Biological molecules Flashcards
(149 cards)
1
Q
When do most atoms tend to be stable
A
When their outermost shell has 8 electrons
2
Q
Describe a covalent bond
A
2 non metals sharing electrons with other atoms, shown by 1 single line
3
Q
How many covalent bonds do oxygen, carbon, nitrogen and hydrogen form
A
hydrogen- 1 oxygen- 2 nitrogen- 3 carbon-4 As they have that number of electrons on outer shell
4
Q
Define condensation reactions
A
- 2 molecules joined together with the removal of water
- almost all happen when 2 -OH groups react together
- involves formation of covalent bonds
5
Q
Define hydrolysis reactions
A
- 2 molecules broken apart with the addition of water
- involves breaking of covalent bonds
6
Q
What are units called that are joined by condensation/broken by hydrolysis reactions called, what is 2 and many called
A
- monomers
- dimers
- polymers
7
Q
What types of molecules are in carbohydrates, what is the monomer and what is the polymer
A
- C, H, O
- monosaccharides e.g. glucose
- polysaccharides e.g. starch
8
Q
What types of molecules are in proteins, what is the monomer and what is the polymer
A
- C, H, O, N, S
- amino acids
- polypeptides and proteins
9
Q
What types of molecules are in nucleic acids , what is the monomer and what is the polymer
A
- C, H, O, N, P (phosphorous)
- nucleotides
- DNA and RNA
10
Q
Describe atoms/bonds in water
A
- water consists of 2 hydrogen atoms, each covalently bonded to 1 oxygen atom
- The oxygen has a greater number of positive protons in ts nucleus- so it exerts a stronger attraction for the shared electrons
- means the oxygen atom becomes slightly negative, and the H atoms become slightly positive
- when this happens, molecule is called polar
11
Q
Describe hydrogen bonding
A
- a hydrogen bond is a weak interaction which happens wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom
- weaker than a covalent bond, but in some polymers thousands and thousands of hydrogen bonds form between chains of monomers- can stabilise the structure of some biological molecules
12
Q
water bonding diagram
A
13
Q
Properties of water- liquid
A
- as in any liquid, water molecules constantly move around
- but unlike any other, as they move they continuously make and break hydrogen bonds
- hydrogen bonds between molecules make it harder for them to escape to become a gas
- by contrast, other less polar but similarly sized molecules (e.g. H2S) are gasses at room temp
- even with H bonds, water has quite a low viscosity- it can flow easily
Because it is liquid at room temp, water can:
- provide habitats for living things in rivers, lakes and seas
- form a major component of the tissues in living organisms
- provide a reaction medium for chemical reactions
- provide an effective transport medium, e.g. in blood and vascular tissue
14
Q
Properties of water-density
A
- when most liquids get colder, they become denser
- if this happened with water, water at top of a pond would freeze and sink- would continue till whole pond full of ice
- water becomes denser as it cools to around 4 degrees C
- as it goes from there to freezing point, because of its polar nature, the water molecules align themselves in a structure which is less dense than liquid water
Because ice is less dense than liquid water:
- aquatic organisms have a stable environment in which to live in through winter
- ponds and other bodies of water are insulated against extreme- layer of ice reduces rate of heat loss from rest of pond
15
Q
Properties of water- solvent
A
- water is good solvent for many substances found in living things, including ionic solutes e.g. sodium chloride, and covalent solutes e.g. glucose
- because water is polar, the positive and negative parts of the water molecule are attracted to the + and - parts of the solute
- the water molecules cluster around these charged parts of the solute molecules or ions, and will help to separate them and keep them apart
- and this point, they dissolve and a solution is formed
Because water is such a good solvent:
- molecules and ions can move around and react together in water, many such reactions happen in the cytoplasm of cells, which is over 70% water
- molecules and ions can be transported around living things whilst dissolved in water
16
Q
Properties of water- cohesion and surface tension
A
- a drop of water on a flat surface doesn’t spread out- can look almost spherical- this is because hydrogen bonding between the molecules pulls them together- the water molecules demonstrate cohesion
- happens at the surface of water too- the water molecules at the surface are all hydrogen bonded to the molecules beneath them and hence more attracted to water molecules below than air above
- means that the surface of water contracts ( because being pulled inwards)- gives the surface of water an ability to resist force applied to it- known as surface tension
Because of cohesion and surface tension:
- columns of water in plant vascular tissue are pulled up the xylem tissue together from the roots
- insects like pond skaters can walk on water
17
Q
Properties of water- specific heat capacity
A
- water temperature is a measure of the kinetic energy of the water molecules
- water molecules held together quite tightly by hydrogen bonds
- therefore, you need to put in a lot of heat energy to increase kinetic energy and temperature
- the amount of heat energy known as SHC- waters is high- 4.2kJ to raise temp of 1kg by 1*C
- means water doesn’t heat up or cool down easily
As water is main component of many living things is water, and many organisms live in water, its high SHC is important:
- living things, including prokaryotes and eukaryotes need a stable temperature for enzyme controlled reactions to happen properly
- aquatic organisms need a stable environment in which to live
18
Q
Properties of water- latent heat of vaporisation
A
- when water evaporates, heat energy, known as the latent heat of vaporisation, helps the molecules to break away from each other to become a gas
- H bonds holding molecules together- means a relatively large amount of energy is needed for water molecules to evapourate- high LHOV
Therefore:
- water can help to cool living things and keep their temperature stable
- e.g. mammals are cooled when sweat evaporates, plants cool when water evaporates from mesophyll cells
19
Q
Properties of water- reactant
A
- water is a reactant in reactions such as photosynthesis, and in hydrolysis reactions such as the digestion of starch, proteins and lipids
- properties as a reaction don’t directory draw on its polarity, but its role as a reactant is extremely important for the digestion and synthesis of large biological molecules
20
Q
List properties of water
A
- Liquid at room temperature
- ice less dense than water
- good solvent
- cohesion and surface tension
- high specific heat capacity
- high latent heat of vapourisation
- good reactant
21
Q
What are carbohydrates
A
- ‘hydrated carbon’- for every carbon atom there are 2 hydrogen and 1 oxygen atoms
- source and store of energy
- structural units
- some also part of other molecules eg nucleic acids and glycolipids
- 3 main types- monosaccharides, disaccharides, polysaccharides
- common mono + di have names ending in -ose
22
Q
What are monosaccharides
A
- simplest carbohydrates
- source of energy in living things
- well suited to this as have large number of carbon-hydrogen bonds
23
Q
Properties of monosaccharides
A
- sugars- sweet
- soluble in water
- insoluble in non-polar solvents
24
Q
Structure of monosaccharides
A
- can exist as straight chains or in ring/cyclic forms
- have backbone of single bonded carbon atoms, with one double-bonded to an oxygen atom to form a carbonyl group
25
Different types of monosaccharides, differences between them
- hexose - 6 C atoms
- Pentose- 5
- tetrose- 4
- triose- 3
- hexose- monomers of more complex carbohydrates, bond together to form disaccharides or polysaccharides
- in solution, triose and tetrose exist as straight chains, , but pentoses and hexoses more likely to be found in ring/cyclic form
26
What can glucose exist as
- a number of different isomers- same formula but atoms arranged differently
- in straight-chain, -H and -OH can be reversed, in ring the -H and -OH on C1 can be above/below plane of ring- important difference in polymerisation
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Disaccharide properties
- sweet
| - soluble in water
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When are disaccharides made
- when 2 monosaccharides are joined togetehr
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2 types of disaccharides, examples
- maltose and lactose- reducing sugars
| - sucrose- non-reducing
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Examples of disaccharides and their components
A (alpha) glucose + A glucose = maltose
A glucose + fructose = sucrose
B (beta) glucose + A glucose = lactose
B glucose + B glucose = cellobiose
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Formation of disaccharides
- condensation reaction
- forms a glycosidic bond
- 2 hydroxyl groups line up next to each other, from which a water molecule is removed
- leaves an oxygen atom acting as link between monosaccharide units
- 1-4 glycosidic linkage
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Breaking down of disaccharides
- hydrolysis reaction
- requires the addition of water
- water provides a hydroxyl group (-OH) and a hydrogen (-H), which helps 1-4 glycosidic bond to break
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A glucose- displayed and molecular formula, role in the body, type of sugar
- C6H12O6
- energy source, component of starch and glycogen which act as energy stores
- hexose
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B glucose- displayed and molecular formula, role in the body, type of sugar
- C6H12O6
