2.1.2 Biological Elements Flashcards
Main elements present in living organisms
Carbon, Hydrogen, Oxygen and Nitrogen (4 main)
Phosphorous and Sulfur (2 extra)
Sodium Potassium and Calcium and Iron (extra)
Biological elements in Carbohydrates
Carbon, Hydrogen and Oxygen (use glucose as example of ration)
Biological elements in lipids
Carbon, hydrogen and oxygen
Biological elements in Proteins
Carbon, hydrogen, oxygen, nitrogen and sulfur
Nucleic acids
Carbon, hydrogen, oxygen, nitrogen and phosphorous
How are carbohydrates polymers?
Long chain molecules linking multiple individual molecules (called monomers) in a repeating manner
Monomers in carbohydrates
Saccharides (sugars)
Monomers in proteins
Amino acids
What causes polarity?
Uneven sharing of electrons in a covalent bond between two atom - making one side delta positive and another side delta negative (regions of positivity and negativity)
O-H bond polarity
Oxygen has a greater share of electrons which makes hydroxyl group polar - O is more negative relative to hydrogen
Water molecule
Polar molecules including water interact with each other as negative and positive regions of the molecule attract each other and form hydrogen bonds
Hydrogen bonds
Relatively weak interactions which break and reform between the constantly moving water molecules - hydrogen bonds are weak interactions but when they occur in high numbers they are strong (giving unique characteristics)
Why does water have a high boiling point?
This is due to hydrogen bonding between water molecules which takes a lot of energy to break the bonds and cause it to become gaseous (evaporate) - therefore latent heat of vaporisation is very high (in order to change state)
Density of water characteristic
More dense in liquid state than solid - as water is cooled BELOW 4 degrees Celsius, hydrogen bonds and the polarity causes repulsion thus producing an open (tetrahedral) lattice which increases the volume and thus decreases density
Cohesion property and example
Water moves as one mass because molecules are attracted to each other (cohesion) due to polarity and in this way plants are able to draw up water through roots (and suck a straw)
Adhesion property and example
Water molecules’ polarity causes it to be attracted to other materials (when you wash your hands, your hands become wet and water does not run straight off)
What causes surface tension?
Water molecules cohesivenss’ to each other > they are adhesive to the air ; creating a “skin” of surface tension
Water as a solvent?
Because it is polar - many organic solvents can be dissolved in it (cytosol of prokaryotes etc) ; many solutes are also polar molecules such as amino acids and proteins therefore water acts as a medium for chemical reactions and helps in the transport of dissolved compounds into and out of the cell
Water as a transport medium?
Cohesion between water molecules means that they stick together
Adhesion means attraction between water and other polar molecules
Effects of adhesion + cohesion results in CAPILLARY ACTION = allowing water to rise up a narrow tube AGAINST Gravity
Water as a coolant?
Because of it’s high SHC and Latent Heat, it helps to buffer temperatures during chemical reactions in prokaryotic and eukaryotic cells because of the large amount of energy required to overcome hydrogen bonding (MAINTAINS constant temperatures in cellular environments - enzymes only active in a narrow temperature range)
Life support for organisms/animals
- Wtaer is stable (temerpature wise too) allowing a constant environment for fish to live in
- Because ice floats it forms on the surface of ponds and lakes rather than at the bottom ; producing an insulating layer above the water below ; aquatic organisms will not be able to survive if entire habitat frozen solid
- Surface tension is strong enough to support pond skaters (small insects)
Carbohydrates formula
Cx(H2O)y
Single sugar unit is called
Monosaccharide
Examples of monosaccharides
Glucose, fructose and ribose
Disaccharide
2 monosaccharides linked together ; lactose and sucrose
Polysaccharide
When two or more monosaccharides are linked they form a polymer called a polysaccharide ; glycogen cellulose and starch
Glucose molecule
C6H12O6 - 6 carbons in a ring therefore hexose monosaccharide
How are carbons numbered?
Clockwise - carbon 1 to carbon 6 (on carbon 5)
Alpha glucose structure describe
Carbon 1 - OH group down 2 - down 3 - up 4 - down 5 - Ch2OH up
Beta glucose structure describe
Carbon 1 - OH group up 2 - down 3 - up 4 - down 5 - ch2oh up
Are glucose molecules soluble?
