2.2 Flashcards
What are monomers?
A small molecule which binds to many other identical molecules to form a polymer
What are polymers?
a large molecule made from many smaller molecules called monomers
What is a condensation reaction?
Reaction that occurs when two molecules are joined together with the removal of water
What is a hydrolysis reaction?
Reaction that occurs when a molecule is split into two smaller molecules with addition of water
What is a monosaccharide?
Monomers from which larger carbohydrates are made
How is a glycosidic bond formed?
A condensation reaction between two monosaccharides
Name three main examples of polysaccharides.
Glycogen, starch, cellulose
Describe Benedict’s test for reducing sugars.
Gently heat a solution of a food sample with an equal volume of Benedict’s solution for five minutes, the solution turns orange/brown if reducing sugars are present
Name two main groups of lipids.
Phospholipids, triglycerides
Give four roles of lipids.
Source of energy, waterproofing, insulation, protection
What is an Ester bond?
A bond formed by a condensation reaction between glycerol and a fatty acid
Describe the emulsion test for lipids.
Mix the sample with ethanol in a clean tube, shake the sample, add water, shake sample again, a cloudy white colour indicates that a lipid is present
What are the monomers that make up protein?
Amino acids
Draw the structure of an amino acid.
R
|
N2N—-C—-COOH
|
HHow is a peptide bond formed?
A condensation reaction between two amino acids
What is a polypeptide?
Many amino acids joined together
Describe the biuret test for protein.
Mix the sample with sodium hydroxide solution at room temperature, add very dilute copper(II) sulphate solution, mix gently, a purple colour indicates that peptide bonds are present
How does an enzyme effect a reaction?
It lowers its activation energy
Give five factors which can effect an enzyme action.
Temperature, pH, enzyme concentration, substrate concentration, inhibitor concentration
What is a competitive inhibitor?
A molecule with a similar shape to the substrate, allowing it to occupy the active site of the enzyme
What is a non-competitive inhibitor?
A molecule that changes the shape of the enzyme by binding somewhere other than the active site.
What is a hydrogen bond?
A weak interaction that can occur wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom
Carbohydrates
A group of molecules containing C, H, O
Glycosidic bond
A bond formed between two monosaccharides by a hydrolysis reaction
Isomers
Same formula but different molecular structure
Lipids
A group of substances that are soluble in alcohol rather than water. Including triglycerides, phosolipids, glycolipids and cholesterol
Macromolecule
Very large organic molecule
Phospholipid
Molecule consisting of glycerol, two fatty acids and one phosphate group
Primary structure
The sequence of amino acids found in a molecule
Quaternary structure
Protein structure where a protein consists of more than one polypeptide chain. For example insulin has a quaternary structure
Secondary structure
The coiling or folding of an amino acid chain, which arises often as a result of hydrogen bond formation between different parts of the chain. The main forms of secondary structure are the helix and the pleated sheet
Tertiary structure
The overall three dimensional shape of a protein molecule, it’s shape arises due to interactions including hydrogen bonding, disulphide bridges, ionic bonds and hydrophobic interactions
fibrous protein
Has a relatively long, thing structure, is insoluble in water and metabolically inactive , often has structural role within organism
Globular protein
Has molecules of relatively spherical shape, which are soluble in water and often have metabolic roles within organisms
Prosthetic group
A non-protein component that forms a permanent part of functioning protein molecule
What gases does human body consist of
Nitrogen, hydrogen, oxygen, carbon, other(trace of potassium, zinc, iron)
3 different types of biological molecules
Carbohydrates, lipids and proteins
How are covalent bonds formed and why do they form
Atoms contain nucleus surrounded by full outer shell and atoms are stable when there outer shell is full. By sharing an electron with another atom they form a strong covalent bond.
What happens during condensation reaction
Two molecules join as water is removed
What happens in hydrolysis reaction and what can a hydrolysis reaction break
Two molecules split apart as water is added, can break a covalent bond
What is it called when two monomers join
Dimer
What is it called when many monomers are joined
Polymer
Give an example of monomers to polymers
In proteins: amino acid -> proteins
What is water made up of
Two hydrogen and one oxygen
Why is water polar
Oxygen has more protons in nucleus so has stronger attraction for shared electrons, this makes oxygen atoms slights negative and hydrogen comes slightly positive
What is a hydrogen bond and when does it occur
It is a weak interaction which happens every time molecules contains slightly negative charge bonded to a slightly positive charged hydrogen atom
Is covalent or hydrogen bond stronger
Covalent
What does carbon having a balance of 4 mean
For every carbon atom there is 4 covalent bonds from it
What are the main 3 elements in organic molecules
Carbon, oxygen, hydrogen
What is the name for when monomers form polymers
Polymerisation
What happens to hydrogen bonds as water moves
They constantly break and make new hydrogen bonds
Why is it hard for water to turn to gas
The hydrogen bonds between molecules make it hard for molecules to escape
Even with hydrogen bonds does what’re have low or high viscosity
Low viscosity
Why is it good that water has low viscosity
Provides habitats for living things in rivers, sea and lakes, form large part of tissue in living organisms, provides reaction medium for chemical reactions, provides effective transport medium (blood)
What would happen if water was less dense
Aquatic animals couldn’t float
Why does ice float on water and why is this different to other liquids
With most liquids they get more dense as they cool, but water only gets mor expense to 4degrees but from freezing water molecules align in a structure less dense than water (due to waters polarity)
Why is it good that ice is less dense than water
Aquatic organisms have stable environment to live in and ponds and other mass waters are insulated against extreme cold as layers of ice reduce heat loss from rest of the pond
Water is a good solvent for many substances in living things, what is an example of this?