- energy source, component of cellulose which provides structural support in plant cell walls
- hexose
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Difference between A and B glucose
Isomers- hydroxyl group on C1 below the plane of ring in A, above in B
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ribose- displayed and molecular formula, role in the body, type of sugar
- C5H10O5
- component of ribonucleic acid (RNA), ATP and NAD
- pentose
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deoxyribose- displayed and molecular formula, role in the body, type of sugar
- C5H10O4
- component of DNA
- Pentose
38
2 types of polysaccharides, example
- homopolysaccharide- made out of 1 type of monomer- starch
| - heteropolysaccharide- more than one- hyaluronic acid in connective tissue
39
Energy source vs store
- source- glucose- reactant in respiration
| - store- starch/glycogen- many joined together
40
Solubility of polysaccharides
- less soluble in water than monosaccharides
- if glucose molecules dissolved in the cytoplasm, the water potential would reduce, and excess water would diffuse in, disrupting the normal workings of the cell
- less soluble because of size and because regions which could H bond with water hidden on inside of structure
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2 types of starch
- amylose
| - amylopectin
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Starch- where is it found
Starch granules in plant cells
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Amylose- structure
- long chain of A glucose
- glycosidic bonds between C1 and C4
- coils into spiral shape, with H bonds holding spiral in place
- hydroxyl groups on C2 situated on the inside of the coil- makes molecule less soluble, allows H bonds to form to maintain coiled structure
44
Amylopectin structure
- chain of A glucose
- glycosidic bonds between C1 and C4
- Also has branches formed by glycosidic bonds between C1 and C6
- also coils into a spiral shape, held together with H bonds, but with branches emerging from the spiral
45
Starch function
Acts as an energy store- g; glucose for respiration
46
How starch's structure is important for its function
- compact- doesn't occupy a large amount of space, occurs in dense granules
- holds glucose molecules in chains so it can easily be 'snipped off' by hydrolysis from the ends when needed for respiration
- branched- allows many glucose molecules to be snipped off at same time when needed for respiration quickly
47
How is starch broken down
- enzyme amylase- hydrolyses 1-4 glycosidic linkages
| - enzyme glucosidase- 1-6 glycosidic linkages (amylopectin)
48
Amylose vs amylopectin displayed formula
49
Where is glycogen found
Dense granules in animals
50
Glycogen structure
- A glucose monomers
- like amylopectin with glycosidic bonds between C1 and C4, and with branches formed by glycosidic bonds between C1 and C6
- 1-4 bonded chains tend to be smaller than amylopectin- has less of a tendency to coil
- however, it has more branches- more compact, easier to remove monomer units as there are more ends
51
Glycogen function
energy store- glucose for respiration
52
How glycogens structure is important for its function
- compact- doesn't occupy much space
- more ends for glucose molecules to be broken off by hydrolysis- more respiration allowed- animals have more metabolic activity
53
glycogen displayed structure
54
Where is cellulose found
- cell walls of plants
55
What type of polysaccharide is starch, describe it
tough, insoluble, fibrous homopolysaccharide
56
Structure of cellulose
- monomer is B glucose- up to 15000 monomers
- every other B glucose molecule is inverted 180 degrees so the hydroxyl groups on C1 and C4 line up
- 1-4 glycosidic bond
- H bonding between roated B-glucose molecules
- hydrogen bonding between the rotated B glucose monomers in different chains- the hydroxyl group sticks out enabling H bonds to be formed between chains
- straight chains lying side by side- not spiraled
- 60-70 chains bound together with H bonds between chains = microfibrills- 10-30 nm in diameter
- then bundle together into macrofibrils- up to 400 microfibrils- embedded in pectins (like glue) to form cell wall
57
How the structure of cellulose supports its function
- having alternating inversions of B glucose molecules, the 1-4 glycosidic bond, and hydrogen bonding between inverted B glucose monomers in each chain prevents spiralling. H bonds in chain give additional strength
- H bonding between molecules in different chains stabilise and give the whole structure additional strength- hydroxyl on C2 sticks out- allows H bonds to be formed between chains
- microfibrils and macrofibrils have very high tensile strength- because of the strength of the glycosidic bonds and because of H bonds between chains- macrofibrils are twice stronger than steel wire of the same diameter
- macrofibrils run in all directions- crisscrossing the wall for extra strength
