biological molecules Flashcards
why is water important?
- water serves as the universal solvent in biological systems
- water makes up 70% or more of the weight of most cells
- many organisms and cells depend on an aqueous extracellular environment for survival
- water has a remarkable capacity to dissolve a great variety of solutes due to its polar nature
what is the bonding of water?
two hydrogen atoms are covalently bonded to one oxygen atom at an angle of 104.5 degrees
why is water a polar molecule?
the oxygen atom is strongly electronegative, while the hydrogen atom is electropositive. there is an unequal distribution of electrons in a water molecule, with a partial negative charge on the oxygen atom, and a partial positive charge on the hydrogen atoms. the water molecule as a whole is uncharged, but the two ends of the molecule have opposite charges
explain the formation of a hydrogen bond
when the electropositive region of the water molecule comes close to an electronegative region of the water molecule, the electrical attraction between them can result in a weak bond called a hydrogen bond
how do oxygen atoms form hydrogen bonds with hydrogen atoms?
each oxygen atom can form hydrogen bonds with two hydrogen atoms,
what is the function of a hydrogen bond?
a hydrogen bond is crucial in maintaining the structure and function of biological molecules, including carbohydrates, proteins and nucleic acids
how do ionic solute compounds dissolve in a liquid?
solvent molecules must overcome the attraction of the positively charged and negative charged ions. as such, the oppositely charged ions become involved in electrostatic interactions with the water molecules, forming hydration spheres where the attraction is neutralised.
definition of hydrophilic?
hydrophilic solutes have an affinity for water and therefore dissolve readily in it. polar molecules and ions/charged molecules are hydrophillic
definition of hydrophobic?
hydrophobic molecules are not very soluble in water, and are non-polar and cannot form hydrogen bonds with water. lipids and some proteins are hydrophobic
definition of amphipathic?
amphipathic molecules have some hydrophobic and hydrophili regions on the same molecule, so some parts of the molecule have an affinity for water while other parts of the molecule do not
how are atoms arranged within a methane molecule?
in the methane molecule, the four bonds are arranged symmetrically as if within a tetrahedron, with the angle between two hydrogen atoms being 109.5 degrees.
what is the function of functional groups?
function groups determine the characteristics and chemical reactivity of the molecules and may take part in the chemical reactions
definition of a macromolecule?
a macromolecule is a giant molecule of high molecular weight, often made of many repeating units, in such a case is therefore a polymer. the repeating units that serve as building blocks of a polymer are called monomers
how are polymers synthesised?
monomers are connected by a condensation reaction in which the two molecules are covalently bonded to each other through loss of a water molecule, also known as a dehydration reaction. this process occurs with the help of enzymes
how are polymers broken down?
polymers are dissembled back into monomers by hydrolysis, where a bond formed between two monomers is broken by the addition of a water molecule
why are lipids not true polymers?
individual lipids are unable to form covalent bonds with one another to form larger molecules, and they are generally not big enough to be considered macromolecules
definition of simple lipids?
simple lipids consist of an alcohol (usually glycerol) linked to one or more fatty acids via an ester linkage (eg. triglyceride)
definition of compounds lipids?
compound lipids are esters of fatty acids, an alcohol and other groups (eg. phospholipids, glycolipids)
definition of derived lipids?
derived lipids are chemically originated components present in the body of plants and animals, and are utilised in other biochemical reactions to produce other essential substances (eg. bile juices, sterols, cholesterol)
what is the molecular formula of glycerol?
C3H8O3, with each carbon bearing a hydroxyl group
what is the chemical composition of fatty acids?
fatty acids are carboxylic acids composed of an acidic carboxyl (COOH) functional group at one end and an attached hydrocarbon chain. the abundance of the non-polar C-H bonds is the reason why fats are hydrophobic
what are the two factors that determine the structure and function of a fatty acid?
- length of hydrocarbon chain
- number and location of double bonds along their carbon skeleton
definition of a saturated fatty acid?
a saturated fatty acid has no double bonds between the carbon atoms (eg. butter is made from saturated fats)
definition of an unsaturated fatty acid?
an unsaturated fatty acid has one or more double bonds, and will have a kink in its tail whenever a double bond occurs, as double bonds are more rigid and form a kink (eg. cooking oil and fish liver oil are generally unsaturated fats)
how is a glyceride formed?
a glyceride is formed when glycerol is linked to one or more fatty acids, resulting in the formation of an ester linkage between a hydroxyl group of glycerol and carboxyl group of a fatty acid, known as a condensation reaction
why does the melting point of fats increase with an increase in hydrocarbon chain length?
the longer the hydrocarbon chains, the more extensive the hydrophobic interactions between the chains, and the more thermal energy is required to break the bonds.
definition of hydrophobic interactions?
hydrophobic interactions are weak bonds that exist between hydrophobic molecules, and is a force of attraction between non-polar molecules
why does the melting point of fats decrease as the degree on unsaturation of fatty acid tails increase?
the kinks where the double bonds are located, prevent the molecules from packing closely. when the fatty acid tails are less closely packed, hydrophobic interactions are less extensive. hence, less thermal energy is required to break enough of these interactions to liquefy the triglycerides
why are triglycerides more efficient energy stores than carbohydrates?
triglycerides have a higher proportion of C and H atoms compared to O atoms, and contain a greater number of C atoms per unit mass than carbohydrates. upon oxidation, triglycerides release a larger amount of energy, and one gram of fat releases more than twice as much energy as a gram of carbohydrates
why are triglycerides a better store of metabolic water?
triglycerides contain two-fold more hydrogen atoms per unit mass than carbohydrates, and release more water when they are oxidised during cellular respiration
why are triglycerides good thermal insulators?
no associated water molecules are stored along with triglycerides and thus they have no extra weight from water of hydration. as such, triglycerides do not affect water potential of cells when stored in large amounts, and fulfils the requirement for an animal’s body mass to be kept to a minimum
why can triglycerides slide under pressure?