Solutes like NaCl and covalent solutes like glucose
How does waters polarity effect is a a solvent
Waters negative and positive parts attract to the solutes negative and positive parts
Why do water molecules attach around charged part of the solute molecules
To help keep them apart so they dissolve and a solution is formed
What two things can molecules and ions do because water is a good solvent
They can move around and react together in water (cytoplasm) and they can dissolve in water and transport around living things
Why does a drop of water on a flat surface not spread out but looks spherical
As hydrogen bonding between molecules pulls them together and water molecules demonstrate cohesion
Why are water molecules more attracted to water molecules than air molecules
As at the surface the water molecules are all hydrogen bonded to molecule beneath them
What happens when water drop touches water
Surface of water contracts as molecules pulled inwards and it gives water surface ability to resist force applied to it (surface tension)
Examples of cohesion and surface tension of water in everyday life
Pond skaters can walk on water and columns of water in plant vascular tissue brought up through xylem tissue from roots
What is amount of high specific heat capacity
4.2kJ of energy to raise the temp of 1kg of water by 1degree
Why does water not heat or cool easily
There are lots of hydrogen bonds holding it together meaning it has high specific heat capacity
Why is it important for organisms that water has high specific heat capacity
Organisms need stable temp for enzyme controlled reactions to happen and aquatic organisms need stable environment to live in
What helps molecules turn into gas from water
Latent heat of vaporisation
Is latent heat of vaporisation high or low in water
High
Why is high latent heat of vaporisation necessary in water
So that water can cool living things and keep their temp stable for example animas cool when sweat evaporates
Examples of where water acts as a reactant
Photosynthesis, hydrolysis reactions
Why is waters properties as a reactant important
Digestion and synthesis or large biological molecules
What does waters properties as a solvent depend on
It’s polarity with H+ and O-
What does it mean if a molecule is polar
There is an unevenly distributed electrical charge, so there are positive and negative regions
What causes waters polarity
Water isn’t a straight chain, so hydrogen bonds form
In the body of its cold outside are body temp doesn’t change and enzymes don’t denature (why)
Water has high specific heat capacity so it’s good at maintaining steady temp
If cohesive forces of water were weaker what would happen to trees
They would be shorter
Why is it important that water is transparent
As few organisms could live without light and it would prevent plants from photosynthesising
What do carbohydrates contain
Hydrogen, carbon, oxygen
What does hydrated carbon mean
For every carbon there are 2 hydrogen and one oxygen atom
What are the 3 different functions of carbohydrates and give examples
Energy source (glucose), energy store (starch), structural units (cellulose)
What are 3 main carbohydrates groups
Monosaccharides, disaccharides and polysaccharides
What is the simplest carbohydrate and what is its purpose
Monosaccharide, important source of energy in longing things
Why are monosaccharides suited to their job
Have a large amount of carbon-hydrogen bonds
What are monosaccharides properties
They are sweet sugars which are soluble in water and insoluble in non-polar solvents
What is the shape of a monosaccharide
Can be straight line, rings or cyclic forms and have a backbone of single bonded carbon atoms with one double bonded to oxygen atom to form carboxyl group
What is the difference between a-glucose and B-glucose
In alpha the -OH group is below on carbon 1 and in B-glucose the -OH group is above
Difference between hexose and pentose in terms of make up
Hexose has 6 carbon atoms and pentose had 5
What does it mean when glucose can exist as a number of isomer when in a straight chain or cyclic form
Molecules with same formula but atoms arranged differently (ring shaped isomers can also form)
When is a ring structure formed in monosaccharides
When oxygen attaches to carbon 1 and carbon 5
Properties of disaccharides
They are sweet and soluble in water
What are the most common disaccharides
Maltose, sucrose and lactose
Which out of maltose, lactose and sucrose are reducing sugars
Maltose and lactose reducing sugars and sucrose non-reducing sugar
A-glucose+a-glucose ->
Maltose
a-glucose+fructose ->
Sucrose
B-galactose+a-glucose ->
Lactose
B-glucose-B-glucose->
Cellobiose
What happens when two monosaccharides bond
Condensation reaction takes place, forming a glycosidic bond
Where does the condensation reaction happen when disaccharides form
Between the 2 -OH groups so only a single oxygen left which binds the two molecules togeteher
How are disaccharides broken into monosaccharides
Hydrolysis reaction
What happens when glycosidic bond formed and hydrolysed by living things
Reaction catalysed by enzymes
What type of bond is a glycosidic bond
Covalent
What is glucose based on how many carbon atoms it contains
6 carbon atoms so is a hexose sugar
What is glucose general formula
C6H12O6
What is glucose purpose and properties
Energy source for most cells and is highly soluble and main form of transporting carbohydrates round the body
What is the term for glucose existing in 2 different forms
Structural isomers
Can pentose sugars form rings
Yes like hexose they are long enough to form rings
What are the most important pentose molecules which are structural isomers
Ribose and Deoxyribose
What is the structural difference of ribose and deoxyribose
Ribose has one H atoms and one OH group attached to carbon 2 and deoxyribose has 2 H atoms and no OH group on carbon 2
How is maltose formed
2 glucose joined by alpha 1-4 glycosidic bond
How is sucrose formed
From glucose and fructose joined by alpha 1-4 glycosidic bond
How is lactose formed
From galactose and glucose joined by beta 1-4 glycosidic bond
