Biological Molecules Flashcards
Elements most common in biological molecules
Carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), sulfur (S)
Elements in carbohydrates
Carbon, hydrogen, oxygen
Elements in lipids
Carbon, hydrogen, oxygen
Elements in proteins
Carbon, hydrogen, oxygen, nitrogen, sometimes sulfur
Elements in nucleic acids
Carbon, hydrogen, oxygen, nitrogen, phosphorus
Element
A substance composed of one type of atom
Molecules
These contain more than one atom and can be either elements
Compounds
Contain either one ionic bond between element or covalent bonds
What structure do ionic compounds have?
Giant lattice structures
Cations
Positively charged ions
Anions
Negatively charged elements
Ions involved in nervous impulse transmission
Calcium, sodium and potassium
Ion involved in determination of pH in solutions
Hydrogen, hydroxide
Ion which is a source of nitrogen for plants
Ammonium, nitrate
Ions - transport of respiratory gases
Hydrogen carbonate, chloride
Ion - nucleic acid band ATP formation
Phosphate
Hydrogen bonding
- Water molecules are polar (i.e. the oxygen atom has a partial negative charge and the hydrogen atoms have partial positive charges)
- As a consequence, the oxygen atom in a water molecule is attracted to hydrogen atoms in neighbouring molecules - this attraction is called a hydrogen bond
Water - good solvent
- Polar water molecules attract (and dissolve) other polar molecules and ions
- Water transports dissolved solutes (e.g. in blood and phloem). Chemical reactions occur in water
Water - high specific heat capacity
- A relatively large amount of energy is required to increase water temperature
- Thermal stability in aquatic environmment and inside organisms
Water - high heat of vapourisation
- Additional energy is needed to change water from liquid to gas
- Thermoregulation - sweating and panting can cool an organism when water on the body is evaporate
Water - cohesion
- Hydrogen bonds cause water molecules to be attracted to each other and flow together
- Surface tension - small organisms can move on the water surface
Water - low density solid (i.e. ice)
- The crystalline structure in ice is less dense than liquid water
- Provides an insulating layer for aquatic habitats in cold climates. The ice surface provides a habitat for some organisms (e.g. polar bears)
Glucose
- 6 carbon atoms (hexose sugar)
- a-glucose - a substrate in respiration (hydroxyl group on the bottom)
- B-glucose - polymerise to form cellulose (hydroxyl group on the top)
Ribose
- 5 carbon atoms (pentose sugars)
- The sugar in RNA nucleotides
Disaccharides
- Two monosaccharides can react together to form a disaccharide - this reaction is called a condensation reaction; it creates a glycosidic bond between the two monosaccharides and produces water
- Disaccharides can be broken down to reform the original two monosaccharides in a hydrolysis reaction
Monosaccharides to disaccharides products
- Glucose + glucose = maltose
- Glucose + galactose = lactose
- Glucose + fructose = sucrose
Glycogen
- Monomer - a-glucose
- Type of glycosidic bonds - 1,4 and 1,6 links
- Branching - yes
- Helical - yes
- Functions - carbohydrate storage in animals
- Properties that suit function - Insoluble, compact due to branching, the number of points at which glucose can be released through hydrolysis is increased by branching
Amylose
- Starch
- a-glucose
- 1,4 links
- No branching
- Helical structure
- Function - carbohydrate storage in plants
- Properties that suit function - Amylose is soluble, helices and branching make starch compact, branching in amylopectin increases the number of points at which glucose can be released through hydrolysis
Anylopectin
- a-glucose
- 1,4 and 1,6 links
- Branching
- No helical structure
- Function - carbohydrate storage in plants
- Properties that suit function - amylose is insoluble, helices and branching make starch compact, branching in amylopectin increases the number of points at which glucose can be released through hydrolysis
Cellulose
- B-glucose
- 1,4 links
- No branching
- No helical structure
- Function - structural support in plant cell walls
- Properties that suit function - insoluble, cross links (hydrogen bonds between chains) increase strength
Benedict’s test
- Used for reducing sugars (e.g. monosaccharides, lactose and maltose) - mix with Benedict’s reagent in boiling tube and heat
- Non-reducing sugars (e.g. sucrose) - after a negative result with the Benedict’s test, boil with dilute HCl. Conduct the Benedict’s test a second time