hydrocarbon tails are non-polar and weak hydrophobic interactions occur between triglyceride molecules. thus, triglycerides are located in adipose tissue around vital organs to cushion and protect vital organs
why can triglycerides act as blubbers in animals?
triglycerides have a lower molecular weight than water per unit volume and are less dense than water
what is the chemical composition of phospholipids?
phospholipids consist of one glycerol and two fatty acids. the third hydroxyl group of glycerol is joined to a negatively-charged phosphate group via a phosphoester linkage. additional small molecules that are usually charged or polar, can be linked to the phosphate group
how do phospholipids behave in water?
the phospholipid is generally ambivalent in water. the hydrocarbon tails are non-polar and hence hydrophobic. the phosphate group and its attachments form a charged hydrophilic head that has an affinity for water
what happens when amphipathic phospholipids are situated in aqueous environments?
three types of lipid aggregates form, serving to shield the hydrophobic tails from the aqueous environment
structure of a micelle?
a micelle is a small, spherical droplet consisting of a phospholipid monolayer, with the phosphate heads on the outside, and the hydrocarbon tails are restricted to the water-free interior of the micelle
what is the structure of a bilayer?
a bilayer is formed when two lipid monolayers combine to form a two-dimensional sheet, where the hydrophilic heads are exposed to the polar exterior while the hydrophobic tails are excluded from water in the non-polar interior
what is the structure of a liposome/vesicle?
a liposome/vesicle is a lipid bilayer folded back on itself to form a hollow sphere. bilayer sheets avoid exposing their hydrophobic edge regions, achieving maximum stability in an aqueous environment. the liposome/vesicle creates a separate aqueous compartment
what is the function of micelles?
micelles are used for the transport of fats between the gut and body tissues
what is the function of the lipid bilayer?
the lipid bilayer forms a selectively permeable cell membrane, forming an effective barrier between the cell and its external environment
what is the function of a liposome/vesicle?
liposomes/vesicles are used for storage and transport of cellular products as well as for digestion of waste, known as phagocytosis. they also serve as vesicles for drug delivery in humans
how is the integrity of the liquid aggregates maintained?
the integrity of the liquid aggregates is maintained due to the large number of hydrophobic and hydrophilic interactions.
how is membrane fluidity maintained in liquid aggregates?
individual hydrophobic interactions are weak, permitting lateral movement of phospholipids, which account for membrane fluidity
why do most phospholipids contain choline?
choline is important for the synthesis of acetylcholine, which is a neurotransmitter that is vital for muscle contractions
what is the chemical composition of glycolipids?
glycolipids are composed of two hydrophobic hydrocarbon tails, and a polar short carbohydrate chain joined to the glycerol’s OH bond via a glycosidic bond with no phosphate
what are the functions of glycolipids?
- serves as a marker that distinguishes one cell from another in cell-cell recognition, where cells recognise other cells by binding to glycolipids
- involved in cell-cell adhesion as a result of this binding
what is the chemical composition of cholesterol?
cholesterol possesses a carbon skeleton made up of three fused six-membered and one five-membered ring
what are the functions of cholesterol?
- serves to regulate membrane fluidity in extreme temperatures
- precursor for the synthesis of bile acids, steroid hormones and vitamin D
what are the functional groups present in carbohydrates?
carbohydrates have a carbonyl group which can exist in the form of a ketone or an aldehyde, and have multiple hydroxyl groups
how many monomers comprise an oligosaccharide?
3-10 monomers
how many monomers comprise a polysaccharide?
10-1000s monomers
what are the basic physical and chemical properties of monosaccharides?
monosaccharides and colourless, crystalline solids that are freely soluble in water but insoluble in nonpolar solvents
what is the chemical formula and nomenclature for monosaccharides?
monosaccharides exist as single sugar units with the general formula (CH2O)n. monosaccharides are name generically according to the number of carbon atoms they contain (eg. glucose is a hexose sugar)
what are the general uses of monosaccharides?
- important as respiratory substrate to produce ATP during cellular respiration
- building blocks for the synthesis of disaccharides and polysaccharides
- raw material for the synthesis of other organic molecules such as nucleotides, amino acids and fatty acids
what is the chemical structure of aldose and ketone sugars
all the carbon atoms of these sugars, except one, have a hydroxyl group attached. the carbon atom that is not attached to a hydroxyl group is attached to a carbonyl group, which is either an aldehyde group or a ketone group
what is the difference between an aldehyde group and a ketone group?
an aldehyde group has a carbon bonded to a hydrogen, oxygen, and variable group R. a ketone group has a carbon bonded to oxygen and two variable groups R1 and R2. as such, aldo sugars have a carbonyl group on carbon atom 1 while keto sugars have a carbonyl group on any of the other carbon atoms. aldehyde groups are easily oxidised to carboxylic acids and thus are strong reducing agents
compare the straight-chain and ring structures of monomers
monosaccharides may exist as linear or ring structures, which exist in a dynamic equilibrium within the cell, meaning that the two forms continuously interconvert with the overall ratio remaining stable. however, the ring structure is the more predominant form, because it is energetically more stable
how is the glucose ring formed from a straight-chain?
the oxygen on carbon 5 links with the carbon comprising the carbonyl group and transfers its hydrogen to the carbonyl oxygen to create a hydroxyl group.
how are the alpha and beta glucose formed and differentiated?
in the ring structure, the anomeric carbon is formed. if a glucose molecule is alpha, the hydroxyl group bonded to the anomeric carbon would lie below the plane of the ring. if a glucose molecule is beta, the hydroxyl group bonded to the anomeric carbon would lie above the plane of the ring/
how is a disaccharide formed?
two monosaccharides form a disaccharide, involving the loss of a single water molecule, through a condensation reaction. they form a glycosidic bond which is defined as the bond formed between the anomeric carbon of one sugar unit and another carbon on the other sugar unit
how can a disaccharide be broken down into its constituent monosaccharides?
a disaccharide can be broken down into monosaccharides through a hydrolysis reaction, involving the addition of one molecule of water in the process via either incubation with dilute acid at 100 degree celcius, or incubation with an enzyme
what is the nomenclature of glycosidic bonds dependent on?
