Biological Molecules Flashcards
Covalent bond
A shared pair of electrons between atoms is called a covalent bond
- carbon forms 4 covalent bonds
Which of these is not a polymer:
A- Carbohydrate
B- Protein
C- Lipid
D- Nucleic acid
C- lipid
Because while they are made of lots of smaller molecules, they are very different to each other
Monomer and polymer: carbohydrates
Monomer
Monosaccharides- glucose (sugars)
Polymer
Polysaccharides- starch, cellulose, glycogen
Monomer and polymer: proteins
Monomer
Amino acids
Polymer
Polypeptides & proteins
Monomers and polymers: Nucleic acids
Monomer
Nucleotides
Polymer
DNA & RNA
Condensation reaction
Joins molecules together
- a water molecule is released
- a covalent bond is formed
- a larger molecule is formed
Hydrolysis reaction
Splitting molecules apart
- water molecule is used
- covalent bond is broken
- smaller molecule is formed
Hydrogen bonds
Form when a slightly positive and negative charge come close
- weak bonds and easily broken
- represented as a dashed line
General formula for carbohydrate
Cn(H2O)n
- always 2 more hydrogen
- usually same C and O
Simple sugars/monosaccharides properties
- contains 3-6 carbons
- soluble in water
- sweet tasting
- form crystals
Which is the most common sugar?
A- Triose sugar (3)
B- Pentose sugar (5)
C- Hexose sugar (6)
C- Hexose sugar (6 carbon monosaccharide)
What is the bond between monosaccharides called
Glycosidic bond
Alpha glucose
OH below
(Google picture :))
Beta glucose
OH above
Maltose
Glucose + glucose
Sucrose
Glucose + fructose
Lactose
Glucose + galactose
Glycosidic bonds in: maltose, lactose, sucrose
Maltose= alpha 1,4 glycosidic bonds
Lactose= beta 1,4 glycosidic bonds
Sucrose= alpha 1,2 glycosidic bonds
Starch: Amylose
- unbranched
- compact
- insoluble
- coiled
iodine makes it go from orange to blue-black
Starch: amylopectin
Branches of a-glucose chains with 1,4 glycosidic bonds joined at ends to another chain by 1,6 glycosidic bonds
- highly branched - can be hydrolysed quickly
- 1,4 bonds between monomers, and 1,6 bonds at branch
What 2 molecules make up starch
- amylose
- amylopectin
Glycogen
Energy store in animals
- alpha glucose
- highly branched - easily hydrolysed
- very compact - good storage molecule
- 1,4 and 1,6 glycosidic bonds
- insoluble in water - do not reduce WP of cells
Cellulose
Polysaccharide found in plants
- main structural component of cell walls
- beta glucose
- joined together by 1,4 glycosidic bonds
- each molecule rotated 180° to each other
- high tensile strength due to many hydrogen bonds that form between the long chains of beta glucose molecules
What is the main component of cell walls in bacteria
Peptidoglycan
What molecule is found in the exoskeleton of insects
Chitin
Reducing sugar
One that reduces another compound and is oxidised
Non reducing sugar
Can’t donate electrons and cannot be oxidised
What are some reducing sugars
- All monosaccharides
- some disaccharides
E.g. glucose, fructose, ribose, maltose
What is not a reducing sugar
SUCROSE
Benedict’s test for reducing sugars
- Sample is placed in boiling tube. For a solid, grind/blend and place in water
- Add an equal volume of Benedict’s reagent
- Heat the mixture gently in a water bath for 5 minutes
Positive result- orange/red
Benedict’s test for non reducing sugars
- Negative test for reducing sugars
- Prepare a fresh sample with water
- Add acid
- Boil
- Add alkali (to neutralise the acid)
- Add Benedict’s reagent
- Heat
Positive result- orange/red
Colorimeters
An instrument that beams a specific wavelength of light through a sample and measures how much of this light is absorbed
Can measure:
- absorbance (how much light is absorbed)
- transmission (how much light is transmitted)
Must be calibrated before taking measurements
- blank placed into colorimeter- should read as 0 as no light absorbed
Results then used to plot a calibration/standard curve
Serial dilution
Created by taking a series of dilutions off a stock solution. The concentration decreases by the same quantity between each test tube
Comparison can be:
- visual
- measured through calibration curve
- measures using a colorimeter
Why is water important
• component of living organisms
• Cooling function
• Habitat
• Transport systems
• Reactant e.g. photosynthesis
• Photosynthesis
Structure of water