What is the general disaccharide formula
C12H22O11
Properties of polysaccharides
Don’t taste sweet and are insoluble in water
Why are polysaccharides good carbohydrate store
They have a compact structure
How is sugar got in polysaccharides
They are insoluble so can’t be diffused but if necessary a hydrolysis reaction can happen to break it off
Examples of polysaccharides
Starch, glycogen and cellulose
What are polysaccharides
Polymers containing many monosaccharides linked by glycosidic bonds
How are polysaccharides and disaccharides similar
Both formed by condensation reaction
Uses of polysaccharides
Mainly used as energy store and as structural components of cells
What are the major polysaccharides
Starch, cellulose and glycogen
What does a hydrolysis redaction do to polysaccharides
Used to break them into monosaccharides, which is the opposite of a condensation reaction
Where is carbohydrates used in plants
Cellulose for structure, glucose for respiration, starch as energy store
What are properties of starch
Major carbohydrate storage molecule in plants, stored as intracellular starch grains or in organelles called plastids, starch produced from glucose made in photosynthesis and broken down in respiration to provide energy
What are the two different types of starch
Amalyose and amylopectin
What is amalose and it’s properties
Long chain of a-glucose and has 1-4 glycosidic bonds, it has helix structure and OHgroup on carbon 2 is on the inside coil making it less soluble so hydrogen bonds form, holding the structure together
What is amylopectin and what is its structure
Long chain of a-glucose with 1-4&1-6 glycosidic bonds to create highly branches structure, this could in spiral shape held with hydrogen bonds with branches emerging from each spiral
What is glycogen and it’s structure
a-glucose molecule with 1-4&1-6 glycosidic bonds, the 1-4 chains are smaller than amylopectin so less likely to coil but it has more branches so is more compact and easier to remove monomer units as there are more ends
What is cellulose
A polysaccharide and main part of cell walls, most abundant organic polymer
What are cellulose properties
It is strong and stops cells bursting when there is excess water, it is also fibrous and tough and insoluble
Why is cellulose a homopolysaccharide
It is made from 15,000 B-glucose molecules bonded through condensation reaction forming 1-4 glycosidic bond
In cellulose why is every over molecule rotated 180degrees and why doesn’t it spiral
-H and -OH are inverted on carbon1 in B-glucose so every other one is rotated and the 1-4 glycosidic bonds prevent spiralling
Why is cellulose strong in terms of molecular structure and how do they form
Hydrogen bonding between rotated B-glucose molecules provide extra strength as -OH groups on carbon 2 struck out allowing them to form between chains
What is the structure of cellulose
Formation of macrofibrils which are embedded in pectin to form cell wall and cross cross in all directions for extra strength
Do animals store carbohydrates as glycogen or starch
Glycogen
Where and how is glycogen stored in animals
As small granules in muscle and liver
Is glycogen more or less dense and soluble than starch and what does this mean
It is less dense and more soluble than starch so can be broken down more rapidly
Why is it important that glycogen can be broken down rapidly
Higher metabolic requirements of animals means we need it more rapidly than plants
What is advantageous about glycogen
It is highly branches and compacted and has free bonds at the end so more glucose can be added easily
Why is cellulose good in plant walls
As the macrofibrils and microfibrils have high tensile strength due for eh strength of the glycosidic bonds and hydrogen bonds between chains
How strong are macrofibrils
Stronger than steel if the same diameter
How to macrofibrils get extra strength
Run is all directions, criss crossing wall
Why is cellulose hard to digest
The glycosidic bonds are hard to break and most animals don’t have the right enzymes to catalyse this reaction
Why is cellulose essential in plants
Plants don’t have ridged skeleton so each cell needs strength to support whole plant
Why is plant cell wall fully permeable
There is space between macrofibrils for water and miners ions to pass on way in and out of the cell
Why is it necessary that cell walls have high tensile strength
Prevents cells bursting when there turgid as turgid cells push against each other holding plants structure and the wall protects delicate membranes
Give an example of another substance that helps macrofibrils provide extra strength
Waxes that block spaces in cell walls to make it waterproof
Give some examples of items that contain cellulose
Cotton, cellophane, paper
What is the structure of a bacteria cells wall
Structure is called peptidoglycan and made from long polysaccharide chains that lie in parallel, cross linked by short peptide chains made from amino acids
How is insects exoskeleton made from chitin different from cellulose and it’s similarities
It has an acetylamino group rather than an OHgroup on carbon2, it forms cross links of long parallel chains of acetylglucosamine in similar way to cellulose
Do glycogen and starch take up lots of room
No they are compact
How are glucose molecules removed from polysaccharides by
Hydrolysis reaction
Is poly or monosaccharides more soluble in water
Monosaccharides
What type of sugar are polysaccharides formed from
Hexose sugar
Is amalyse branched
No it has a helix structure
Where is glycogen within a cell
In the cytoplasm
What is structure of microfibrils in cell wall
60-70 chains of them massed together to form microfibrils
What are microfibrils embedded in
Hemicellulose and pectin
What is hemicellulose
Short polysaccharides that bing tightly (not covalent) to surface of cellulose microfibrils and to each other
What are pectins
Polysaccharides in cell walls which have negative charge
How are lipids stored
As adipose tissue
What is the purpose of adipose tissue
It provides heat insulation in mammals underneath skin and around delicate organs like kidneys to act as a cushion in impacts