- the numbering of the carbons attached to the hydroxyl groups involved
- the orientation of the hydroxyl groups, determining the configuration of the representation of the glycosidic bond
what is the principle of the benedict’s test for reducing sugars?
the benedict’s test makes use of the ability of a free carbonyl group in a reducing sugar to reduce copper from Cu2+ to Cu+. under alkaline conditions, copper (II) sulfate, which exists as a blue solution, is reduced to insoluble copper (II) oxide, which exists as a brick-red precipitate
why can non-reducing sugars not participate in the redox-reactions characteristic of reducing sugars?
non-reducing sugars like sucrose have no free carbonyl group linked in a glycosidic bond. as such, non-reducing sugars will need to undergo acid hydrolysis to break the sugar down into reducing sugars first
what are the observations present in benedict’s test?
if reducing sugars are not present, benedict’s solution will remain blue, and with increasing quantities of reducing sugars present, the suspension formed with gradually turn from green to yellow to orange and then to brick-red
what are the two types of polysaccharides present?
storage polysaccharides (eg. starch, glycogen) which are hydrolysed as needed to provide simple sugars for cells, and structural polysaccharides which serve as structural materials for structural support in the cell
what is the function of alpha(1,4) glycosidic bonds?
they allow for the formation of linear, unbranched chains, found in unbranched amylose, as well as in amylopectin and glycogen
what is the function of alpha(1,6) glycosidic bonds?
they give rise to branches in the chain, and are found where branches occur in amylopectin and glycogen
what are the functions of starch in plant cells?
starch serves as a carbon source, consisting of only alpha glucose monomers and both unbranched amylose (10-30%) and branches amylopectin (70-90%). they are stored in plant cells as starch grains either within the chloroplasts, or within the amyloplasts which are specialised plastids for starch storage
what are the structure and chemical properties of amylose?
amylose exists as an unbranched chain that consists of hundreds to thousands of alpha glucose residues joined by alpha(1.4) glycosidic bonds. forming a helical structure with 6 glucose units per turn that is compact. since amylose is bulky, amylose is poorly soluble in water and thus does not exert osmotic influence in the cell
what is the principle behind the test for starch?
the centre of the starch helix is hydrophobic in nature and is where iodine in potassium iodine solution packs within the core of the helix to give rise to a blue-black colouration
what are the observations present for starch test?
if the sample turns blue-black in colour, there is a presence of starch. if the sample remains yellow/brown in colour, there is an absence of starch
what is the structure of amylopectin?
amylopectin is a more complex form of starch which consists of alpha glucose residues, and contains both alpha(1.4) and alpha(1,6) glycosidic bonds. branch points occur at every 12-30 residues and average branch length is between 24-30 residues.
what is the purpose behind the many branch ends in amylopectin?
the many branch ends allow a larger number of enzymes to act on it at any one time so it can be easily hydrolysed
what is the purpose behind the extensive branches in amylopectin?
the extensive branching causes amylopectin to be highly compact
why do starch, cellulose and glycogen not affect the water potential within cells and living organisms?
starch and glycogen are large molecules and are insoluble
why do glycogen and starch act as large stores of carbon (respiratory substrate)?
starch and glycogen are composed of several hundreds to thousands of glucose monomers
why is starch easily hydrolysed by enzymes present in plants
glucose units are linked by alpha(1,4) glycosidic bonds, which gives rise to straight chains of glucose
why is amylose compact in structure?
amylose molecules are helical in shape
why is amylopectin compact, with a large number of free ends available for hydrolysis by amylase at any one time?
amylopectin molecules are highly branches due to the presence of alpha(1,6) glycosidic bonds
why are starch and glycogen unreactive and chemically-stable compounds?
the anomeric carbon is involved in glycosidic bond formation, leaving few free anomeric hydroxyl groups
where is glycogen mainly found in the body?
glycogen is found mainly in the liver, accounting for 10% of liver mass and skeletal muscle, accounting for 1-2% of the muscle mass in the form of cytoplasmic granules
what is the function of glycogen?
in the liver, it is used as a source of glucose to maintain blood sugar levels. in the muscle, it serves as a fuel source to generate ATP for muscle contraction.
what is the structure of glycogen?
glycogen consists only of alpha glucose, and has a similar structure to amylopectin but it is more extensively branched. alpha(1,6) glycosidic bonds occur every 8-12 glucose units
what happens when glycogen is suspended in water?
it gives a red-violet colour with iodine in potassium iodide solution
why are alpha(1,4) glycosidic bonds in glycogen easily hydrolysed by enzymes glycogen phosphorylase?
glucose unit are linked by alpha(1,4) glycosidic bonds
why is glycogen is highly compact, and have a larger number of free ends available for hydrolysis by amylase at any one time?
glycogen is highly branched due to the presence of alpha(1,6) glycosidic bonds
what is the chemical structure of cellulose?
cellulose is made up of beta-glucose, and hence a beta glycosidic bond is formed between the glucose monomers. alternate monomers are inverted to obtain beta(1,4) glycosidic bonds, forming a long, unbranched straight chain of up to 10000 beta-glucose molecules.
how are cellulose chains arranged?
many chains run parallel to each other and their hydroxyl groups project outwards from each chain. extensive hydrogen bonds from between the protruding hydroxyl groups of neighbouring chains, allowing the establishment of rigid cross-links between chains, later associating in groups to form microfibrils, which consist of 60-70 cellulose chains and can attain a diameter of up to 25nm. microfibrils associated with other non-cellulose polysaccharides, and are arranged to form macrofibrils
what properties do cellulose cell walls have?
- cellulose cell walls have high tensile strength that confers cellulose considerable stability, as the cellulose fibres are laid down in different orientations in the different layers of the plant cell wall, permitting the cell wall to withstand forces exerted in all directions
- full permeability to water and solutes, important for the proper functioning of plant cells
why is cellulose stable?
beta glucose units are linked by beta(1,4) glycosidic bonds. amylase can only hydrolyse alpha(1,4) glycosidic bonds found in starch, and few organisms produce cellulase
how does cellulose provide high tensile strength for structural support?