- Negative result - blue
- Positive result (i.e. the carbohydrate is present) - low = green, medium = orange, high = red
Iodine test
- Starch
- Mix iodine/potassium iodide solution for with the sample
- Negative result - yellow/brown
- Positive result - purple/black
Polysaccharides
- Polysaccharides are long carbohydrate molecules (polymers) formed when many monosaccharides bond together in condensation reactions
- Examples: glycogen, amylose, amylopectin, cellulose
Colorimetry
A colorimeter can be used to to assess the concentration of sugar in a solution
Colorimeter method
- Insert a red filter
- Use a cuvette of distilled water (calibrate) the colorimeter
- Construct a calibration curve for each solution, and plot a graph of transmission
NOT FINISHED
Biosensors
These represent a method for determining the concentration of sugars in a solution. These machines require a recognition molecule that will bind the carbohydrate being assessed. The extent to which the carbohydrate binds determines the reading on the biosensor display. Unlike the Benedict’s test, biosensors detect specific sugars (e.g. glucose)
Triglyceride
- Glycerol (head) and 3 tails attached via ester bonds
- Properties - compact and insoluble
- Roles - Energy storage and insulation
Phospholipid
- Properties - Hydrophilic head and hydrophobic tails
- Roles - Membrane structure
Cholesterol
- Properties - small; both hydrophilic and hydrophobic
- Role - membrane stability and steroid hormones
Synthesis of triglycerides
A triglyceride comprises a glycerol molecule and 3 fatty acids. Each fatty acid undergoes a condensation reaction with one of the OH (alcohol) groups in glycerol. A hydrolysis reaction breaks down the triglyceride into the original glycerol and fatty acids
Saturated vs unsaturated
- Fatty acids can be either saturated (no C=C double bonds) or unsaturated (at least one C=C double bond)
- Evidence exists that excessive consumption of saturated triglycerides raises the risk of coronary heart disease
Emulsion test
- Mix your sample with ethanol
- Mix with water and shake
- The formation of a white emulsion on top of the solution indicates the presence of a lipid
Amino acid
- All amino acids contain a central carbon atom, an amine group, a carboxyl group, and a hydrogen atom
- The identity of an amino acid is determined by its R group; this is different in each of the 20 amino acids found in organisms
Rf value calculation
Rf = distance moved by the amino acid/distance moved by the solvent
Polypeptides
Amino acid monomers are joined by condensation reactions. A peptide bond is formed between two amino acid, producing a dipeptide. A polypeptide is formed when many amino acids bond together. This occurs at ribosomes during translation. Peptide bonds are broken in hydrolysis reactions
Levels of protein structure
- A polypeptide produced during translation is called the primary structure of a protein
- However, proteins are move complex than a sequence of amino acids in a chain
- They fold and coil into shapes specific to their functions; these are called secondary and tertiary structures
Bonds involved in secondary structure, and shape
Hydrogen bonds, a-helix or B-pleated sheet
Bonds involved in tertiary structure, and shape
- Hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions
- A specific 3D shape
Quaternary structures
- Produced when two or more polypeptides associate, for example, haemoglobin consists of 4 polypeptide subunits and collagen comprises 3 polypeptides
- Prosthetic groups can also be present in quaternary structures
Globular proteins
- Shape: compact and spherical
- Bonding/structure: hydrophilic R-groups on the outside, and hydrophobic R-groups on the inside
- Water solubility: soluble
- Conjugation (i.e. in the presence of a prosthetic group): sometimes
- Functions: enzymes (e.g. catalase), hormones (e.g. insulin), membrane proteins, antibodies, transport proteins (e.g. haemoglobin, which has 4 polypeptides in its quaternary structure, each carrying a haem prosthetic group)
Fibrous proteins
- Shape: long and linear
- Bonding/structure: a limited range of amino acids, often with a repetitive sequence, oraganised and strong structures
- Water solubility: insoluble
- Conjugation (i.e. in the presence of a prosthetic group): no
- Functions: structural roles, for example, keratin (in skin, hair and nails), collagen (in connective tissues in tendons, skin and ligaments)