What is the properties of lipids
Diverse group of compounds which are insoluble in water but soluble in organic solvents like ethanol
What is the most commun type of lipid
Triglycerides
Give examples of lipids
Triglyceride, waxes, steroids and cholesterol
Why are lipids insoluble in water
They are not polar
Why aren’t triglycerides, phospholipids and steroids monomers
They are macromolecules as they have different molecules binding them together
What do lipids contain in terms of atoms
Lots of hydrogen and carbon but little oxygen
What are triglycerides made up of
Glycerol and 3 fatty acids
What is a complete fatty acid
Fatty acids we eat not produce
How does glycerol and fatty acid bond to make triglyceride
Condensation reaction forming 3 water molecules and 3 ester bonds
What bond holds lipids together
Ester bond
What is glycerols structure and properties
Has 3 carbon atoms and is alcoholic so has 3 OH groups which are important to triglycerides structure
What is the structure of a fatty acid
Have a carboxyl group on one end attached to hydrocarbon tail (made of only one carbon and hydrogen atom), they can be from 2-20 carbon long
In fatty acid when carboxyl group ionises what is produces and why does it make it an acid
A H+ and COO- group and this makes it an acid as it can produce free H+ ions
What is the structural difference between saturated and unsaturated fatty acid
When it’s saturated there are no c=c bonds but if it’s unsaturated there are c=c so less hydrogen atoms bonded to molecule
What does a single c=c bond make a fatty acid acid and what does more than one c=c bond make a fatty acid
Monosaturated and more make it polysaturated
How does having one or more c=c chain change the shape of hydrocarbon and what does this do
It gives a link where the double bond is which push molecules slightly apart making them more fluid
When forming a triglyceride where is the condensation reaction formed
Between -COOH group of fatty acid and -OH group of glycerol
What is an ester bond
Covalent bond formed during condensation reaction holding lipids together
How are triglycerides used as an energy source
Broken down in respiration to release energy and ATP
How are triglycerides broken down
Hydrolyse ester bonds, then glycerol and fatty acids can be broken down to CO2 and H2O
Does respiration of lipids produce more or less water than respiration of sugar
More
Why are triglycerides good energy store
Insoluble in water as not polar so can be stored without affecting water potential of a cell
Does fat or glucose release more energy and why
Fat, 1g of fat releases twice as much energy as 1g of glucose because lipids have higher proportion of hydrogen than carbohydrates and little oxygen
In what ways is lipid a good insulator
In whales acts as heat insulation known as blubber, is an electrical insulator in nerve cells and allows hibinating animals to store extra fat
Why is it good that fat is buoyancy
Fat less dense than water so aquatic animals have fat to stay afloat
Do lipids or carbohydrates contain more oxygen
Carbohydrates have more oxygen than lipids
What are the two groups of lipids
Fats and oils and steroids and terpenes
At room temp is fat solid or liquid
Solid
Do either glycerol or fatty acids have structural variations
Only one sort of glycerol but fatty acid has many variations
What disease can high triglycerides levels cause and what happens
Coronary heart disease - causes mass build up of connective tissue and fat in artery walls which slows blood flow and could cause a clot
Why is fat a good insulator
As it conducts heat slowly
What is the difference is structure of a phospholipid
Phospholipid have one less fatty acid which is replaced with a phosphate group compared to triglycerides
Where is an ester bond formed on phospholipid
Condensation reaction between OH group on phosphate acid molecule and one of 3 OH groups on glycerol form
Do fatty acids in phospholipids have even or odd amount of carbons
Even (18/16)
Is a phospholipid saturated or unsaturated
Usually one chain is saturated and one is unsaturated
What happens to the phosphate group of phospholipid in water
Phosphate group has negative charge, making it polar (attracted to water)
Why are fatty acid tails repelled by water
They are non polar
What is the name given to head and tail of phospholipid
Hydrophilic and hydrophobic
Why are phospholipid AMPHIPATIC
As the head is hydrophilic and tail is hydrophobic
What type of lipids are amphiphatic and what aren’t
Membrane lipids are but lipids involved in storage aren’t
In phospholipid lipid is tail hydrophobic or hydrophilic
Hydrophobic
Is phospholipid is phosphate hydrophilic or hydrophobic
Hydrophilic
What happens to to amphamatic phospholipids in water (layers)
May form layers on surface with heads in water and tails sticking out of water
What does an amphamatic phospholipid do in water (sphere)
Form micelles,bring ball with tails pointing inwards and hydrophilic heads pointing outwards creating a spherical shape
What are amphamatic phospholipids good for
Good at forming membranes around cells and organelles as inside and outside the cells is an aquatic solution
What shape do phospholipids go into when they act as a membrane
Form a bilayer with heads on outside and tails on inside aquatic solution
Can phospholipids move around when there in a bilayer
They can move around in there but won’t move anywhere where there hydrophobic tail is exposed to water which gives membrane stability
How permeable is the phospholipid bilayer as a membrane and what does this mean
Semi-permeable as it only lets small and non polar molecules move through tail in bilayer which controls what goes in and out of the cells and keeps it functioning properly
What do cholesterol
A steroid alcohol which is a type for lipid made from neither fatty acid or glycerol
What is cholesterol structure
Has 4 carbon based rings or isoprene units
Is cholesterol large or small and is it hydrophobic or philic
It’s a small and hydrophobic molecule
Why is it good that cholesterol is hydrophobic
So it can sit in the hydrophobic part of bilayer