- alternate inverted beta-glucose units linked by beta(1,4) glycosidic bonds allow cellulose to from long, unbranched and straight chains.
- there is extensive hydrogen bonds form between parallel chains
- straight parallel chains can be grouped into microfibrils, which eventually cluster into macrofibrils
how are proteins diverse in their structure?
proteins range in size from relatively small peptides to huge polymers with molecular weights in the millions. proteins exhibit enormous diversity of biological function and thus each protein has a specific three-dimensional (3D) conformation
what elements do proteins contain?
proteins contain carbon, hydrogen, oxygen, nitrogen and in some cases, sulfur
how are proteins constructed?
proteins are polymers constructed from a set of 20 different amino acids. amino acids are covalently joined together by peptide bonds to form a polypeptides. polypeptides fold into a specific 3D conformation to form a functional protein
which two factors affect the function of a protein?
- nature of the amino acids present in the protein
- 3D conformation of the protein molecule
what are the differences between fibrous proteins and globular proteins?
- in fibrous proteins, polypeptides chains are elongated and wound around each other to form rope-like structure, while in globular proteins, polypeptide chains are folded, bent and twisted to form a compact and spheroidal structure
- in fibrous proteins, each polypeptide chain has a repetitive amino acid sequences, while in globular proteins, each polypeptide chain has a specific and non-repetitive amino acid sequence
- in fibrous proteins, the length of the polypeptides chain may vary in two samples of the same protein, while in globular proteins, the length of polypeptide is always identical in two samples of the same protein
- fibrous proteins have stable structures due to the numerous intra and inter-molecular hydrogen and covalent bonds, while globular proteins have relatively unstable structures due to numerous intra and inter molecular non-covalent bonds
- fibrous proteins are generally insoluble in water, while globular proteins are generally more soluble in water
- fibrous proteins perform structural functions while globular proteins perform metabolic functions
what is the function of enzymatic proteins?
enzymatic proteins perform selective acceleration of chemical reactions
what is the function of defensive proteins?
defensive proteins protect the body against disease and foreign particles. (eg. antibodies recognise and bind to antibodies on viruses and bacteria)
what is the function of storage proteins?
storage proteins aid in the storage of amino acids (eg. casein, the protein in milk, in the major source of amino acids for baby mammals)
what is the function of transport proteins?
transport proteins aid in the transport of substances in and out of the cell, or from one region to another (eg. haemoglobin transports oxygen from the lungs to other parts of the body)
what is the function of hormonal proteins?
hormonal proteins aid in the coordination of an organism’s activities (eg. insulin secreted by the pancreas, causes other tissues to take up glucose, lowering blood sugar concentration)
what is the function of receptor proteins?
receptor proteins aid in the response of cell to chemical stimuli
what is the function of contractile and motor particles?
contractile and motor particles aid in movement of the body (eg. actin and myosin are responsible for the contraction of muscles)
what is the function of structural proteins?
structural proteins provide support for the cell or body (eg. keratin is the protein of hair and other skin appendages)
what is the definition of a simple protein?
a simple protein is a protein where only amino acids form the structure of simple proteins (eg. histones in nucleoproteins, globulins in blood fibrinogen and antibodies, and albumins)
what is the definition of conjugated proteins?
conjugated proteins are proteins combined with a non-protein component, known as a cofactor. a cofactor can be inorganic or organic in nature. if an organic cofactor is tightly bound to a protein, it is known as a prosthetic group (eg. glycoproteins with carbohydrates, chromoprotein with pigment, lipoprotein with lipid)
how many amino acids are present in a cell?
more than 60 different kinds of amino acids are present in a cell, but only 20 are fundamental amino acids used in protein synthesis.
why do animals need to obtain essential amino acids from their diet?
unlike plants, animals are unable to synthesise all the amino acids that they need and must obtain ‘ready-made’ amino acids directly from their diet.
what is the definition of derivatives?
derivatives are a small number of rare amino acids that occur in the proteins of living organisms, and are made from some of the 20 fundamental amino acids (eg. hydroxyproline is a derivative of proline)
how are derivatives obtained?
DNA does not code for these derivatives are they are modified after incorporation into a polypeptide chain
what is carbon covalently attached to in an amino acid?
- a basic amine group (NH2)
- an acidic carboxylic group (COOH)
- a hydrogen atom
- a variable group R
what are the physical properties of amino acids?
amino acids are colourless and crystalline solids with relatively high melting points.
what are the chemical properties of amino acids?
amino acids are insoluble in organic solvents but soluble in water to form ions. this is because the amine and carboxylic group can readily ionise
how are zwitterions formed?
- a hydrogen ion is lost from the carboxylic group, making it negatively charged
- this hydrogen ion associated with the amine group, making it positively charged
- since the resulting amino acid contains one positive and one negative charged, it is electrically neutral and dipolar
why are amino acids amphoteric?
amino acids are amphoteric as they exist as zwitterions in aqueous medium, and have both acidic and basic properties in aqueous solution.
what is the definition of a buffer?
a buffer is defined as a substance that can resist changes in pH in a solution when small amounts of an acid or alkali is added to it
what happens to an amino acid when acid is added to it?
the carboxylic group takes up a hydrogen ion and becomes H3N-RCH-COOH
what happens to an amino acid when an alkali is added to it?
the amine group loses a hydrogen ion which combines and neutralises the OH- in the alkali. as such, the amino acid becomes H2N-RCH-COO-
how many amino acids are classified as having non-polar R groups?
9 amino acids
what are the chemical properties of non-polar R groups?
these R groups are hydrocarbon in nature, and are thus hydrophobic and unreactive, tending to become localised in the interior, meaning they shield away from the aqueous medium of the polypeptide
how many amino acids have polar R groups?
