair, skin and nails
- It contains many sulfur-containing R-groups called cysteine, which results in the presence of many strong di-sulfide bridges
- This confers it with strength and inflexibility
- The more disulfide bonds, the less flexible it will be (this is what determines the difference between hair and nails)
What are the properties and functions of elastin?
- It is present in elastic fibres in muscular walls, such as those in blood vessels and alveoli
- It confers these muscular walls with not only the ability to stretch but to recoil once force is removed
What are the properties and functions of collagen?
- Collagen forms connective tissue found in skin, tendons, ligaments and the nervous system
- It is flexible but strong, and less elastic than elastin
What are the biological functions of calcium ions?
- They regulate the transmission of electrical impulses between neurones
- They are also essential in muscular contraction; they allow for actin to interact with myosin, stimulating contractions
What are the biological functions of sodium ions?
- They facilitate the conveyance of glucose and other small molecules across cell membranes through co-transport mechanisms
- They are essential for the transmission of nerve impulses
What are the biological functions of potassium ions?
- They are essential for nerve transmission
- They regulate water potential, serving two important roles: opening and closing guard cells around stomata and allowing for the reabsorption of water in kidneys
What are the biological functions of hydrogen ions?
- They determine the pH of solutions and can be used as a buffer, allowing enzymes to function optimally
- They catalyse some reactions
What are the biological functions of ammonium ions?
- They act as intermediate ions in the deamination of amino acids
- They are an essential source of nitrogen for nitrate ions in plants
What are the biological functions of nitrate ions?
- They provide an essential source of nitrogen for protein synthesis
- They are essential for growth and repair in plants
What are the biological functions of hydrogen carbonate ions?
- They act as a pH buffer
- They are used to transport carbon dioxide in the bloodstream
What are the biological functions of chloride ions?
- They act as a pH buffer
- They work with sodium and potassium ions to regulate membrane potential, offsetting excess positive charge
What are the biological functions of phosphate ions?
- They are an essential component of nucleotides, such as those found in DNA, RNA and ATP
- They are an essential component of phospholipids, which are necessary for the formation of cell membranes
What are the biological functions of hydroxide ions?
- They act as a pH determiner
- They catalyse some reactions
What is the chemical test for proteins?
- Add biuret reagent to the sample
- Biuret reagent consists of a strong alkali, like sodium hydroxide, and copper (II) sulfate
- The copper (II) atoms accept pairs of electrons from nitrogen atoms in peptide bonds, forming violet-coloured complexes
- Thus, the solution will go violet or purple (from blue) if protein is present
- The extent to which it is purple indicates the number of peptide bonds present in the sample
What is the chemical test for reducing sugars?
All monosaccharides and disaccharides (except sucrose) are reducing sugars
- Place the sample, dissolved in water, in a boiling tube
- Add Benedict’s reagent (copper (II) sulfate solution)
- Heat in a water bath for around five minutes
- The reducing sugars will reduce the copper (II) ions to copper (I) ions
- Remove the precipitate
- If the test is positive, the colour change will be blue to brick-red
The test can be semi-qualitative without additional equipment as the proportion of brick-red colour to blue colour indicates the concentration of reducing sugar
What is the chemical test for non-reducing sugars?
Most commonly sucrose
- Boil a solution of the non-reducing sugar in a dilute acid like hydrochloric acid
- Repeat the test for reducing sugars and observe a positive result
- This works because the acid hydrolyses the non-reducing sugar into reducing sugars (glucose and fructose are formed in the case of sucrose)
What is the chemical test for starch?
- Add iodine dissolved in potassium iodide to the sample
- The solution will change from yellow/brown to blue/black if starch is present
It is only amylose that reacts with the iodine to form a blue-black complex. Amylopectin does not give a positive result on its own
What is the chemical test for lipids?
- Mix the sample with ethanol
- Mix the resultant solution with water
- A white emulsion should form on top of the solution if the sample consists of lipids
- This is because lipids are not water soluble, so will not remain in solution if the solution is too aqueous
How can colorimetry be used to quantitatively test for the presence of biological molecules?
- For the Biuret test and Benedict’s test, the colour produced is dependent on the concentration of sample present
- Colorimeters measure the absorbance or the transmission of light; they are inversely proportional to one another, so either works
- Example: To determine the concentration of glucose in a solution, you would use a red light filter to allow red light to pass through, and measure the absorbance of red light by the solution. The lower the absorbance of red light, the higher the concentration of glucose as it is reflecting more red light back, so must be more red in colour.
- Colorimeters should be calibrated with distilled water first
- If blue light is being shined through the solution in the example, a blue light filter should be used and absorbance will increase as glucose concentration increases
What is an alternative method of quantitatively testing for the presence of biological molecules?
- Biosensors
- This involves allowing the sample to interact with a biological component like DNA
- A transducer will detect a change that occurs as a result of this interaction, such as a change in pH or electrical activity, and display this change on a monitor
How can paper chromatography be used to separate biological molecules?
Using the example of amino acids
- Amino acids are added along a pencil line on one end of some chromatography paper (the stationary phase) using capillary tubes
- The end is submerged in several organic solvents (the mobile phase), which carry amino acids up the paper over the course of several hours
- The amino acids’ solubility (dictated by their size and charge) determines how far they move up the paper
- The paper is sprayed with ninhydrin to accentuate the spots
- When analysing the chromatogram, the retention factor value can be calculated by dividing the distance each amino moved up the paper by the distance the solvent moved up the factor
- By comparing the obtained Rf values with known Rf values of amino acids, the amino acids can be identified
Thin layer chromatography can also be used. In TLC, the stationary phase is a thin layer of gel like silica gel