What does cholesterol do
Regulated fluidity of membrane preventing it from coming to fluid or too stiff
Where is cholesterol made and found
Made in liver of animal and cholesterol derives in plants membranes called stigmasterol which is slight different from cholesterol
What are examples of things made from cholesterol
Testosterone, oestrogen and vitamin d
Why can steroid hormones made of cholesterol pass through cell membranes
They are small and hydrophobic
Is the phosphate group acidic or alkaline
Acidic
How is phospholipid formed
Phosphoric acid reacts with one of 3 OH groups of glycerol and other 2 OH react with fatty acid
What is the most known steroid
Cholesterol
Is all cholesterol bad
No some is essential
Where is essential cholesterol found
Membrane of animals cells to keep them fluid
What happens when cholesterol interacts with hydrocarbon chains of phospholipid molecule
Chances stability and flexibility of membrane
Why and what part of phospholipid is insoluble in water
Long hydrocarbon chain is insoluble but end of glycerol molecule is soluble as it has polar groups
What is a mono layer
Formed when fat is half in contact with air and half with water, head in water and tail out of water
What happens to fat when in water surface with isn’t in contact with air
Bilayer like plasma membrane
What are proteins
Large monomers made of amino acids
What is proteins function (structure)
Structural components in animals (muscles made from protein)
What is function of protein (enzymes)
Tendency to adopt specific shapes make proteins important as enzymes
Do both animals and plants need amino acids to make proteins
Yes
Do animals make all there proteins
They make some but must I gets others
What’s an essential amino acid
Amino acids which we must ingests and cannot produce
When can plants make amino acids
If they have a fixed access to nitrogen
What is an amino acids structure
They each contain oxygen, carbon, hydrogen, nitrogen and sometimes sulfur
What does each protein chain of amino acids have
An amino group (NH2) and a carboxyl group (COOH) at the other end
What does r mean on amino acid structure
Varys depending on which amino acid it is
How can r groups vary
By size, charge, polarity, if there hydrophobic or hydrophilic
How are amino acids bonded
Amino acid joined together by condensation reaction forming covalent peptide bond
How do you break a peptide bond
Hydrolysis reaction (addition of water)
Give an example of when peptide bonds are broken
Protease in intestines breakers down peptide bonds during digestion and can break down hormones so effect isn’t permanent
What is the name of two amino acids bonded
Dipeptide
What is a long chain of amino acids called
Polypeptides
How many polypeptides does a protein have
Of at least one but sometimes more bonded together
How does structure of protein differ from lipids and carbohydrates
Contains nitrogen and sometimes sulfur which others don’t
What is glycines R on amino acid
H-hydrogen
How many proteins used in biosynthesis of proteins
20
Why can amino acids act as buffers
They have a positive and negative charged region
Which part of amino acid is possible and negative
Amine group is positive and carboxyl group negative (NH3+ —RCH—COO-)
What does buffer mean
Amino acids can combine with acid or alkali substances as they can resist change of pH on addition of acid or alkali
Give an example of amino acids acting as a buffer
If acidic hydrogen taken up by -COOH group, decreasing acidity of surrounding (NH3+ — RCH —COOH) and if alkane hydrogen ions released from amino group, increases acidity round it (NH2 — RCH — COO-)
Why is it important that proteins are buffers
Useful in blood, tissue fluid and within cell to help keep pH stable which important in homeostasis
What is primary structure
Sequence of amino acids in a protein chain
Why is order and number of amino acids important
Changing just one amino acid can alter function of the protein
Why is there a large variety of proteins
20 different amino acids which can all be arranged differently and chains usually 100 amino acids long so 20*100 ways of rearranging amino acids
What does function of protein depend on based on shape
Whether it’s a primary, secondary, tertiary or quarternary structure
What is a secondary structure
Chain of amino acid which isn’t straight but twisted into shape, some are a-helixes and some are B-pleated sheets
How many amino acids does a secondary a-helix structure have
36 amino acids per 10 turns of helix
How is secondary helix structure held together
Hydrogen bonds between NHgroup of amino acid and COgroup of another (4 places ahead in chain)
What is B-pleated structure and how is it held togeteher
Folds slightly in a zigzag and hydrogen bonds between NH group of one amino acid and CO group further down the chain to hold sheet together
Why are a-helix and b-pleated strong
hydrogen bonds are weak but there are many of them so makes them stable at optimal pH and temp
When is tertiary structure formed
when coils and pleats from secondary structure start to fold along with areas of straight chain of amino acids
Why does tertiary structure have precise structure
Held firmly in place by bonds between amino acids which lie close to each other
What shape do tertiary structure adopt in fibrous and globular proteins
Supercoiled in fibrous and spherical in globular
What bonds found in tertiary structure
Ionic bond between a positive R and a negative R, disulphides bond between the sulfur, hydrogen bond between NH and OC
What is a quarternary structure
Many proteins made up of more than one polypeptide chain
What bonds do quaternary have
Same as tertiary, disuflide, hydrogen, ionic
When do hydrogen bonds form in proteins
When hydrogen atom has slight + charge and other atom has slight - charge which e.g. hydrogen bond may form between amino group of one amino acid and carboxyl soup for another amino acid
What do ionic bonds form between and what do these form into
Carboxyl and amino groups that are part of R group, which ionise into NH3+ and COO-
Why does ionic bond form when something + and -