6 amino acids
what are the chemical properties of these amino acids?
these amino acids have polar R groups with no net charge, and are hydrophilic in nature (eg. OH and NH groups)
how many amino acids have charged R groups?
five amino acids
what are the chemical properties of charged amino acids?
these amino acids contain either a negatively or positively charged R group, making them hydrophilic. Acidic amino acids have a net negative charge when ionised in water, owing to the presence of a carboxyl group in the R group. basic amino acids have a net positive charge when ionised in water, owing to the presence of an amine group in the R group
how is a peptide bond formed?
it is formed when two amino acids are joined to each other covalently, forming a CN bond, between the amine group and the carboxyl group of the amino acids, through a condensation reaction
what is the structure of a polypeptide?
each polypeptide consists of many amino acids joined together in a head-to-tail fashion by peptide bonds in a specific linear amino acid sequence. a polypeptide includes a free amine and carboxyl group, and a R group
what are the properties of polypeptides?
- the presence of free amine and carboxyl groups confers the polypeptide the ability to buffer solutions, although not to as great an extent as free amino acids
- the R groups of some amino acids are able to ionise, conferring additional buffering capacity on the polypeptide
- the R group with specific chemical and physical characteristics also results in variations in length and sequence of the polypeptides, contributing to the diversity of proteins
what is the principle of the biuret test?
the biuret test detects peptide bonds and thus all proteins give a positive result. nitrogen atoms in peptide bonds complexes with Cu2+ ions to give a purple colouration
what is the definition of primary structure of a protein?
the primary structure is defined as the unique number and linear sequence of amino acids that constitute the polypeptide chain
how are polypeptides given their unique sequence?
proteins are synthesised in vivo by the stepwise polymerisation of amino acids in the order specified by the sequence of nucleotides in a gene
how does the primary structure of an amino acids affect the protein’s structure and function?
the secondary, tertiary and quaternary structures are direct consequences of the primary structure. the amino acid R groups will determine the type and location of bonds present at higher levels of organisation in the protein. additionally, size, charge, polarity and hydrophobicity of the R groups will affect the 3D conformation of the protein
what is the definition of secondary structure of a protein?
certain sequences of amino acids form hydrogen bonds that cause the region to fold into a spiral (alpha helix) or pleated sheet (beta sheet).
how does a protein take the form of an extended spiral spring?
- it is stabilised by intrachain hydrogen bonds, which occur between CO and NH groups of the peptide backbone. the hydrogen bond is formed between the O atom of the CO group and the H atom of the NH group situated four amino acid residues ahead in the linear sequence
- the hydrogen bonds formed are parallel to the main axis of the helix, and this brings maximum stability to the alpha helix.
- the alpha helix makes one complete turn for every 3.6 amino acids
- the R groups of the amino acid residues project outside the helix, perpendicular to the main axis, preventing steric interference with the polypeptide backbone and with each other
what may interfere with the formation of the alpha helix?
proline and hydroxyproline insert a kink and disrupt the formation of the alpha helix. amino acids with bulky R groups if present in large numbers can also interfere with the formation of the alpha helix
how is the beta-pleated sheet formed?
- like the alpha helix, it is stabilised by hydrogen bonds which occur between CO and NH groups of the polypeptide backbone
- hydrogen bonds occur between CO and NH groups within the same polypeptide chain (intrachain sheets) or between CO and NH groups of neighbouring polypeptide chains (interchain sheets)
what varieties do beta-pleated sheets come in?
- the antiparallel beta-pleated sheet in which neighbouring hydrogen bonded polypeptide segments run in opposite N-terminus to C-terminus directions
- the parallel beta-pleated sheet in which the hydrogen-bonded segments run in the same N-terminus to C-terminus direction
what may interfere with the formation of beta-pleated sheets?
amino acids with bulky R groups interfere with the formation of the beta-pleated sheet by causing steric hindrance, and as a result amino acid residues usually have small R groups
what is the definition of tertiary structure of a protein?
the tertiary structure refers to the further bending, twisting and folding of the polypeptide chain with the secondary structures to give an overall specific 3D conformation
what 4 types of R group interactions determine the 3D conformation of the protein?
- ionic bonds, hydrogen bonds and hydrophobic interactions
- covalent bonds, in particular disulfide bonds
how are disulfide bonds formed in a protein?
it is formed by oxidation of the sulfhydryl groups of any two cysteine residues in the same polypeptide chain or in different chains, forming a covalent SS bond
how are ionic bonds formed in a protein?
some amino acid R groups are positively charged while others are negatively charged. these oppositely charged R groups may form ionic bonds which are relatively weak in the aqueous cellular environment and may be broken by changes in the pH of the surrounding medium
how are hydrophobic interactions formed in a protein?
the polypeptide folds so as to shield hydrophobic R groups from the aqueous environment. interactions occur between hydrophobic R groups of amino acid residues
what is the definition of a domain in proteins?
a domain is a distinct, discrete, locally folded structural unit, each with its own specific function. most domains consist of 100-200 amino acid residues and neighbouring domains are usually connected by one or two polypeptide segments.
what is the definition of the quaternary structure of a protein?
quaternary structure is the overall protein structure that results from the associated of two or more polypeptide chains to form a functional protein. each polypeptide adopts a tertiary structure and is called a protein subunit. proteins with more than one subunit are known as multimeric proteins
what is the structure of haemoglobin?
- haemoglobin is a multimeric protein, made out of two alpha chains (containing 141 amino acids) and two beta chains (containing 146 amino acids).
- each polypeptide chain consists of eight alpha helices connected by non-helical segments, stabilised by hydrogen bonds
- the two subunits in each dimer are held together primarily by hydrophobic interactions, but ionic and hydrogen bonds also occur
- the four subunits form a globular molecule that is held by multiple non-covalent interactions
what is the function of haemoglobin?
haemoglobin is an oxygen binding protein, giving red blood cells their colour. haemoglobin transports oxygen in the blood from the lungs to other tissues in the body, in order to supply cells with the oxygen required for aerobic respiration.
how does the structure of haemoglobin relate to its function?
