Topic 2 - Molecular Biology Flashcards
properties of carbon compounds
- carbon forms covalent bonds with other atoms
- each carbon atom can form up to 4 covalent bonds (this is more than most other atoms)
- so carbon compounds can have complex structures
types of carbon compounds
- carbohydrates
- lipids
- proteins
- nucleic acids
carbohydrates
- made up of CHO
- ratio of H:O is 2:1 (hence the -hydrate)
lipids
- made up of CHO
- insoluble in water
- contains less O than carbohydrates
types of lipids
- steroids
- waxes
- fatty acids
- triglycerides
triglycerides
- fats if solid at room temperature
- oils if liquid at room temperature
proteins
- made up of 1 or more amino acid chains
- almost all the amino acids will contain CHON, but 2 of them also contain S
nucleic acids
- chains of nucleotides
- contains CHONP
types of nucleic acids
- DNA
- RNA
ribose
- C5H10O5
- 5-membered ring with a side chain
- 4 carbon atoms are in the ring while 1 forms a side chain
- hydroxyl (OH) groups on carbon atoms 1, 2, 3, and 5 point up, down, down, up respectively
glucose
- C6H10O6
- 6-membered ring with side chain
- 5 carbon atoms in the ring with 1 in the side chain
- in alpha glucose (most common), hydroxyl (OH) groups on carbon atoms 1, 2, 3, 4 point down, down, up, down respectively
- but in beta glucose, which is used in plants to make cellulose, the OH group on C atom 1 points up
amino acids
the central C atom is bonded to:
- an amine group (hence the term ‘amino acid’)
- a carboxyl group (making the molecule an acid)
- a H atom
- the R group (variable part of amino acids)
metabolism
- web of all enzyme-catalysed reactions in a cell/organism
- consists of pathways in which 1 type of molecule is transformed into another over a series of steps
- consists of over 1k reactions
types of metabolism
- anabolism
- catabolism
anabolism
- synthesis of complex molecules from simpler molecules
- requires energy (usually in ATP form)
examples of anabolic reactions
- formation of macromolecules from monomers by condensation reactions
- protein synthesis using ribosomes
- DNA synthesis during replication
- photosynthesis
- synthesis of complex carbohydrates (e.g. starch, cellulose, glycogen)
catabolism
- breakdown of complex molecules into simpler molecules
- releases energy and in some cases this energy is captured in the form of ATP
examples of catabolic reactions
- digestion of food in the mouth/stomach/small intestine
- cell respiration in which glucose/lipids are oxidized to CO2 and water
- digestion of complex carbon compounds in dead organic matter by decomposers
properties of water molecules
- formed by covalent bonds between an O atom and 2 H atoms
- the bonds between H and O involve unequal sharing of e-s (so it’s a polar covalent bond)
- H is partially positive while O is partially negative
- water molecules are v-shaped so the 2 H atoms form a pole while the one O atom forms an opposite pole
hydrogen bonds
- attraction between a partially positive H atom and a partially negative atom when both are in polar covalent bonds with other atoms
- kinda like an affair :)
- it’s a weak intermolecular force but since there are so many water molecules per unit volume of water, there are a LOT of hydrogen bonds
cohesion
binding together of 2 molecules of the same type
adhesion
binding together of 2 molecules of different types
significance of hydrogen bonds with regard to the properties of water
- cohesion: hydrogen bonds form between water molecules, causing them to stick to each other
- adhesion: hydrogen bonds can form between water molecules and other polar molecules
- high specific heat capacity/latent heat of vaporization/boiling point: hydrogen bonds restrict the motion of water molecules, so more energy (higher temp) is required to break those bonds
- solvent properties: water can form hydrogen bonds with other polar molecules, as its O pole is attracted to positive ions while its H pole is attracted to negative ions, causing them to dissolve
applications of water’s cohesive properties
- useful for water transport in plants
- water is sucked through xylem vessels at low pressure
- this can only work if the water molecules aren’t separated by the suction forces
applications of water’s adhesive properties
- in leaves, water keeps cell walls moist
- by adhering to cellulose molecules in cell walls
- if water evaporates and is lost from the leaf, adhesive forces will cause water to be drawn out from the nearest xylem vessel, thereby maintaining the walls’ moisture
- so that the walls can continue to absorb CO2
applications of water’s thermal properties
- as water has a high specific heat capacity, its temperature will remain relatively stable
- so it’s a thermally stable habitat for aquatic life
- as water has a high latent heat of vaporization, it absorbs heat (energy)
- this makes it an effective coolant
- as water has a high boiling point, it is in liquid state for the majority of habitats on Earth
applications of water’s solvent properties
cytoplasm is an example of a complex mixture of dissolved substances in which metabolic chemical reactions occur
hydrophilic
- substances that are chemically attracted to water
- they will dissolve in water
- they are polar
hydrophobic
- substances that dissolve in other solvents but not in water
- they are non-polar
- all lipids are hydrophobic
hydrophobic interactions
forces causing non-polar molecules to join together into groups in water
why do hydrophobic interactions occur?
