Chapter 3 Biological Molecules Flashcards
Elements present in: Carbohydrates Lipids Proteins Nucleic acids Phospholipid
Carbon, hydrogen, oxygen
Carbon, hydrogen, oxygen
Carbon, hydrogen, oxygen, nitrogen, sulphur
Carbon, hydrogen, oxygen, nitrogen, phosphorous
Carbon, hydrogen, oxygen, phosphorous
What is the structure of water?
- H-O-H
- the distribution of electrons between the covalently bonded atoms is not equal
- causing a slightly negative charge on oxygen and slightly positive charge on hydrogen
- the negative oxygen attracts the hydrogen of other water molecules
- this attraction is hydrogen bonding
Why do hydrogen bonds give water a high specific heat capacity and latent heat?
The hydrogen bonds can absorb a lot of energy
It takes a lot of energy to heat the hydrogen bonds
It takes a lot of energy to break the hydrogen bonds between water
- when sweat evaporates it cools the skin
What is cohesion (water)?
Cohesion is the attraction between molecules of the same type
Water is very cohesive because it is polar
This helps water to flow - making it good for transport
Causes water to move as a mass
Why does waters polarity make it a good solvent?
Because water is polar, the slightly negative/positive ends will be attracted to the negative and positive ions
This means the ions will get totally surrounded and dissolve
Transports useful ions around the body
Why is water less dense when it is solid?
When water freezes the hydrogen bonds fix the position of polar molecules further apart in a
Giant
Open lattice structure
Allows ice to float
What are carbohydrates?
Molecules that contain oxygen, carbon and hydrogen
Can be broken down into glucose so that energy can be transferred to ATP through respiration
What is a monosaccharide?
A single sugar unit
Glucose, sucrose, galactose, ribose
What is a disaccharide?
Formed from 2 monosaccarides
G + G = maltose
G + S = fructose
G + G = lactose
What is a polysaccharide?
Polymers made of 2 or more monosaccharides
Glycogen, starch, cellulose
Glucose
Alpha
Beta
Alpha - c1 = c4
Beta - c1 / c4
CH2OH - c6
Glucose = polar and soluble in water - hydrogen bonds between hydroxyl group and water
Alpha glucose condensation
Glucose + glucose –> maltose + water
1,4 glycosidic bond
2 hydrogens and 1 oxygen is removed to form water
Glycosidic bonds
Amylose (poly alpha glucose)
Amylopectin
Glycogen (alpha)
Cellulose (beta)
1,4 (unbranched)
1,4 + 1,6
1,4 + 1,6
1,4 (unbranched)
What is a reducing sugar?
Saccharides that can donate electrons or reduce another molecule or chemical
Monosaccharides
Testing for carbohydrates (reducing sugars)
Benedicts test
- put liquid sample in boiling tube
- add equal volume of benedicts reagent
- heat in a boiling water bath for 5 mins
- reducing sugars react with copper ions - less blue colour
- blue green yellow red precipitate colour scale
Testing for carbohydrates (non-reducing)
- sucrose is boiled with dilute HCL
- hydrolysed it into fructose and glucose which are reducing sugars
- add equal volumes of Benedicts reagent
- boiling water bath
- colour precipitate
Iodine test for starch
- add drops of potassium iodine into the solution
- If starch is present solution changes from yellow/brown to purple/black
Using the colorimeter to measure the absorbante of light by a coloured solution
Filter added Calibrated with water Benedict's test Resulting solutions filtered The transmission percentage is measured Calibration curve plotted 3/6 repeated for unknown solution
What are lipids?
Hydrogen, carbon, oxygen
Group of large complex molecules with a large molecular weight
GLYCEROL + FATTY ACIDS
Functions of lipids (7)
Membrane formation Hormone production Electrical insulators Waterproofing Thermal insulation Cushions vital organs Buoyancy
What is a triglyceride?
Glycerol + 3 fatty acids
The hydroxyl groups interact creating 3 water molecules and ester bonds between the glycerol and fatty acids
What are saturated and unsaturated fatty acids?
Saturated = no double bonds - fats = solids, closer together
Unsaturated = double bonds - oils = kink so they can’t pack as close together
What are phospholipids?
Has a phosphate group covalently attached to third hydroxyl group of the glycerol replacing a fatty acid
Glycerol + phosphate group + 2 fatty acids
What are the qualities of phospholipids?
They have a hydrophilic head and hydrophobic tails
Forms a bilayer
Separates the aqueous environment
Water soluble molecules can’t pass through
Surfactants - lower the surface tension of water
What is the structure of cholesterol?
Hydrophobic
Four carbon ring structure
Hydrocarbon chain
A hydrophilic hydroxyl group
What is the role of cholesterol?
Maintains the fluidity of the cell membrane and integrity
Stabilises the membrane
Reduces permeability to some soultes
Identification of lipids
Emulsion test
Mix sample with ethanol then with water and shake
If white emulsion forms on top a lipid is present
What are peptides?
Polymers made up of amino acids - proteins are one or more polypeptides
What are ….. amino acids?