- each polypeptide chain is folded such that amino acid residues located at the surface of a subunit are generally hydrophilic, while those buried in the interior of the molecule are mostly hydrophobic, making haemoglobin soluble in an aqueous medium, and hence a good transport protein for oxygen in blood
- the folding of the polypeptide chain also allows the formation of a hydrophobic cleft to allow for the haem prosthetic group to bind. each haem group will bind 1 molecule of oxygen and thus each haemoglobin molecule will bind to 4 molecules of oxygen
- the haem group consists of an iron ion held in a porphyrin ring. the iron ion binds one of the oxygen atoms in a molecule of oxygen. the iron and combine reversibly with oxygen and hence enhances the release of oxygen in metabolically active tissues
- as Fe2+ in the first haemoglobin subunit binds 1 molecule of oxygen, the F helix is pulled closer to the haem group, creating a strain on the other subunits, such that the previously obscured haem groups are revealed. the remaining subunits change their 3D conformation slightly , allowing their respective haem groups to bind to oxygen more readily. thus haemoglobin is known as an allosteric protein, and this mechanism is known as cooperative binding
what is the structure of collagen?
- a single collagen molecule consists of three polypeptide chains, with each polypeptide consisting of a repeating tripeptide sequence of glycine - X - Y where X is often proline, and Y is often hydroxyproline or hydroxylysine.
- each collagen polypeptide assumes a left-handed helical conformation with about three residues per turn known as the collagen helix or an alpha chain
- three parallel alpha chains wind around each other with a gentle, right-handed, rope-like twists to form tropocollagen
what are the features of tropocollagen?
- every third residue of each polypeptide passes through the centre of the triple-helix, which is crowded that only the small R group of glycine can fit in. this allows the three helical alpha chains to pack tightly together, providing high tensile strengh
- the residues in the X and Y positions are located on the outside of the triple helix, where there is room for the bulky R groups of proline and other residues
- proline with its ring structure, stabilises the rigid three-stranded collagen helix
- the tropocollagen is held together by an extensive network of hydrogen bonds, formed between the NH group of glycine in one alpha chain, and the CO group of another amino acid in a neighbouring alpha chain. hydroxyl groups of hydroxyproline and hydroxylysine also participate in hydrogen bonding
- covalent cross-links are also present within tropocollagen molecules to further impart the collagen fibre with high tensile strenght.
what is the function of collagen?
collagen fibres are the major stress-bearing components of connective tissues such as bone, teeth, cartilage and more, as it has great tensile strength and is able to provide bone with the required flexibility, structure and strength. tendons also have the strength and structure required to transmit muscular contraction etc.
how is a collagen fibre formed?
- many of the tropocollagen molecules lie side by side, linked to each other by covalent cross-links between the carboxyl end of one molecule and the amino end of another, giving rise to a collagen fibril
- tropocollagen molecules are arranged in a staggered manner with each other, stabilised by hydrophobic interactions between tropocollagen molecules, conferring it greater strength.
definition of denaturation of a protein?
denaturation is the loss of the specific 3D conformation of a protein molecule
when does denaturation occur?
denaturation occurs when the bonds that maintain the conformation of the protein is broken and the protein unfolds. thus, it can no longer perform its normal function. it may be temporary or permanently damaged, but the primary structure remains unaffected.
what is the definition of renaturation of a protein?
renaturation is when certain proteins can regain their specific 3D conformation and their biological activity if returned to conditions in which the 3D conformation is stable
what does denaturation disrupt?
denaturation disrupts R group interactions such as disulfide bonds, ionic bonds, hydrogen bonds and hydrophobic interactions, as well as hydrogen bonds formed between the NH and CO groups of the polypeptide backbone
how does heat cause denaturation?
excessive heat increases vibrations of the atoms, leading to disruption of non-covalent bonds
how does changes in pH cause denaturation?
drastic changes in pH changes the charges in the acidic and basic R groups, leading to disruption of ionic bonds and hydrogen bonds
how does organic solvents cause denaturation?
transfer of a protein from an aqueous environment to an organic solvent can disrupt hydrophobic interactions that make up the stable core of globular proteins. the protein turns inside out and the hydrophobic regions changes place with the hydrophilic regions
how does the addition of urea and detergents cause denaturation?
addition of chemicals can disrupt ionic and hydrogen bonds that maintain the protein’s conformation
how do the structural features of the G-protein linked receptor allow for it to carry out its function?
- the GPLR has seven transmembrane a helices. The exterior surfaces of the a helices facing the non-polar fatty acid tails of the phospholipid molecules in the cell surface membrane have many non-polar R groups which interact with the fatty acid tails. This allows the GPLR to be stably embedded in the cell surface membrane to serve as a cell surface receptor
- the specific loops between the transmembrane helices of GPLR form an extracellular ligand-binding site, and a cytoplasmic G-protein binding site. the extracellular ligand-binding site of the GPLR has a complementary shape to the ligand to allow binding of the ligand. the cytoplasmic G-protein binding site has a complementary shape to the G-protein and allows binding of G-protein to the cytoplasmic G-protein binding site of GPLR in the cytoplasm
what is the definition of an enzyme?
an enzyme is a biological catalyst that increases the rate of a chemical reaction by lowering the activation energy of a reaction, while remaining unchanged itself at the end
how do reactants behave throughout an energy profile diagram?
- the uphill portion of the energy profile represents the initial investment of energy required to start a reaction, also known as the activation energy
- at the summit, reactants are in an unstable transition state, where bonds can be broken/formed
- once the appropriate bonds have been broken/formed, the molecules settle into their new bonding arrangement to form the product
what is the effect of an enzyme on the reactant molecules?
- the activation energy is lowered in a enzyme-catalysed reaction
- more reactant molecules can summount the energy barrier to reach the transition state to be converted into product molecules
what are the properties of enzymes?