- there is a slight attraction between non-polar molecules
- moreover, water molecules are more attracted to each other than to non-polar molecules
- so water can form more hydrogen bonds with each other
transporting sodium chloride in blood
- NaCl is an ionic compound
- so it’s freely soluble in water
- it is carried by plasma in dissolved state
transporting amino acids in blood
- they are soluble in water
- but their solubility depends on the R group (some are hydrophilic, others are hydrophobic)
- to be carried in the blood plasma, they have to be soluble enough to dissolve
transporting glucose in blood
- glucose is polar
- so it’s freely soluble
transporting oxygen in blood
- oxygen is non-polar but due to its small size it can dissolve in water
- however, water will become saturated with oxygen even at low concentrations
- furthermore, the higher the temp of water, the lower the solubility of oxygen
- blood plasma at body temp cannot carry enough oxygen to facilitate aerobic respiration
- this problem is overcome by the presence of haemoglobin in red blood cells
- haemoglobin has binding sites for oxygen to increase the capacity of blood for oxygen transport
transporting fat molecules in blood
- fats are entirely nonpolar
- they are also larger than oxygen so they’re insoluble in water
- so they’re carried in blood using lipoprotein complexes
lipoprotein complex
- a group of molecules with a single phospholipid layer on the outside
- there are also proteins on the monolayer, hence the name
- they can store fats on the inside
transporting cholesterol in blood
- cholesterol molecules are largely hydrophobic
- so they are insoluble in water
- they are transported in lipoprotein complexes (like fats)
- but unlike fats, which are stored behind the monolayer, cholesterol molecules are positioned in the monolayer
monosaccharide
single sugar unit
examples of monosaccharides
- glucose
- fructose
- ribose
- galactose
disaccharide
two monosaccharides linked together
examples of disaccharides
- maltose
- sucrose
- lactose
polysaccharides
many monosaccharides linked together
examples of polysaccharides
- starch
- glycogen
how do monosaccharides combine?