Positive and negative groups are strongly attracted to each other forming ionic bond
What in an amino acid contains sulfur
In the R group but only certain amino acids like cysteine
Where are disulphides links formed between and how strong are they
Formed between r group of two cysteines and are strong covalent bonds
Where do hydrophobic parts of r group associate together and hydrophilic parts
In middle of polypeptide to avoid water contact so hydrophilic parts found near edge to be close to water
What do hydrophobic and hydrophilic interactions cause and what does this mean
Can cause twisting of amino acid chain which changes protein shape and can influence its functions as most proteins surrounded by water in living organisms
What bonds are there in primary structure
Only covalent peptide bonds between each amino acid
What bonds do secondary structures have
Hydrogen bonds
What are two different secondary structures
B-pleated sheet and a-helixes
Where are a-helixes found
In hair (keratin) and enzymes and antibodies
Why does b-helix have relatively flat structure
Hydrogen bonds between parallel chains which then becomes folded
B-pleated or a-helix more common
A-helixes
Where are b-pleated sheets found
Silk and strong and thick protein and structures
What may the structure of polypeptide be in tertiary structure
Cross links formed between either hydrogen, ionic or disulphide bonds
Examples of proteins joined with other molecules
Glycoproteins - protein and carbohydrates
What is it called when protein and other molecule joined
Conjugated protein
Where may you find glycoproteins
Mucus, connective tissue, eukaryotic plasma membrane
Use of lipoproteins
Transport soluble lipids round the body
When is quarternary structure present
Only present when 2 or more polypeptide chains
Give an example of quaternary structure and its function
Haemoglobin in red blood cells contains tightly packed polypeptide chains which has spatial arrangement vital for efficient functioning of molecule
What are inorganic ions essential for
Constituents of skeletal structures, maintains osmotic pressure and constituent of soft tissue, nerve impulse transmission and muscle contraction, activator for enzymes, hormone and vitamins
What is a cation
Positive ions
Is calcium cation or anion
Cation (ca*2+)
What is calcium’s structural use
Increases fidgety in bones, teeth, cartilage and component of exoskeleton of crustances)
How is calcium useful in human body
Clotting blood and activator for severe enzymes (lipase, ATPase, chlorinerase), stimulates muscle contraction and regulates transmission of nerve impulses, regulates permeability of cell
Who is calcium important in plants
In their cell wall development and middle lamella between cell walls
Is sodium cation or anion
Cation (Na+)
How is sodium useful in human body
Involved in regulation of osmotic pressure, controls water levels and maintains pH, affects absorption of carbs in intestines and water in kidneys, contributes to nervous transmission and muscle contraction
How is sodium useful in plants
Constituent in vacuole to maintain turgidity
Is potassium cation or anion
Cation (K+)
How is potassium useful in animals
Involved in water levels in body fluid and pH maintenance, assists active transport of cells across membranes, involved in synthesis of glycogen, protein and glucose breakdown, contributes to nerve transmission and muscle contraction
How is potassium used in plants
In flowering plants it generates healthy leaves and flowers , component of vacuole in plant to maintain turgidity
Is hydrogen cation or anion
cation (H+)
Hydrogen use in plants
Involved in Photosynthesis and respiration
Hydrogen use in animals
Involved in transport of oxygen, CO2 in the blood and involved in pH regulation of blood
Is ammonium cation or anion
Cation (HH4+)
Use of ammonium in human body
Essential component of nucleic acid, maintains pH in human body, component of nitrogen cells
Use of ammonium in plant and human
Component or amino acid, proteins, chlorophyll and some hormones like insulin
Is nitrate cation or anion
Anion (NO8-)
Uses of nitrate
Component of amino acid, proteins, vitamins, chlorophyll, essential in nucleic acids and some hormones made of proteins, also component of nitrogen cycle
Is hydrocarbonate cation or anion
Anion (HCO3-)
Uses of hydrocarbonate in human body
Involved in blood pH regulation and involved in CO2 transport in and out of blood
Is chloride cation or anion
Anion (cl-)
Uses of chloride in human body
Helps urine production in kidney by maintaining water balance, involved in CO2 transport in and out of blood, regulates affinity of haemoglobin to oxygen, involved in blood pH regulation and used to produce HCL in stomach
Is phosphate cation or anion
Anion (PO4*3-)
Use of phosphate in human
Increases bone, teeth, cartilage ridgity, component of phospholipid, ATP, nucleic acids, several important enzymes, involved in regulation of blood pH
Use of phosphate in plants
Helps root growth in plants
Is hydroxide cation or anion
Anion (OH-)
Hydroxide use in body
Regulation of blood pH
What’s a macronutrient
Ions required in large amounts
What’s a micronutrient
Ions required in small amounts
If human or plant has deficiency what does this mean
Doesn’t consume enough of certain ions or particular ions
What does cobalt defficency lead to
Anaemia
What does copper defficency in plants lead to
Young shoots dying back
What are some functions for minerals in large organic molecules
molecules, e.g. proteins contain sulfur and nitrogen, enzymes contain metal ions like copper, ion, zinc, phospholipid and nucleic acids contain phosphorus
Function of minerals in small organic molecules
ATP contains phosphorus (phosphorus also required for activation of small organic molecules), e.g.glucose has phosphorus added before freak down in respiration, hormone thyroxine has iodine
What is the functions of minerals in certain pigments
Haemoglobin and chlorophyll both contain iron and magnesium
Function of minerals as structures
Calcium and phosphate found in bonds and calcium found in plant cell wall