- enzymes are effective in small amounts - they remain chemically unaltered at the end of the reaction
- enzymes are extremely efficient - enzyme-catalysed reactions are highly efficient, proceeding 10^3 to 10^8 times faster than uncatalysed reactions
- enzymes have a high degree of specificity - most enzymes are specific to one type of substrate molecule
- enzymes can be denatured by heat and they act most efficiently at an optimum temperature
- enzymes are affected by pH and they act most efficiently at their optimum pH
- enzyme activity can be regulated by activators and inhibitors.
what is the basic structure of enzymes?
most enzymes are globular proteins. therefore, enzymes have a specific 3D conformation that is necessary for their action. this 3D structure must be maintained for an enzyme to remain functional. like any other protein, an enzyme can be denatured when the bonds holding them in the specific 3D conformation are disrupted
what are catalytic amino acid residues involved in?
the R groups of catalytic amino acid residues are directly involved in the catalytic activity of the substrate and enzyme (eg. making or breaking bonds once the substrate is bound)
what are binding amino acid residues involved in?
the R groups of binding amino acid residues hold the substrates in position via non-covalent bonds while catalysis takes place
what are structural amino acid residues involved in?
structural amino acid residues are involved in maintaining the specific 3D conformation of the active site, as welll as the enzyme as a whole
what are non-essential amino acid residues involved in?
non-essential amino acid residues have no specific functions and can be removed or replaced without the loss of the enzyme’s catalytic function
what is the primary structure of an enzyme?
the primary structure of the enzyme consists of a unique number and linear sequence of amino acids. the structural residues interact to maintain the 3D conformation of the protein. a few of the residues are on the surface of the folded protein, and are non-essential.
what are the three main types of cofactors found that interact with enzymes?
- inorganic metal ions
- coenzymes
- prosthetic group
what are the properties and functions of inorganic small ions?
- these ions are mostly small divalent ions (eg. calcium ions)
- they may either be a component of an active site, of affect enzyme activity through allosteric regulation.
- they usually bind reversible to the enzyme and act by altering the enzyme’s active/allosteric sites to facillitate the catalytic reaction carried out by the enzyme
what are the properties and functions of coenzymes?
- they loosely associate with the enzyme during the reaction, and act as transient carriers of specific function groups, hydrogens or electrons
- most coenzymes are derived from vitamins
what are the properties and functions of prosthetic groups?
- prosthetic groups are tightly bound to the enzyme on a permanent basis
what is the definition of an effective collision?
when an enzyme and substrate collide in the correct orientation, the substrate will be bound the the enzyme at a specific site on the enzyme called the active site
how is an enzyme-substrate complex formed?
- the substrate molecule is held between the active site by binding amino acid residues by non-covalent bonds such as hydrogen and ionic bonds between the R groups of the binding amino acids.
- the R groups of the catalytic amino acid residues at the active site catalyse the conversion of the substrate to product
- the alteration in chemical conformation results in the product molecule being released from the active site as it is no longer complementary to the active site structure. the enzyme active site is free for the binding of another substrate molecule
how do enzymes lower activation energy of a reaction?
- enzymes orient the substrates in close proximity, in the correct orientation to undergo chemical reactions
- enzymes strain critical bonds in the substrate molecule, allowing the substrates to attain their unstable transition state
- enzymes provide a microenvironment that favours the reaction (eg. the presence of specific amino acids/ions at the active site may result in a specific set of molecular conditions
what does the lock and key mechanism suggest?
the mechanism suggests that there is a complementary shape or conformation between the substrate and the active site of the enzyme, in the same way that a key fits into a lock very precisely. the enzyme is viewed as a rigid structure, where only substrates that are exactly complementary to the conformation of the active site are able to bind to the active site for catalysis
what does the induced fit hypothesis suggest?
the hypothesis suggests that one enzyme is able to catalyse reactions for a variety of substrates that share similar structural or chemical properties.
enzymes exhibit active site flexibility, where enzymes do not have a rigid conformation and can allow more than one type of substrate to bind.
how does the induced fit hypothesis work?
upon binding of substrate, the active site changes its conformation slightly to bind the substrate even more firmly so that the R groups of the catalytic amino acids at the active site are moulded into a specific conformation, and brought into close proximity to the chemical bonds in the substrate hence facilitating catalysis where the substrate is converted to product
what is the principle of limiting factors?
- the rate of a biochemical process, which consists of a series of reactions, is limited by the slowest reaction in the series
- when a biochemical process is affected by several factors, its rate is limited by that factor which is in the shortest supply, known as the limiting factor
- when the supply of the limiting factor is increased, it will lead to an increase in the rate of reaction
explain the relationship between substrate concentration and rate of enzymatic reaction
at low substrate concentration, not all the active sites of the enzymes are occupied, and the rate is limited by the concentration of substrate. an increase in substrate concentration increases the frequency of effective collisions between the active site and substrate molecules, increasing the number of ES complexes formed per unit time and the amount of product formed per unit time, resulting in a proportional increase in the rate of reaction
at high substrate concentration, the active site of every enzyme is occupied at any given moment, and rate is limited by saturation of active sites. substrate concentration is no longer the limiting factor and enzyme concentration is the limiting factor, resulting in the rate of reaction reaching a plateau
explain the relationship between enzyme concentration and the rate of reaction
at low enzyme concentrations, the increase in enzyme concentration provides more active sits, and thus increases the frequency of effective collision between substrates and active sites. more ES complexes are formed per unit time, resulting in an increase in the amount of product formed per unit time, resulting in an increase in the rate of reaction
at high enzyme concentrations, the enzyme concentration is no longer a limiting factor, and there are not enough substrate molecules competing for the active sites available. substrate concentration is the limiting factor and thus the rate of reaction reaches a plateau
explain the relationship between temperature and rate of reaction
at low temperatures near or below freezing point, enzymes are inactivated. increasing temperatures increase the kinetic energy of the substrate and enzyme molecules, increasing the frequency of effective collision between substrate and active sites. the formation of ES complexes and product per unit time increases and the rate of reaction increases.