- hard to digest cellulose because glycosidic bonds between the glucose molecules are less easy to break- most animals don't have enzyme to catalyst reaction
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Structure for function of cell wall as a whole
- because plants don't have rigid skeleton, each cell needs to have strength to support the whole plant
- space between macrofibrils for water and mineral ions to pass on their way into and out of the cell- makes the cell wall fully permeable
- the wall has high tensile strength- prevents plant cells from bursting when they are turgid- helps support whole plant- turdgid cells press against eachoter, supporting the structure of the plant as a whole- also protects delicate cell membrane
- the macrofibril structure can be reinforced with other substances for extra support, or to make the walls waterproof. For example, cutin and suberin are waxes that bloc the spaces in the cell wall, and make it more waterproof. Lignin (a polymer of phenylpropane units) performs the same function for xylem vessels. I the woody part of tree trunks, cell walls are extra thick to withstand the weight.
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How has cellulose been used by humans
- cotton- 90% cellulose
- cellophane and celluloid (used to be used in photographic film) also derived from cellulose
- one of main components of paper is cellulose
- rayon (viscose) is a semi-synthetic fibre produced from cellulose- similar properties to silk
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2 other examples of structural polysaccharides
Bacterial cell walls:
- whole structure surrounding the cell is s
a peptidoglycan- made from long polysaccharide chains that lie in parallel, cross-linked by short peptide chains (made of amino acids)
Exoskeletons:
- insect and crustacean exoskeletons are made of chitin
- differs from cellulose as it has an acetylamino rather than hydroxyl group group on C2
- forms cross-links between long parallel chains of acetylglucosamine, in a similar way to celluose
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3 most important lipids for humans
- Triglycerides
- Phospholipids
- steroids
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Properties of lipids
- contain large amounts of carbon and hydrogen- smaller amounts of oxygen
- Insoluble in water (as not polar)- don't attract water molecules
- dissolve in alcohol
- macromolecules
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Components of a triglyceride
- Glycerol
| - 3x fatty acids
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Special type of fatty acid (how is made in body)
Some must be ingested 'complete'- essential fatty acids- we can make many though
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Structure (with displayed formula) of glycerol
- alcholol so has free -OH groups (hydroxyl)
| - three -OH groups
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Fatty acid structure (with displayed formula)
- carboxyl group (-COOH) on one end
- attached to hydrocarbon tail (made of only carbon and hydrogen atoms)
- 2-20 carbons long
- Carboxyl group ionises into a H+ and a -COO- group
- structure is therefor an acid as it can produce free H+ ions
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2 types of fatty acids- describe, implications of this
- saturated- no double C bonds
- unsaturated- double bond between 2 of the C atoms- fewer H atoms can be bonded to the molecule
- single c=c bound- monounsaturated (e.g. oleic acid), more than one makes it polyunsaturated (e.g. linoleic acid)
- having one or more c=c bonds changes shape of hydrocarbon tail- gives kink in tail where double bond is
- kinks push molecules apart slightly- makes them more fluid
- more unsaturated makes melting point lower
- animal lipids often contain a lot of saturated fatty acids- often solid at 20 degrees C
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Formation of a triglyceride (with displayed formula)
- 3 x condensation reactions between -COOH (carboxyl group) of the fatty acid and the -OH (hydroxyl) group of the glycerol
- 3 x ester bonds formed (covalent) as 3 -OH on glycerol
- 3 x water molecules released
- fatty acids may be same o different- e.g. some may be saturated vs unsaturated
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triglyceride displayed formula
70
Triglyceride breaking
- 3x hydrolysis reactions
- 3 x water molecules needed
- 3 x ester bonds broken
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Functions of triglycerides
Energy source:
- can be broken down in respiration to release energy and generate ATP
- first step is to hydrolysed ester bonds, and then both glycerol and fatty acids can be broken down completely to carbon dioxide and water
- respiration of a lipid produces more water than respiration of a sugar
Energy store:
- because triglycerides are insoluble in water, they can be stored without affecting the water potential of the cell
- mammals store fat in adipose cells under the skin
- one gram of fat releases twice as much energy as 1g of glucose as lipids have a higher proportion of hydrogen atoms than the carbohydrates, and also no oxygen atoms
Insulation:
- adipose tissue is a storage location for lipid in whales (blubber)- acting as a heat insulator
- lipid in nerve cells acts as an electrical insulator
- animals preparing for hibernation store extra fat
Buoyancy:
- because fat is less dense than water, it is used by aquatic mammals to help them stay afloat
Protection:
- humans have fat around delicate organs, such as their kidneys, to act as a shock absorber
- the peptidoglycan cell wall of some bacteria is covered in a lipid-rich outer coat
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Structure of phospholipids
- similar to triglycerides
- 1 of fatty acids replaced by phosphate group
- 3 x condensation reactions
- 3 x water molecules released
- 2 x ester bonds
- 1 x phosphate ester bond- OH group on phosphoric acid molecule (H3PO4), and one of 3 -OH on glycerol
- most of fatty acids found in phospholipids have even number of C atoms- 16 or 18
- commonly, one is saturated and 1 is unsaturated
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Behaviour of phospholipids in water
- phosphate group- negative charge- polar (hydrophilic)
- fatty acid- non-polar- hydrophobic
- means phospholipid molecule is amphipathic
- membrane lipids tend to be amphipathic, whereas those involved in storage aren't
- In water phospholipids that are amphipathic may form a layer on the surface of water, with the heads in the water, and the tails sticking up out of te water
- may also form micelles- tiny balls with the tails tucked away inside, and the heads pointing outwards into the water
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Describe the use of phospholipids in membranes (and why they act as good ones)
- inside and outside a cell membrane is an aqueous solution
- the phospholipids form a bilayer- 2 rows of phospholipids with tails pointing in and heads pointing out
- between 20 and 80% of membranes in plant and animal cells are made of phospholipids (bacterial membranes tend to contain a greater proportion of protein)
Why they make a good membrane:
- individual phospholipids are free to move around in their layer, but will not move into any position where their hydrophobic tails are exposed to water- gives membrane some stability
- membrane is selectively permeable- only possible for small and non-polar molecules (e.g. oxygen and carbon dioxide) to pass through tails in bilayer- lets the cell control what goes into and comes out of the cell- keeps cell functioning properly
75
Properties of cholesterol
- steroid alcohol (sterol)
- type of lipid not made from glycerol or fatty acids
- small
- hydrophobic molecule- can sit in the middle of the hydrophobic part of bilayer
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Cholesterol structure
- consists of 4 carbon-based rings (isoprene units)
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Cholesterol in plants vs animals
Animals- mainly made in the liver
Plants- also have cholesterol derivative in membranes- stigmasterol- only difference is double bond between C22 and C23
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Cholesterol function
- maintains stability/fluidity in membranes
- makes us steroid hormones oestrogen, testosterone and vitamin D- can pass through hydrophobic part of cell membranes- steroids also abundant in plants, and on ingestion and absorption some can be converted into animal hormones
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2 types of ions, examples
Cations- positive- calcium, sodium, hydrogen, potassium,ammonium
Anions- negative- nitrate, hydrogen carbonate
80
Calcium functions
Ca2+:
- increases rigidity of bones, teeth and cartilage, component of exoskeleton of crustaceans
- important in clotting blood and muscle contraction
- activator for several enzymes- e.g. lipase, ATPase, cholinsterase
- stimulates muscle contraction and regulates the transmission of nerve impulses
- regulates permeability of cell membranes
- important for cell wall development in plants, and in formation of middle lamella between cell walls
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sodium functions
Na+
- involved in the regulation of osmotic pressure, control of water levels in body fluid and maintenance of pH
- affects absorption of carbohydrate in the intestine, and water in the kidney
- contributes to nervous transmission and muscle contraction
- constituent of vacuole in plants- helps maintain turgidity
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Pottassium functions
K+
- involved in control of water levels in body fluid and maintenance of pH
- assists active transport of materials across cell membrane