Yes because of the hydrogen bonds formed between hydroxyl groups and water molecules ; glucose can be dissolved into the cytosol of the cell
Condensation reaction between 2 alpha glucose
Carbon 1 and Carbon 4 - OH groups both down close together ; they react to form O bond with H2O as by-product
Bond forms between 1 and 4 - 1,4 glycosidic bond ( COVALENT BOND)
2 a-glucose bonded together
Maltose - disaccharide
Other hexose monosaccharides
Fructose (fruit) and galactose
Sucrose?
Disaccharide formed by fructose + glucose
Lactose?
Glucose + galactose (milk) - disaccharide
Ribose?
It is a pentode monosaccharides - 5 carbon atoms ; present in RNA nucleotides and deoxyribose in DNA nucleotides
What is starch?
Made up of two polysaccharides and glucose made by photosynthesis in plant cells is stored as starch ; it is a chemical energy store
Amylose
Polysaccharide made by alpha glucose molecules joining together using 1-4 glycosidic bonds ; allowing it to twist to form a helix which is further stabilised by hydrogen bonding between different molecules making it more compact and thus less soluble than the glucose molecules
Amylopectin
Also made up of 1-4 bonds between alpha glucose BUT there are also some glycosidic bonds between carbon 1 and carbon 6 causing amylopectin to have a branched structure with the branching occurring every 25 glucose subunits
Glycogen
Functionally equivalent energy storage molecule to starch in animals and fungi BUT is more branched than amylopectin which means it is more compact and less space is needed for storage ; cooling is ideal for storage in animal. Branching results in many free ends where glucose molecules can be added or removed which speeds up the processes of storing or releasing glucose molecules (for respiration maybe) by the cell
Key properties of branched polysaccharides
Insoluble, compact and branched allowing them to carry out storage roles
Hydrolysis reactions
Exothermic reaction - when during respiration the stored energy is released as ATP for the organism to use ; this is caused due to hydrolysis, addition of water molecules to break up the glycosidic bond (CATALYSED BY ENZYMES)
Beta glucose molecules
Unable to join together same as alpha glucose because hydroxyl groups too far apart therefore every alternate beta glucose molecules is turned upside down
Beta glucose switched
ANTI-CLOCKWISE Carbon 1 - hydroxyl group down Carbon 2- hydroxyl group up 3 - down 4 - up 5 - ch2oh down
Cellulose
Polysaccharide unable to twist or coil or form branches so it is a straight chain ; cellulose chains form hydrogen bonds with each other (OH and O) forming microfibrils - join together to form macrofibrils which are combined to produce fibres -> strong and insoluble and used to make cell walls which are also a part of our diet ; break down to form roughage etc
Benedicts test for reducing sugars
All monosaccharides are reducing sugars (and maltose and lactose - disaccharides)
Benedicts reagent is alkaline copper sulfate ; place sample in boiling water with equal volume of benedicts and heat for 5 minutes
If reducing sugars are present then they will cause Cu2+ ions to gain an electron forming Cu+ (reduction) which forms a brick red precipitate
More reducing sugars = more precipitate and less Cu2+ ions left ; this is QUALITATIVE
Range of colours in benedicts
Green - low concentration of reducing sugars
Yellow/amber - medium concentration
Red - high concentration
Non-reducing sugars
Negative with benedicts because not reducing (SUCROSE)
If sucrose is boiled with HCl it is hydrolysed to glucose and fructose which are both monosaccharides and thus reducing sugars giving a positive result
Iodine test for starch
Few drops of iodine dissolved in potassium iodide - if solution changes colour from yellow to purple/black then starch is present in sample
Reagent strips
Can be used to test for presence of reducing sugars (glucose) and ADVANTAGE IS THAT MORE ACCURATE CONCENTRATION OF SUGAR CAN BE MATCHED TO COLOUR PRODUCED
Lipids contain what elements?
Carbon, hydrogen and oxygen
Fats and oils difference
Fats are solid lipids at room temperature and oils are liquid lipids at room temperature
Why does oil and water not mix?