as the temperature continues to increase beyond the optimum temperature, thermal agitation of enzyme molecule disrupts the hydrogen bonds, ionic bonds and non-covalent interactions that stabilise the specific 3D conformation of the protein molecule, and the enzyme is no longer a complementary fit with the substrate. the enzyme is denatured and loses its catalytic function, resulting in the frequency of effective collisions between substrate and active sites to decrease. the rate of formation of enzyme substrate complexes drop and rate of reaction decreases
explain the relationship between pH and the rate of reaction
- when there is a lower pH, more hydrogen ions are available to neutralise negative charges present in the enzyme. when there is a higher pH, less hydrogen ions are available to neutralise negative charged present in the enzyme. changes in ionisation of amino acids disrupts the ionic/hydrogen bonds that maintain the 3D conformation of the enzyme
- conformation of the active site is no longer complementary to the substrate, and no ES complex can be formed
- substrate cannot be held in its correct orientation in the active site of catalysis to occur
- R groups on catalytic amino acid residues no longer possess the correct ionisation to catalyse the required reaction
what is the definition of the maximal reaction velocity?
the maximal reaction velocity reflects the maximum rate that a reaction can proceed in the presence of a specific concentration of enzyme and excess substrate
what is the definition of the michaelis constant?
the michaelis constant is measured as the substrate concentration that allows an enzyme-catalysed reaction to proceed at half the maximum velocity. enzymes with a low michaelis constant value exhibit a high affinity for their substrate, while enzymes with a high michaelis constant value exhibit a low affinity for their substrate
what is the definition of an inhibitor?
inhibitors are a small variety of molecules which can reduce the rate of an enzyme-catalysed reaction.
definition and mechanisms of a competitive inhibitor?
competitive inhibitors are structurally similar to the substrate molecule and compete with the substrate for binding to the active site. although it is not acted upon by the enzyme, it remains bound to the active site and prevents substrate binding to the active site
explain the relationship between substrate concentration and rate of reaction WITH a competitive inhibitor
an increase in substrate concentration reduces the effect of inhibition, as the substrate and inhibitor are in direct competition for the enzyme’s active sites and the greater the proportion of the substrate molecules, the greater the chance a substrate can out-compete the inhibitor to enter the active site. the rate of reaction almost equivalent to Vmax can be attained. as such, the final amount of product formed is the same
what is the definition and mechanisms of a non-competitive inhibitor?
non-competitive inhibitors bear no structural resemblance to the substrate and does not compete with the substrate for the active site. the inhibitor binds to a part of the enzyme that is not the active site and this alters the 3D conformation of the enzyme. the enzyme molecule no longer has an active site that is complementary in conformation to the substrate and does not bind to the enzyme active site.
explain the relationship between substrate concentration and rate of reaction WITH a non-competitive inhibitor
the binding of a non-competitive inhibitor to a site other than the enzymes’s active site causes a change in 3D conformation of the enzyme’s active site, preventing substrate molecules from binding. a certain proportion of the enzyme molecules are rendered inactive, and Vmx is lower. as the substrate and the inhibitor are not in direct competition for the same site, an increase in substrate concentration has no effect on the inhibition. Km remains unchanged, as the affinity of the enzyme for substrate remains unaffected. thus, the final amount of product formed is the same
what is the basic structure of an allosterically regulated enzyme?
most allosterically regulated enzymes are composed of two or more polypeptide chains and it is a multi-subunit enzyme. each subunit has its own active site, and allosteric sites are usually located where subunits are joined
what happens to an allosterically regulated enzyme when it undergoes allosteric activation?
when an activator binds, it stabilises the active form of the enzyme and increases the affinity of the enzyme for its substrate.
what happens when an allosterically regulated enzyme undergoes allosteric inhibition?
when an inhibitor binds to the allosteric site, it stabilises the inactive form of the enzyme and decreases the affinity of the enzyme for its substrate
why does the rate of an allosteric enzyme-catalysed reaction have a sigmodal shape?
the binding of an activator to an allosteric site induces a favourable conformation change in the active sites of all the subunits of the enzyme. this significantly amplifies the response of the enzyme to substrates. the amplification results in the sudden steep rise in the rate of reaction.
how does the graph for an allosterically activated enzyme reaction apply to the mechanism of cooperativity?
binding of one substrate molecule to an active site of a multimeric enzyme triggers the same favourable conformational change in the active sites of all other subunits of the enzyme. cooperativity amplifies the response of enzyme to substrate. one substrate molecule primes an enzyme to accept additional substrate molecules
what are the mechanisms of reversible inhibition?
the inhibitor binds to the enzyme via weak non-covalent bonds such as hydrogen bonds and hydrophobic interactions. the effect of inhibitor is temporary, and can be easily removed causing no permanent damage to the enzyme.
what are the mechanisms of irreversible inhibition?
the inhibitor binds to the enzyme via covalent bonds, and this causes permanent damage to the enzyme molecule so that it is unable to carry out catalytic activity
where are intracellular enzymes located?
- in the cytosol or nucleus
- inside membrane-bound organelles (eg. mitochondria, chloroplast, lysosomes)
- attached to the plasma membrane
- attached to membranes of organelles (eg. mitochondria and chloroplast)
what are the advantages of metabolic pathways catalysed by enzymes?
- reactants may be modified in a series of small steps, enabling energy to be released in a controlled amounts, and minor adjustments to be made to the structure of molecules
- each step is catalysed by a specific enzyme allowing for regulation and control of metabolism as each enzyme is a point of control of the overall pathway. enzymes specific to the reaction are regulated by different inhibitators/activators, hence allowing for a finely balanced portioning of cell metabolites among different pathways
- the steps in the pathway may be spatially arranged so that the product of one reaction is ideally located to become the substrate of the next enzyme. this permits the build-up of high local concentrations of substrate molecules and biochemical reactions can proceed rapidly
what are the mechanisms of end-product inhibition?
when the end-product of a metabolic pathway accumulates, it may act as an inhibitor on the enzyme controlling the preceding steps of the pathway. the binding may alter the conformation of the active site of the enzyme and lower its affinity for its substrate, or block the entry of the substrate into the active site