2 hydrogen ions (+) and 1 oxygen (-)
Why is water a good solvent
- Polarity
- Hydrogen bonding
- Bond angle
Polar & non polar
Polar- will dissolve
Non polar- won’t dissolve
Polarity
- Each hydrogen atom shares its electron with the atom of oxygen
- Because the oxygen atom has more protons than hydrogen atoms, it pulls more strongly on these free electrons
Hydrogen bonding
• when water molecules get closer together, the oppositely charged parts of the molecule attract each other, forming hydrogen bonds
• We call this cohesion
• At room temperature, water forms a lattice
Cohesion between water molecules
- at air water surface, cohesion produces surface tension
- within a column of water, cohesion explains why the column doesn’t break
E.g. xylem during transpiration
Properties of water
- universal solvent
- liquid at room temperature
- specific heat capacity
- latent heat of vaporisation
- latent heat of fusion
- density
- capillarity / cohesion
- surface tension
Universal solvent
Because it has polar molecules, water is attracted to any substance that is also polar substances that can become part of water hydrogen bonded structure and will dissolve (hydrophilic)
Triglycerides and large polymers won’t dissolve
(Also non polar)
Liquid at room temperature
Helps cells transport and use substances like oxygen or nutrients
Specific heat capacity
Lots of energy needed to change the temperature of water
- therefore environment outside of organisms resist temperature changes that could cause it damage e.g. lake
Latent heat of fusion
High latent heat of fusion prevents the liquid environment of cells from freezing and tearing the cells apart, as liquid water temperatures can drop to around -10°C before it begins to freeze
Latent heat of vaporisation
Lots of energy is needed to evaporate
- it draws the thermal energy from the surface, cooling it as the water evaporates from it (e.g. sweating)
Density
- density decreases when freezing as molecules spread out
- ice forms on the surface of water which means that organisms can live below
- ice insulates the water below, meaning aquatic organisms don’t freeze and can move around
Capillarity/cohesion
• adhesion makes water stick to other polar substances, effectively making it ‘wet’
• Upward movement in xylem of tall plants, such as trees, against gravity
• Also important is waters transparency
• Water being transparent and colourless transmits sunlight, enabling aquatic plants to photosynthesise, and enabling us to see, as our eyes are coated in water
Surface tension
pond skaters and other in class ‘insecta’ are able to glide on surface of ponds
• Water moves up xylem tissue without breaking apart
Basic structure of amino acid
Amine group
Carboxyl group
H. H. =O
N ———C ——— C
H. R. -OH
Elastin
Cross linking and coiling for strength
- skin, lungs, bladder, blood vessels
Pepsin
Single polypeptide chain, 327 amino acids
- symmetrical tertiary structure
- mainly acidic R groups (stable)
Conjugated protein
One with a prosthetic group (non protein component)
Function of proteins
• structural- muscle, bone
• Carrier and channel proteins
• All enzymes
• Many hormones
• Antibodies
Fibrous proteins
• Structural role
• relatively long and thin
• Insoluble in water
• Metabolically inactive
E.g. collagen, keratin, elastin
Globular proteins
• Metabolic role
• relatively spherical in shape
• Interact with water
E.g. haemoglobin, insulin, pepsin
Collagen
Structural role
- fibrous protein
- high tensile strength
- not elastic
- flexible
- insoluble
Haemoglobin
- Globular protein
- soluble
- has a haem group
- metabolic role
Primary structure
- sequence of amino acids bonded by covalent peptide bonds
- specific for each protein
Only peptide bonds
Secondary structure
- occurs when the negatively charged nitrogen and oxygen atoms interact with positively charged hydrogen atoms to form hydrogen bonds
2 shapes can form:
- alpha helix- Occurs when hydrogen bonds form between every fourth peptide bond
- beta pleated sheets- forms when the protein folds so that 2 parts of the polypeptide chain are parallel to each other
Most fibrous proteins have secondary structures e.g. collagen, keratin
Has peptide and hydrogen bonds
Tertiary structure
Further conformational change of secondary structure leads to additional bonds forming between the R groups