- through a condensation reaction
- involves a loss of OH from one molecule and H from another
- anabolic process (energy required)
structure of cellulose
- glucose’s beta isomer forms a diagonal chain
- formed via condensation reactions
- each beta glucose molecule is oriented upwards/downwards in alternate fashion
- this is because the OH groups in C 1 and 4 on beta glucose points in opposite directions
- so for a condensation rxn to occur, each molecule has to be at 180 degrees to the previous one
- instead of being curved, cellulose forms a straight chain
- cellulose molecules are unbranched chains of beta glucose
- this allows them to form bundles of cellulose, with hydrogen bonds linking them together
cellulose microfibrils
- bundles formed from cellulose molecules
- high tensile strength
- its strength prevents the cell from bursting even at very high pressures due to osmosis
function of cellulose
used as the basis of plant cell walls
structure of starch
- made by linking alpha glucose molecules together
- formed via condensation reactions
- the OH groups in C 1 and 4 on alpha glucose points in the same direction
- so all molecules can be positioned similarly
- this causes starch to form a curved chain, not straight
forms of starch
- amylose
- amylopectin
differences in structure between amylose and amylopectin
amylose: the glucose chain is unbranched and forms a helix
amylopectin: the chain is branched so it has a more globular shape
function of starch
- it’s only made in plant cells
- starch is hydrophilic but too large to be soluble in water
- so they’re useful for storing glucose
- a concentrated glucose solution would cause too much water to enter a cell via osmosis
- so starch can store glucose (i.e. energy) without endangering the cell
- there is no fixed size
- so it’s easy to add/remove extra glucose molecules
- this can be done at any of the ends of a molecule (regardless of whether they have branches or not)
structure of glycogen
- similar to amylopectin starch but more branching occurs
- so the molecule is more compact
function of glycogen
- made by animals and some fungi
- same function as starch in plants
- glycogen is hydrophilic but too large to be soluble in water
- so they’re useful for storing glucose
- a concentrated glucose solution would cause too much water to enter a cell via osmosis
- so glycogen can store glucose (i.e. energy) without endangering the cell
- there is no fixed size
- so it’s easy to add/remove extra glucose molecules
- this can be done at any of the ends of a molecule (regardless of whether they have branches or not)
lipids
- diverse group of carbon compounds
- all are insoluble in water
- fats are liquid at body temp but solid at room temp
- oils are liquid at both body temp and room temp
how are triglycerides formed?
- combining 3 fatty acids with 1 glycerol
- each of the fatty acids is linked to the glycerol via a condensation rxn
- they are linked via ester bonds
ester bond
- bond formed when an acid reacts with the OH group in an alcohol
- in triglycerides it’s between -COOH (fatty acid) and -OH (glycerol)
function of triglyceride
- energy store
- energy from them can be released via aerobic cell respiration
- they are also used to insulate heat (e.g. in the blubber of Arctic aquatic mammals)
where are lipids stored?
- specialized cells called adipose tissue
- they’re located right below the skin and around some organs (e.g. kidneys)
lipids vs carbohydrates
- compared to carbohydrates, at the same mass lipids can release double the amount of energy in cell respiration
- fats form pure droplets in cells (no water) while carbohydrates are associated with water (each glycogen molecule is bonded to 2 water molecules)
- lipids are poor heat conductors so they can insulate heat
- lipids are liquid at body temp so they can act as shock absorbers
- this is why they are stored in subcutaneous adipose tissue near the skin, and around important organs
why is glycogen still stored if lipids are so efficient?
- lipids are more ideal for long-term storage
- but glycogen can be broken down to glucose and transported easily and rapidly
- fats can’t be mobilized as rapidly
- also, glucose can be used in both aerobic and anaerobic respiration while fats can only be used in aerobic
- so they are efficient for short-term storage
- the liver stores 150 g of glycogen and some muscles store 2% glycogen by mass
BMI formula
BMI = mass (in kg) / height^2 (in metres)
the unit is kg m^-2
nomogram
type of chart used to calculate BMI
obesity
- due to excessive food intake and insufficient exercise
- this causes accumulation of fat in the adipose tissues
- obesity increases the risk of conditions (e.g. coronary heart disease)
- significantly reduces life expectancy
structure of fatty acids
- unbranched chain of C atoms
- with H atoms linked to them by single covalent bonds
- at one end of the chain there’s an acidic part (carboxyl group, -COOH)
- there are usually 14-20 C atoms
saturated fatty acids
- C atoms are bonded to each other via single bonds
- so it contains as much hydrogen as possible (thereby being ‘saturated’)
unsaturated fatty acids
- 1 or more double bonds between C atoms
- it doesn’t contain as much H as its potential (thereby being ‘unsaturated’)
