2: Molecular biology Flashcards
What must cells of living organisms do to stay alive?
- Replicate their DNA
- Cell respiration
- Synthesise their own proteins
- Photosynthesis
What is metabolism?
The sum of all chemical reactions in an organism
What are the main classes of carbon compounds?
Carbohydrates, lipids, proteins and nucleic acids
Carbohydrate profile
- Consists of C, H and O
- Functions as a source of energy
- Important as a recognition molecule (glycoproteins) and as a structural component (DNA/RNA)
Monosaccharide –> starch –> granules in chloroplasts
Lipid profile
- Contain C, H, and O
- Non-polar, hydrophobic
- Major component of cell membranes
- Function as long-term energy storage (fats and oils)
- Function as a signalling molecule (steroids)
Fatty acid –> triglyceride –> adipose cells
Protein profile
- Contain C, H, O and N (and S)
- Consist of amino acids arranged into linear chain(s)
- Function as regulatory molecules involved in catalysis (all enzymes are proteins)
- Function as structural molecules and for cellular signalling
Amino acid –> polypeptide –> intermediate filament
Nucleic acid profile
- Contain C, H, O, N and P
- Genetic material of all cells and determines the inherited features of an organism
- DNA: code for protein assembly, RNA: manufacturing of proteins
Nucleotide –> DNA –> chromosome
What is a catalyst?
A substance that increases the rate of a reaction and is reusable for many reactions
What is an enzyme?
A protein molecule which catalyses only one reaction
What is a chain of reactions?
When the product of one reaction is catalysed by another enzyme
What is anabolism?
Metabolic reactions that build up complex molecules (macromolecules) from simpler ones (monomers) via condensation reactions
What is a condensation reaction?
Reaction that occurs when monomers are covalently joined and water is produced as a by-product
Types of condensation reactions for the four organic compound types:
- Monosaccharides: glycosidic linkages
- Amino acids: peptide bonds
- Fatty acids: ester linkages
- Nucleotides: phosphodiester bonds
What is catabolism?
Metabolic reactions that break complex molecules (macromolecules) into simpler molecules (monomers) via hydrolysis reactions
What are hydrolysis reactions?
Reactions that require water molecules to break the bonds within the polymer
Why is carbon the basis of organic life?
Can form four covalent bonds which are stable
What is urea?
A component of urine which is produced in the liver tissue of many animals. Can be synthesised from inorganic compounds, falsifying the theory of vitalism (meaning it can only be made in living organisms)
Structure of organic monomers
- Monosaccharides: ring structures
- Fatty acids: chains of hydrocarbons (unsaturated/saturated)
- Amino acids: anime group, hydrogen, carboxyl group and variable group (R)
- Nucleotides: pentose sugar, phosphate group and nitrogenous base
Water profile
- Polar (contains non-equally shared elections)
- Molecules can be pulled together by hydrogen bonds
What are the properties of water?
It is: cohesive, adhesive, thermal and solvent
Water cohesiveness explanation
Cohere due to hydrogen bonds between molecules.
Example: Columns of water in xylem vessels rarely break despite suction forces.
Water adhesiveness explanation
Dipolarity of water molecules adheres water to polar surfaces.
Example: Keeping cell walls moist by drawing out water from xylem vessels due to adhesive forces between water and cellulose.
Water thermality explanation
Hydrogen bonding causes water to have high melting and boiling points, high latent heat of vaporization and high specific heat capacity.
Example: Allows water to be stable (temp change relatively slow, effective coolant in humans)
Water solubility explanation
Dipolarity allows many substances to dissolve in water, including ions and polar molecules.
Example: Water is usually the medium for metabolic reactions.
How is water used as a coolant in sweat?
- Hydrogen bonds between water molecules must be broken upon vaporization
- Energy is taken from body heat (heat energy) to break the bonds
- Sweat is secreted by glands in the skin
- The body heat is absorbed by the sweat (water)
- The temperature of the tissue decreases
What does it mean to be hydrophilic?
To be polar and water soluble
What does it mean to be hydrophobic?
To be non-polar and water insoluble
Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood
- Glucose and amino acids: polar, soluble due to positive and negative charges
- Sodium chloride: polar, transported as ions (split by water)
- Cholesterol: non-polar, attaches to polar proteins, hydrophilic end is soluble
- Lipids: non-polar, attaches to polar proteins, carried by lipoprotein complexes
- Oxygen: non-polar, carried by haemoglobin
Comparison of thermal properties of water with methane
Water has a higher melting point, specific heat capacity, latent heat of vaporization and boiling point than methane. This is because hydrogen bonds restrict the movement of water molecules and much heat energy is needed to break these bonds.
Outline the role of condensation and hydrolysis in the relationship between amino acids and polypeptides.
- Condensation is two molecules joined by a covalent bond with the loss of a water molecule.
- An example condensation is the formation of a peptide bond between amino acids.
- The covalent bond forms between the carboxyl end of one amino acid and the amino end of other.
- Many amino acids joined by condensation form a polypeptide.
- Hydrolysis is the addition of water to break a large molecule into smaller ones.
- Polypeptides are broken down into amino acids by hydrolysis.