Non essential
Essential
Conditionally essential
All have different R groups
- our body can make them from other amino acids 5
- can only be obtained from what we eat 9
- only needed by infants 6
Synthesis of peptides
Amino acids join when the amine and carboxylic acid groups react through condensation reactions
OH from carboxylic and H from amine = water
Peptide bond formed between amino acids = dipeptide
What enzyme catalyses polypeptide synthesis?
Peptidyl transferase
Separating amino acids using TLC
The rate the organic solvent moves depends on the interactions they form with the silica stationary phase
- silica gel is applied to the surface
- draw pencil line and spot the amino acids onto the line
- place plate into a jar containing the organic solvent
- remove plate and draw a line on the solvent front
- plate is sprayed with NINHYDRIN SPRAY- amino acids turn brown
- RF = component distance/ solvent front
Levels of protein structure
Primary structure
The sequence in which the amino acids are joined
Bonds
- peptide
Secondary structure
Local folding of the polypeptide chain into
alpha helix or
beta pleated sheet - parallel polypeptide chains
Bonds
- hydrogen bonds form within the amino acid chain
Tertiary structure
The folding of the protein into its final shape
- the coiling or folding of secondary structure brings the the R groups closer together so they interact
R group interactions:
- weak interactions = polar and non polar R groups- hydro
- hydrogen bonds
- ionic bonds = opposite charged R groups
- disulfide bonds = only form between R groups that contain sulfure atoms
Quaternary structure
Results from the association of two or more individual proteins called subunits
Between different protein molecules
What enzyme catalysés the breakdown of peptides?
Proteases
Identification of proteins
Biuret test
- 3cm of liquid sample is mixed with equal volumes of 10% NaOH solution
- 1% copper sulfate drops are added until the sample students blue
- leave for 5 mins
- if it changes lilac peptide bonds are present
What are globular proteins?
- compact, water soluble and spherical
- the tertiary structure is folded so that the hydrophilic r groups are on the outside of the protein and the hydrophobic r groups are kept away from the aqueous environment
Soluble in water
Examples of globular proteins… (insulin)
Insulin - hormone - regulation of blood glucose levels
Need to be soluble because are transported in the bloodstream
Fit in receptors on the cell membrane so need to be a specific shape
2 polypeptide chains with disulfide bonds
What are conjugated proteins?
Globular proteins that contain a non protein component called prosthetic group
Examples of conjugated proteins (haemoglobin)
Haemoglobin
Red oxygen carrying pigment found in blood cells
Quaternary protein made from 2 alpha and 2 beta subunits
prosthetic groups is called haem
each haem contains iron
oxygen binds to iron
Examples of conjugated proteins (catalase)
Enzyme
Quaternary group containing 4 haem groups
The presence of iron II ions allow it to interact with hydrogen peroxide and speed up its breakdown
*Hp- byproduct of metabolism that is damaging to cells
What are fibrous proteins?
Formed from long insoluble molecules - have a lot of hydrophobic r groups of amino acids in primary structure
Amino acid sequence is repetitive = organised structures
Contain a limited range of amino acids with small r groups
Not folded into complex 3D shapes unlike globular
Examples of fibrous proteins
Collage
Collagen
- made up of 3 polypeptides wound together in a rope structure
connective tissue
- bone, skin, muscle
How are nucleotides linked together?
- condensation reactions
- phosphodiester bonds formed when phosphate group on the 5th carbon of the pentose sugar forms a covalent bond with the hydroxyl group on the 3rd carbon of the adjacent sugar
DNA EXTRACTION
1) use blender to break up the sample
2) mix the sample with detergent - break the cell membrane
3) add salt - break the hydrogen bonds between DNA and water
4) incubate the solution in a water bath
5) cool down and filter
6) add protease enzymes to mixture = break down proteins bound to DNA
7) add a layer of cold ethanol
* DNA white precipitation removed with rod
Glycosidic Ester Peptide Hydrogen Phosphodiester
Disaccharides Glycerol + fatty acids Between amino acids Between water molecules Between nucleotides
What is the role of rRNA?
Plays a biochemical role in catalysing the reaction
Maintains the structural stability of the protein synthesis sequence
What is the role of tRNA?
Transfer RNA
A strand of RNA folded in a way that 3 bases are exposed (anticodon)
They carry an amino acid corresponding to that codon to form the amino sequence chain that forms the primary structure of the protein
What is mRNA?
Carries mRNA to the site of protein synthesis
What are the steps of translation?
The mRNA binds to the small sub unit of ribosome
The tRNA with the complementary anticodon binds to the mRNA and carries the amino acid
Another tRNA binds to and carries the next codon
The first amino acid is transferred to the second amino acid by the formation of peptide bonds which is catalysed by peptidyl transferase , which is an rRNA component
Why do cells require energy?
For synthesis
For movement
For transport
Atp
Nitrogenous base (always adenine)
Pentose sugar
3 phosphate groups
How atp releases energy
Hydrolysed into adp - supplies energy
Properties of ATP
Small
Water soluble
Releases energy
Easily regenerated
Example of fibrous proteins
Keratin
Keratin
- large portion of sulfur containing amino acid
= disulfide bonds = strong
can be either flexible or hard
- hair , nails
Example of fibrous protein
Elastin
Elastin
- quaternary protein made from stretchy tropoelastin molecules
- gives flexibility to vessel walls
found in elastic connective tissue
- skin, vessels