Lipids are non-polar cause of the even distribution of outer electrons ; creating no positive or negative areas and thus nit being soluble in water
What are lipids?
Macromolecules which are built from monomers like polysaccharides
Triglyceride
Combines one glycerol molecule with 3 fatty acids which are alcohol (OH) with 3 carboxyl groups (COOH)
Reaction to form triglycerides
Hydroxyl groups interact leading to the formation of 3 water molecules and bonds between the fatty acids and the glycerol molecule (O-C=O ester bond) ; this reaction is called esterification which is another condensation reaction
Fatty acid structure
COOH - (CH2)n - ends chain with CH3
Hydrolysis of triglycerides?
3 water molecules need to be supplied to reverse the reaction that formed the triglyceride ; hydrolysis
Saturated
Fatty acid chains which are saturated have no double bonds present because all the carbon atoms form the maximum number of bonds with hydrogen atoms
Monounsaturated
Single double bond
Polyunsaturated
2 or more double bonds
What does it mean for a fatty acid chain to be unsaturated?
The presence of double bonds causes the molecule to kink or bend and they therefore cannot pack so closely together which makes them liquids (oils) at room temperature instead of fats
Plants contain what type of triglycerides?
Unsaturated - thus as oils which are healthier than saturated fats
Elements in phospholipids
Carbon, hydrogen, oxygen and phosphorous ; they contain the PO43- ions which are found in the cytoplasm of every cell ; they are soluble in the cytosol ; one of the fatty acid chain in a triglyceride is replaced with a phosphate head to make it a phospholipid
Polarity in a phospholipid
Non-polar tail (fatty acid chain - just C and H atoms so no proper difference in electronegativity) and a charged polar head with the phosphate group. The non polar tails repel water (hydrophobic) and the polar heads interact with water (hydrophilic)
What does this difference in polarity cause?
They form a layer with the phosphate heads in the water and the fatty acid tails sticking out (surfactants) - they can also form structures based on a two layered i layer formation with all the hydrophobic tails pointing inwards (mycelle) and the hydrophilic heads on the outside ; this allows them TO SEPARATE AN AQUEOUS ENVIRONMENT FROM CYTOSOL ; endosymbiosis theory
Sterols structure
Alcohol molecules based on a 4 carbon ring structure with an OH at the end ; resulting in dual hydrophilic/hydrophobic characteristics ; hydroxyl group is polar and thus rest is hydrophobic
Cholesterol role
Manufactured in liver - positions itself between phospholipids with the hydroxyl group at the periphery of the membrane adding stability and regulating fluidity by keeping membranes fluid at low temperatures and stoping them becoming too fluid at high temperatures
Roles of lipids
Because they are non polar Membrane formation - hydrophobic barriers Hormone production Electrical insulation Water proofing
Lipids in long term energy storage
Thermal insulation to reduce heat loss - buoyancy for animals like whales and cushioning to protect vital organs
Presence of lipids test
Emulsion test - sample is mixed with ethanol and the resulting solution is mixed with water and shaken, forming a white emulsion as a layer on top of the solution which indicates the presence of a lipid ; if it is clear it is negative
Elements in protein
Carbon, hydrogen, oxygen and nitrogen
What are peptides?
They are polymers made up of amino acid molecules - protein consists of one or more polypeptides arranged as a complex macromolecule and they have specific biological functions
Structure of amino acids?
Central carbon atom attached to an amine NH2 group, a carboxyl COOH group, hydrogen and an R group (which differs)
How many different amino acids found in the body?
20
How does a peptide bond form?
Through a condensation reaction including amine and carboxyl idc acid groups - R groups are not involved - OH in the COOH reacts with H in NH2 ; forms water as a by product and a dipeptide is formed as a result (with a peptide bond)
How is a polypeptide formed?
Many amino acids are joined together by peptide bonds - this is catalysed by the enzyme peptidyl transferase present in ribosomes
What factors affect the shape of the polypeptide chains?
Different R groups interact forming different types of bonds (folding in different ways)
Presence of different sequences of amino acids leads to different structures with different shapes being produced ; VERY specific for the different functions
Primary structure?