- involved in synthesis of glycogen and protein, and breakdown of glucose
- generates healthy leaves and flowers in flowering plants
- contributes to nervous transmission and muscle contraction
- component of the vacuole in plants, helping to maintain turgidity
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Hydrogen functions
H+
- involved in photosynthesis and respiration
- involved in transport of oxygen and carbon dioxide in blood
- involved in regulation of blood pH
84
Ammonium functions
NH4 +
- component of amino acids, proteins, vitamins and chlorophyll
- some hormones made of proteins e.g. insulin
- essential component o nucleic acids
- involved in the maintenance of pH in the human body
- component of nitrogen cycle
85
Nitrate functions
NO3 -
- component of amino acids, proteins, vitamins and chlorophyll
- some hormones made of proteins, which contain nitrogen, e.g. insulin
- essential component o nucleic acids
- component of nitrogen cycle
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Hydrogencrabonate functions
HCO3 -
- involved in regulation of blood pH
- involved in the transport of carbon dioxide into and out of blood
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What are proteins
Large polymers compromised of long chains of amino acids
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Functions of proteins
- form structural components of animals in particular- e.g. muscles are made of protein
- their tendency to adopt specific shapes makes protein important as enzymes, antibodies and some hormones
- membranes have protein constituents that act as carriers and pores for active transport across the membrane and facilitated diffusion
89
Describe protein creation in animals vs plants
both need amino acids to make protein
- animals- can make some but need to ingest the others (essential amino acids)
- plants- can make all the amino acids they need , but only if they can access fixed nitrogen e.g. nitrate
90
Describe the structure of amino acids, give 3 examples, displayed formula
- each amino acid contains hydrogen, carbon, oxygen and nitrogen
- some contain sulfur
- over 500, but only 20 proteinogenic (found in proteins)
- 1 amine group (-NH2) at one end
- 1 carboxyl group (-COOH) at the other end
- R group- representative of a different group- different for each amino acid- for example:
- glycine- H- simplest amino acid
- Alanine- CH3
- Cysteine- CH3S
R groups can vary by size, charge and polarity- some hydrophobic and some hydrophilic
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amino acid names
- almost all end in -ine
| - only exceptions are those which have an acidic R group, e.g. aspartic and glutamic acid
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What can amino acids act as
Buffers
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Describe how amino acids can act as buffers
When pH is too LOW:
- the amino group can accept a H+ ion
- Changes from NH2 to NH3+
- -NH2 + H+ ---> NH3+ (reversible)
When pH is too HIGH:
- The carboxyl group can give up a H+ ion
- Changes from COOH to COO
- -COOH ---> - COO- + H+
Means amino acid has acidic and basic properties- known as amphoteric
- in long chain of amino acids, there are amine and carboxyl groups on each end, but also many on R groups that have same buffering effect
- helps regulate changes in pH- byffering- helps resist large changes
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name of 2 and multiple amino acids joined
Dipeptide is 2
Polypeptide is more
always joined in same way regardless of R group
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Describe formation of dipeptide/joining of amino acids
- condensation reaction
- releases water molecule using OH of carboxyl group and H of amino group
- covalent peptide bond formed
- bond is the c = O and N-H in middle
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Describe formation of dipeptide/joining of amino acids
- condensation reaction
- releases water molecule using OH of carboxyl group and H of amino group
- covalent peptide bond formed
- bond is the c = O and N-H in middle
97
describe breaking of multiple amino acids
- hydrolysis reaction
- water molecule added
- peptide bond broken
- enzyme used
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use of enzymes in dipeptide breakage/formation
- enzymes needed to catalyse the hydrolysis/condensation reactions
- e.g. protease enzymes in the intestine break peptide bonds during digestion
- also break down protein hormones so their effects arent permanent
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names of structures of proteins
- primary
- secondary
- tertiary
- quaternary
100
primary structure of proteins
- sequence of amino acids
- number and order of amino acids important as just one change can change function
- 20 amino acids- at every point in chain there are 20 alternatives- most proteins at least 100 amino acids long- 20^100 possible ways of ordering 100 amino acids