Main functions of carbohydrates
- Monosaccharides: energy source
- Disaccharides: transport form
- Polysaccharides: storage form, cell recognition
Structure and function of cellulose and starch in plants and glycogen in humans
- Cellulose: Linear form, alternating orientation, beta-D-glucose subunits, 1-4 bonds, commonly used by plant cells within plant cell walls
- Starch: Linear and helical form (amylose) / highly branched form (amylopectin), same orientation, alpha-D-glucose subunits, 1-4 bonds (amylose) / 1-4 and 1-6 (amylopectin), commonly used by plants to store glucose for later use
- Glycogen: Highly branched form, same orientation, alpha-D-glucose subunits, 1-4 and 1-6 bonds, commonly used by humans to store glucose for later use
Different forms of fatty acids
- Saturated: all carbon atoms connected by single covalent bonds, max hydrogen
- Unsaturated: contains one or more double bonds, hydrogen can be added (mono/poly)
Different forms of unsaturated fatty acids
- Cis isomers: H-bonds on same side of double bond, healthier
- Trans isomers: H-bonds on opposite sides of double bond, unhealthy (trans fats)
Health risks of trans fats and saturated fatty acids
- Both raise cholesterol levels
- Cannot dissolve in blood, must be packages with proteins to form lipoproteins for transport
- Trans fats increase LDL levels and decrease HDL levels, and saturated fats increase LDL levels
- High cholesterol leads to the hardening and narrowing of arteries, resulting in CHD
- High concentrations of trans fats have been found in the arteries of patients who died from CHD
- Positive correlation between saturated fatty acid intake and rates of CHD
Main types of lipids and their structures
- Triglycerides: made from three fatty acids and one glycerol by condensation reactions
- Phospholipids: made from two fatty acids and one glycerol, with a phosphate ground instead of the third fatty acid
- Steroids: made from a quadruple ring structure
Why are lipids more suitable for long-term energy storage in humans than carbohydrates?
- The amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates
- The same amount of energy stored as a lipid rather than a carbohydrate can be stored in half the body mass
- Lipids are six times more efficient in the amount of energy that can be stored per gram of body mass due to no association with water
Body mass index formula
(weight in kilograms)/(height in meters)^2
How many animo acids are there?
20
What are the amino acid variations/exceptions?
Selenocysteine and pyrrolysine
Why do animo acids give a huge range of possible polypeptides?
The side chains will have distinct chemical properties (charged, non-polar, polar) causing the protein to fold and function differently
What is a gene?
A sequence of DNA which encodes a polypeptide sequence
How is a gene sequence converted into a polypeptide sequence?
Transcription and translation
Exceptions to one gene coding for one polypeptide:
- Genes may be alternatively spliced to generate variants
- Genes are transcribed but never translated
- Genes may be mutated
When is a single polypeptide considered a protein?
When it does not require one or more polypeptides to begin its function
Examples of proteins:
- Myoglobin: single polypeptide found in muscle cells which can bind to an oxygen molecule that is released after hard exercise
- Haemoglobin: composed of four polypeptides found within red blood cells that can bind to four oxygen molecules, only when all four polypeptides are bonded to each other
The three-dimensional conformation of a protein
- Primary structure: order of the amino acid sequence
- Secondary structure: alpha helices (coiled) and beta-pleated sheets (directionally-oriented staggered strand) resulting from hydrogen bonds forming between amine and carboxyl groups
- Tertiary structure: determined by the interactions between the variable side chains
- Quaternary structure: proteins that consist of more than one polypeptide chain linked together
How is the globular structure of proteins stabilised?
Intramolecular bonds
Examples of proteins in living organisms and their functions:
- Structure: collagen, spider silk
- Hormones: insulin, glucagon
- Immunity: immunoglobulins
- Transport: haemoglobin
- Sensation: rhodopsin
- Movement: actin, myosin
- Enzymes: rubisco, catalase
Rubisco function
- Enzyme that catalyses photosynthesis
- Fixes CO2 from the atmosphere
Insulin function
- Hormone dissolved in blood
- Binds to insulin receptors in the membranes of body cells
- Cells absorb glucose and lower blood glucose concentration
Immunoglobin function
- Antibody that binds antigens on pathogens
- Immune system produces huge range of immunoglobins with different binding sites
- Allows specific immunity against different diseases
Rhodopsin function
- Pigment that makes rod cells of retina light-sensitive
- Non-amino acid part absorbs photon of light, sending nerve impulse
Collagen function
- Structural protein
- Prevents tearing in skin
- Prevents fractures in bones
- Gives tensile strength to tendons and ligaments
Spider slik function
- Structural protein
- High tensile strength
- Resists breakage
What is denaturation?
A structural change in a protein that results in the loss of its biological properties
What causes the denaturation of proteins?
- Heat breaks intramolecular bonds (due to vibrations), which is almost always irreversible
- Heating an egg white denatures albumin proteins, making them insoluble and solid
- pH must stay around the optimum level to keep its conformation normal
- Deviating the pH too far from the optimum will break intramolecular bonds
What is a proteome?
All of the proteins produced by a cell, a tissue or an organism
What is an enzyme?
A protein with a specific three-dimensional shape, where part of that is an area called an active site
What is a substrate?
A reactant in an enzyme-catalysed reaction
What does it mean to be substrate-specific?
When molecules other than the substrate do not fit or are not attracted so do not bind