- Tertiary structure determines function
The additional bonds are:
- Hydrogen
- Disulfide
- ionic
- weak hydrophobic interactions
Most common is globular proteins
Quaternary structure
Exists in proteins that have more than one polypeptide chain working together as a functional macromolecule e.g. haemoglobin
- each polypeptide chain in the quaternary structure is referred to as a subunit of the protein
Lipids
- fats solid at room temp
- oils liquid at room temp
- insoluble
Triglycerides, phospholipids, sterols
What so lipids dissolve in
Organic solvents e.g. alcohol
Do not dissolve in water
Role of lipids in organisms
• solvent
• Storage
• Thermal insulator
• Energy source
• Waxy cuticle of leaves- prevent it drying out
• Myelin sheath of neurones- electrical insulation
• Phospholipid bilayers
• Stored as adipose tissue in cells
• Organ cushioning
Triglycerides
- non polar, hydrophobic molecules
- made of glycerol and 3 fatty acids
Fatty acid
A molecule with a hydrocarbon chain and carboxylic acid (contains carboxyl group (COOH)
Shorthand chemical formula for fatty acid is RCOOH
Ester bond
the bond formed when an organic acid such as a fatty acid joined to an alcohol such as glycerol by a condensation reaction (a triglyceride with 3 fatty acids joined to a glycerol has 3 ester bonds)
Saturated and unsaturated fatty acid
Saturated
Have no double bonds between carbons
Unsaturated
At least one double bond between carbons
Monounsaturated: one double carbon bond along the molecule
Polyunsaturated: multiple double carbon bonds along the molecule
Presence of a double bond causes kinks/bends - can’t be closely packed making them liquid at room temp.
Triglycerides vs phospholipids
Similarities
• both contain a glycerol base
• Both contain fatty acid
• Both lipids
• Both have ester bonds holding fatty acids to glycerol
Differences
• phospholipid has 2 fatty acids whereas triglyceride has 3
• Phospholipid has one phosphate ion bonded to the glycerol
Phospholipids
Phosphate head is polar- soluble in water (hydrophilic)
Fatty acid tails are non polar and therefore insoluble in water (hydrophobic)
Phosphate— glycerol — 2 fatty acids
Sterols
Lipid structure (not fat or oil)
- manufactured in liver and intestines
- increases membrane stability
- regulation - fluid at low temperatures and stops them becoming too fluid at high temperatures
Examples of sterols
- cholesterol
- vitamin D
- steroid hormones
- bile
Why is data and nutritional studies often flawed
• people digest and metabolise food differently and usually they don’t study the long term impacts
• People have different diets
• Who’s done the study, are they biased e.g. only looking for results to back up what they want
• May only study one group of people e.g. kids
Emulsion test- lipids
- Add 2cm3 of food sample to test tube and grind sample if solid
- Add 5cm3 of ethanol
- Add 5cm3 of water and shake
Positive = cloudy emulsion
Negative = clear
Biuret test- proteins
- Add food sample to test tube
- Add Biuret solution (sodium hydroxide + copper surface)
Positive = purple
Negative = blue
Thin layer chromatography (TLC)
Technique to analyse small samples via separation
- speed depends on solubility and polarity
- use UV light to see dots that are white/transparent
non polar will travel quickly
polar will stick to surface and travel slowly
Stationary phase
Not moving
- thin metal sheet coated in silica or alumina
- molecules stick to the surface
Mobile phase
Moving
- flows over the stationary phase
- polar solvents: water, alcohol
- non polar solvents: alkanes
Rf value
Distance travelled by pigment divided by the disatnce travelled by the solvent
distance traveled by solute
Distance traveled by solvent
Ways to see the chromatogram
Ninhydrin
- used to see amino acids
- see as brown or purple spots
UV light
Iodine
- enclose the plate with a few iodine crystals
- iodine forms a gas which binds to the molecules in each of the spots
Advantages of TLC
• The mobile phase moves more quickly through the stationary phase
• The mobile phase moves more evenly through the stationary phase
• There are a range of absorbencies for the stationary phase
• Show a greater separation of components in the mixture
Elements of carbohydrate, lipids, proteins, nucleic acids
Carbohydrates + lipids =C,H,O
Amino acids= C, H, O, N
Nucleic acids= C, H, O, N, S