- fatty acids with only 1 double bond are called ‘monounsaturated fatty acids’
- fatty acids with > 1 double bond are called ‘polyunsaturated fatty acids’
types of unsaturated fatty acids
- cis-fatty acids
- trans-fatty acids
cis-fatty acids
- AKA oils
- when hydrogen atoms are on the same side of the 2 C atoms that are double bonded, the molecule is called a cis-fatty acid
- there is a bend in the hydrocarbon chain at the double bond
- due to this, triglycerides containing cis fatty acids are not as good at packing together in regular arrays compared to saturated fatty acids
- so their melting points are lower
- they’re liquid at room temp
trans-fatty acids
- when hydrogen atoms are on opposite sides of the 2 C atoms that are double bonded
- they don’t have a bend in the hydrocarbon chain at the double bond
- higher melting point
- solid at room temp
- they’re produced artificially in by partial hydrogenation of vegetable/fish oils
- this is done to produce solid fats for margarine and other processed foods
health risks of fats
- coronary heart disease: coronary arteries become partially blocked by fatty deposits
- this leads to blood clot formations and heart attacks
- a positive correlation between saturated fatty acid intake and CHD rates has been found
- but this doesn’t prove the existence of a causation link
- the Maasai tribe in Kenya have a saturated fats-rich diet but CHD rates are exceedingly low among them
- furthermore, diets rich in olive oil (cis-monounsaturated fatty acids) are staples in Mediterranean countries but their populations have low CHD rates
- there’s also a positive correlation between trans-fat intake and CHD rates
- a tentative causation link has been established
- because fatty deposits in the diseased arteries of CHD patients have been found to contain high concentrations of trans-fats
polypeptides
- amino acid chains
- made by linking amino acids together via condensation reactions
- this happens on ribosomes via translation
- polypeptides are the main components of proteins
- in many proteins, they are the only component
- some proteins contain only 1 polypeptide while other proteins contain 2+
production of polypeptides from amino acids
- condensation reaction between two amino acids
- an OH (from -COOH/carboxyl group) of one amino acid and a H (from -NH2/amine group) of another amino acid are removed to form H2O
- a peptide bond forms between the 2 amino acids
dipeptide
2 amino acids that are bonded together by a peptide bond
oligopeptides
chains that are made up of < 20 amino acids
similarities between amino acids in ribosomes
- C atom in the center
the C atom is bonded to:
- an amine group
- a carboxyl group
- a H atom
- an R (variable) group
polypeptide diversity
- and ribosomes link amino acids together one at a time
- amino acids can be linked together in any sequence
- the number of possible amino acid sequences can be calculated with dipeptides (i.e. 20^(number of amino acids))
- 20 coz most organisms make proteins using the same 20 amino acids
role of genes in polypeptide production
- the number of possible sequences is infinite
- but only a small percentage of those are produced by living organisms
- the information needed to code polypeptides are stored in the base sequence of a gene
- 3 bases of a gene is needed to code for 1 amino acid in a polypeptide (e.g. if a polypeptide needs 400 amino acids, the gene sequence will theoretically have 1200 bases)
- however, the gene sequence is always longer in reality (due to extra start/stop sequences in the beginning, end, and at certain points in the middle)
how many polypeptides are needed to synthesize a protein?
- some proteins are single polypeptides
- others require more polypeptides to be linked together
lysozyme
- enzyme in secretions (e.g. in nasal mucus and tears)
- kills some bacteria by digesting peptidoglycan in their cell walls
peptidoglycan
a component of bacterial cell walls
structure of integrin
- membrane protein with 2 polypeptides
- both polypeptides have a hydrophobic section (which is embedded in the membrane)
- so the 2 polypeptides can either be adjacent to each other or can unfold/move apart when they’re working
function of integrin
- membrane protein
- used to make connections between structures inside and outside a cell
structure of collagen
- 3 long polypeptides
- wounded together to form a rope-like molecule
- collectively, they have greater tensile strength together than they would have individually
- the winding allows a bit of stretching to occur
- this reduces the chance of the molecule breaking
function of collagen
- structural protein in tendons, ligaments, skin & blood vessel walls
- provides high tensile strength but limited stretching/flexibility
structure of hemoglobin
- 4 polypeptides
- with associated non-polypeptide structures
- collectively, these 4 polypeptides interact to transport oxygen more effectively than they would have separately
function of hemoglobin
- transport protein in RBCs
- binds oxygen in the lungs and releases them in tissues with a reduced oxygen concentration
protein conformation
- 3-D structure of proteins
- determined by the amino acid sequence of a protein as well as its constituent polypeptides