Sequence in which amino acids are joined ; this will influence how polypeptides fold to give the protein it’s final shape - in turn determining it’s function BUT ONLY BOND IS PEPTIDE BOND
Secondary structure
The oxygen and hydrogen and nitrogen (NOT R GROUPS) interact and HYDROGEN BONDS may form
Alpha helix
Hydrogen bonds within the amino acid chain pull it into a coil shape called an alpha helix
Beta pleated sheet
The chains lie parallel to each other and hydrogen bonds join individual amino acids (H and O) together - forming a sheet like structure which makes it appear pleated
Tertiary structure
Overall 3D shape ; folding of protein ; the coiling in the secondary structure brings R-groups close enough to interact, causing further folding to occur
Interactions between R Groups
Hydrophobic and hydrophilic interactions - weak interactions between polar and non-polar R Groups
Hydrogen bonds - weakest
Ionic - oppositely charged R groups
Disulfide bridges - covalent and strongest (only form between R groups that contain sulfur atoms)
Quaternary structure
Two or more polypeptide chains ; interactions between these subunits are the same as they are in the tertiary structure except between whole protein molecules rather than one amino acid/polypeptide chain
Hydrophilic and hydrophobic interactions
Proteins are assembled in the aqueous environment of the cytoplasm so the way in which a protein folds will also depend on the R groups - hydrophilic groups are on the outside and the hydrophobic groups are on the inside of the molecule shielded from the water
Breakdown of peptides
Peptides are created by amino acids linking together in condensation reactions - protease enzymes catalyse the reverse reaction turning peptides back into their constituent amino acids ; a water molecule is used to break the peptide bond in a hydrolysis reaction - reforming the amine and carboxylic acid groups
Globular proteins
Compact, water soluble and usually roughly spherical ; R-groups interact so that hydrophobic R groups away from aqueous environment and hydrophilic R groups on outside (soluble)
Insulin
Globular - hormone, soluble in blood stream and very specific on cell membrane to have effect and thus precise shapes
Conjugated proteins
Globular proteins that contain non-protein components called prosthetic groups (without them they are called simple proteins)
Types of conjugated proteins
Lipids or carbohydrates may combine with proteins forming lipoproteins or glycoproteins (Haem groups - Fe2+ ions are present in Catalase and haemoglobin)
Structure of haemoglobin
4 polypeptides (quaternary structure) with 2 alpha and 2 beta subunits ; each subunit contains a prosthetic haem group and the iron is able to combine reversibly with oxygen allowing it to transport oxygen around the body and changing shape when delivering oxygen around the body
Catalase structure
Enzyme with 4 haem prosthetic groups - presence of Fe2+ allows it to interact with hydrogen peroxide and speed up its breakdown to water and oxygen (catalyse prevents build up of hydrogen peroxide as a byproduct of metabolism so it does not damage cells)
Fibrous proteins
Long, insoluble molecules due to a high proportion of amino acids with hydrophobic R groups in their primary structure; limited range of amino acids and this is quite repetitive => very organised structures reflected in the roles fibrous proteins may have (keratin, elastin, collagen etc) ; THESE ARE NOT FOLDED INTO 3D SHAPES LIKE GLOBULAR PROTEINS
Keratin
Has a lot of cysteine which forms disulfide bridges forming inflexible and strong materials ; degree of disulfide bonds determines flexibility (hair more flexible than nails)
Elastin
Present in walls of blood vessels allowing them to expand when needed (especially in arteries high blood pressure) - quaternary protein made from many stretchy tropoelastin molecules
Collagen
Connective tissue - 3 polypeptides wound together in a rope like structure
Elastin structure
Link many soluble teopoelastin proteins to make a very large stable cross linked structure- stretch and recoil because of aggregation of teopoelastin with interactions between hydrophobic areas (covalent cross linking stabilises structure)
Collagen structure
3 polypeptide chains wound around each other to form a triple helix - every third amino acid is glycine which allows it to be closely packed and many hydrogen bonds form between polypeptide chains forming quaternary protein with staggered ends