Function of minerals in determining anion-cation balance in cells
Sodium and potassium and chloride ions, important especially on nerves, muscles and sensory cells involved in impulse transmission
Function of minerals in determining water potential
Mineral salts and other solutes determine water potential of cells and body fluids, most organisms water potential canning function outside of narrow limits
What is a qualitative test
Test for a substance, not how much substance there is
What three types of carbohydrates can you test for
Starch, reducing sugars, non-reducing sugars
How do u test for starch
Add iodine to sample and if starch present goes from yellow-brown to blue-black
What does potassium iodine change colour when starch is present
When starch dissolved in potassium iodine, iodine forms a triiodide ion (I3-) which slips into middle of amaloyse helix causing colour change
What are reducing sugars
Monosaccharides and some disaccharides, they can give or reduce electron to other molecules
Method for test for reducing sugars
Heat the sample with Benedict’s solution and the colour will change from blue -> green -> yellow -> orange-red
Why does solution change colour in reducing sugars test
Benedict’s contains Cu2+ ions which are reduced to Cu+ ions forming orange-red copper oxide called precipitate as comes out of solution and forms solid
How do you test for non-reducing sugars
Boil sample with hydrochloric acid to hydrolysis the sample, then cool sample and use hydrogen carbonate to neutralise it, test for reducing sugars, green, yellow, organs, red all indicate presence of non reducing sugar
What test do you use to test for lipids
Emulsion test
Method for emulsion test
Take sample and mix with ethanol, then remove some of it and add water to a new test tube with it in, a colour white emulsion indicates presence of lipids
Why in emulsion test is lipids on top of the water
Made it tiny lipid droplets which come out of solution when mixed with water
What test do you use to test for proteins
Biuret test
Method of biuret test
Add biuret onto sample and if protein present will turn from blue to lilac
Why does colour change in biuret test
Colour formed by complex between nitrogen atoms in peptide chain and Cu2+ ions, so test really tests for presence of peptide bonds
What equipment would you use for a quantitive test for reducing sugars
Colorimeter
What is colorimetry
Try to quantify sugar concentration in original sample by assessing how these two variables changed
How does a colorimeter work
By shinning light through same, for reducing sugars you would use centrifuge to separate precipitate and excess Benedict’s solution (supernatant)
You would use a pipette to remove supernatant into cuvette which is placed into colorimeter and colorimeter need resetting to 100% transmission by using a blank after each reading
Why must there be no finger prints on curvette
Made of glass or plastic so fingerprints would affect light transmission
Why are colour filters used on colorimeter
For more accuracy, red filters detect how much light passes through filter in percentage transmission
Is the solution was red what colour light filter would be the best and worst to use
Blue = best and red= worst as blue would be absorbed by red solution but red light would just be reflected
What happens in colorimeter if there is lots of unreacted copper silva the and supernatant is still blue
Absorption of red light is high and percentage transmission would be low
What happen when the supernatant has a little unreacted copper surface and supernatant less blue
Absorption of red light low and percentage transmission is high
What blank is often used to reset colorimeter
Water
How do u make a calibration curve
Take series of known concentrations for reducing sugars, using a sample of each do Benedict’s test and then use colorimeter to record percentage transmission of light through each supernatant to the concentration of reducing sugar, you can then use this curve to found out how much sugar a sample has with only knowing light transmission or concentration
What is a biosensor
Uses biological or chemical variable which can’t easily by measured and transferred into electrical signal, they can detect water contamination and pathogens and toxins in food and can detect air born bacteria used in bioterorism programmes
Fibrous proteins
Have regular and repetitive sequences of amino acids and usually insoluble in water so they can form fibres, usually have structural function
Examples of fibrous proteins
Collagen, elastin (connective tissue), keratin (in hair)
Globular proteins
Rolls up into almost spherical shape, hydrophobic R groups turn into centre and hydrophilic ones on outside making it soluble in water as water molecules cluster and bond round them
Uses of globular proteins
Specific shape do function as enzymes, hormones(insulin), haemoglobin
Collagen function
To provide mechanical strength
Collagen use in artery walls
Layers of collagen prevent artery busting when in high pressure from blood pumping to heart
Collagen use in tendon and connective muscle
Tendon and connective tissue made from collagen to allow them to pull on bones
Collagen use in bones
Bones made from collagen and reinforced with calcium phosphate to make them hard
What tissue and bone like structure can collagen make
Cartilage and connective tissue
What is Keratin
Rich in cysteine so lots of disulphides bonds formed between peptide chains and hydrogen bonds making it very strong
Where is keratin found
Wherever body part needs to be hard and strong
Examples of where keratin is found
Fingernails, hair, claws, hooves, horns, scales, fur and feathers
What does keratin provide
Mechanical protection and impermeable barrier to prevent infection and waterproof protecting entry of water-born pollutants
Structure and properties of elastin
Cross-linked coiling makes elastin structure strong and extensive
Where is elastin found
Living things where they must stretch or adapt their shape as part of life’s process
Function of elastin in skin
Means skin can stretch round our bones and muscles, without it after being pinched skin wouldn’t recoil
What is use of elastin in lungs
Allows them to inflate and deflate
Use of elastin in bladder
Allows bladder to expand and hold urine
Elastin use in blood vessels
Like collagen, it helps blood vessels stretch and recoil as blood pumped through them helping to maintain pressure wave of blood
What structure is haemoglobin and how many polypeptides is it made of
Quaternary structure made of 4 polypeptides, has 2 a-globin chains and 2 B-globin chains and each of these has its own tertiary structure, but fitted together forms haemoglobin molecule
How is haemoglobin held together
By bonds and interactions giving it very specific shape
What does it mean that haemoglobin is a prosthetic group
At one position on outside of each chain, theres a space where haem group help and this group called prosthetic group
Function of haemoglobin
Carry oxygen from lungs to tissues
How does haemoglobin pick up oxygen from lungs
Oxygen molecules bond to iron in each 4 haem groups of haemoglobin molecule causing it to go from purple-red to bright red and oxygen released by haemoglobin when it reaches the tissue
What is insulin made of
2 polypeptide chains, A chain starts with section of a-helix and B chain ends with B-pleated which both fold into tertiary structure and joined by disulphides links
Why is insulin soluble
As amino acids with hydrophilic R group on outside of molecule
What is insulin function
It binds to glycoprotein receptors on outside of muscle and fat cells to increase their glucose uptake from the blood, which increases glucose rate of consumption
What is pepsin
Enzyme that digests protein I stomach, made of 327 amino acids in single polypeptide chain
What structure is pepsin
Fold into symmetrical tertiary structure
Why is pepsin very stable in stomach acidic environment
As has very few amino acids with basic R groups but 43 acidic amino acids, meaning there are few basic groups to except H+ions so little effect on enzyme structure
What binds hold pepsin tertiary structure together
Hydrogen bonds and 2 disulphides bridges
Example of when it is useful to be able to predict the shape of protein
Predicting occurrence of biologically active binding sites on a protein molecule can help identify medicines
What are the two types of predicting a protein shape
Ab inito protein molecule, comparative protein modelling
What is Ab initial protein modelling
Model built based on physical and electrical properties of an atom in an amino acid sequence, in this there are multiple solutions to same amino acid sequence and other methods need applying to reduce number of solutions
What is comparative protein modelling
One approach is protein threading which scans amino acids sequence against a database of solved structures and produces set of possible models which would match the sequence
Why is it important enzymes have a globular structure
As globular structures are tightly fixed and enzymes role depends on its shape
Properties of globular properties
Used in buffering and usually water soluble
What is a collid
Particle that remains dispersed in solution rather than dissolving, settling or floating
Give examples of collids
Many larger molecules such as proteins and lipids
Why are proteins and lipids collids
Too small to settle out under gravity but to large to dissolve as large SA making them readily available for chemical reactions
What type of structure is antibodies
Globular protein
What is most globular proteins function
Involved in transport out of cells and around body
Is steel or collagen stronger
Collagen
Structure of collagen
3 polypeptide chains coiled round each other in triple helix (rope like) structure
What is Transamination
Process of synthesising non-essential amino acids
What can an error in synthesis of proteins cause
Sickle cell animea of cystic fibrosis
How can you separate proteins from solvent
Electrophoresis, progressive hydrolysis and chromatography
Principal of chromatography
To separate mixture into constituents (eg. Biological molecules)
What are the two stages of chromatography
Stationary and mobile phase
What is the stationary phase
Chromatography paper or thin layer chromatography (TLC)plate (made form cellulose), in both cases there are free OH groups pointing out in contact with mobile phase
Mobile phase
Solvent for biological molecules (use of water for polar molecules or ethanol for non-polar molecule) mobile phase flows through and across stationary phase carrying biological molecule with it
What is the practical for separating amino acid from solution
1.wear eye protection. 2.draw pencil line on chromatography paper and put tiny dot to show where solution solution mixture will be placed 3.put solution mix on for 6times and allows to dry in between each using capillary tube 4.place into solvent below pencil line 5. Cover beaker with watch glass 6.let solvent run till just below top of paper, then remove from solvent and allow to dry
What happen in chromatography practical
As solvent travels up the less soluble component of solution will travel slower, you can use Rf value to help identify components
How does chromatography work in colourless molecules like protein
You can use UV so paper will flow except where pigment is, you can use Ninhydrin to see amino acid, when you spray paper amino acids become brown or purple, or iodine crystals in a closed container with paper and iodine binds to each molecule in each spot making them visible
What does the soles of a complement in solution depend on
Solubility in given solvent and polarity
How does chromatography work
Exposed OH groups make surface of paper very polar allowing hydrogen bonds to form with molecule and other interactions
What happens to highly polar solute in chromatography and low polar
Stick to surface being absorbed, so move slower but non-polar solute will travel fast
What should you do in chromatography if two molecules travel at same speed
Change the solvent or the pH
What is chromatography commonly used for
Used to monitor progress of reactions as it works relatively quick and also urine testing for illegal drugs in athletes