- order in primary structure will determine shape of protein molecule through its other structures- determines function
- peptide bonds only
101
secondary structure of proteins
- primary structure twists into shape called secondary structure- a helix or b Pleated sheet - both use only H bonds. Even though H bonds are relatively weak, many are formed, so makes both type of structures stable at optimum temperatures and pH
- some chains don't adopt regular structure, and some may have more than 1 secondary structure different ends of the chain
a (alpha) helix:
- 36 amino acids per 10 turns of helix
- helix held together by hydrogen bonds between the -NH group of one amino acid and the -CO group of another 4 places ahead of it in the chain
B (beta) pleased sheet:
- fold very slightly in zig-zag structure
- Hydrogen bonds between -NH group of one amino acid and the -CO group of another further down the strand holding the sheet together
102
Tertiary structure of proteins
- coils and pleats (secondary structure) themselves start to fold, along with areas of straight chains of amino acids
- very precise shape held firmly in place by bonds between amino acids which lie close to each other
- tertiary structure may adopt a supercoiled shape (e.g. in fibrous proteins), or a more spherical shape ( in globular protein)
- hydrogen bonds, disulphide links, ionic bonds and hydrophilic and hydrophobic interactions
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Quaternary structure of proteins
- multiple polypeptide chains arranged to make complete protein molecules
- may also be held together with same types of bond that hold the tertiary structure
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Describe hydrogen bonds in protein
- form between H atoms with a slight positive charge and other atoms with a slight negative charge
- in amino acids, they form in hydroxyl, carboxyl and amino groups
- for example, hydrogen bonds may form between the amino group of one ami no acid and the carboxyl group of another
- may also form between polar areas of the R groups
on different amino acids- these in particular are involved in keeping the tertiary and quaternary structure of the protein in the correct shape
- presence of multiple hydrogen bonds can give protein molecules a lot of strength
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Describe disulphide links in proteins
- The R group of the amino acid cysteine contains sulphur
- disulphide bridges formed between the R group of 2 cysteines
- these are strong covalent bonds
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Ionic bonds in proteins
- can form between those carboxyl groups and amino groups that are part of R groups ( as ones not part of R groups only on end of chain)
- these ionise into NH3+ and COO-
positive and negative groups like this are strongly attracted to each other to form an ionic bond
107
describe hydrophobic and hydrophilic interactions in proteins
- hydrophobic parts of the R groups tend to associate together in he centre of the polypeptide to avoid water
- in the same way,hydrophilic parts are found at the edge of the polypeptide to be close to water
- hydrophobic and hydrophilic interactions cause twisting of the amino acid chain, which changes the shape of the protein
- these interactions can be a very important influence given that most proteins are to be found surrounded by water inside a living organism
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levels of protein structure picture
109
tertiary protein structre diagram
110
order types of bonding in tertiary structure of protein from strongest to weakest
- ionic bonds
- disulfide links
- hydrogen bonds
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2 types of proteins
- Fibrous
| - Globular
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Properties and examples of fibrous proteins
- relatively long, thin structure
- regular, repetitive sequences of amino acids
- means they can form fibres
- insoluble in water
- structural role- metabolically inactive
- collagen and elastin- connective tissue
- keratin - hair
113
Collagen structure
- almost every 3rd amino acid is glycine
- also lots of proline and hydroxyproline
- primary structure- helix shape
- hydrogen and covalent bonds hold 3 helixes together- tropocollagen/ triple helix
- covalent cross-linkages hold these together- staggered (like bricks)- extra strength
- many of these are a collagen fibril
- many of these make collagen fibre
114
Collagen function
Provides mechanical strength:
- artery walls- prevents artery bursting when withstanding high pressure from blood being pumped by heart
- tendons- made of collagen- connect muscles to bones- allow them to pull on bones
- bones- made from collagen- reinforced with calcium phosphate- makes them hard
- cartilage and connective tissue- made from collagen
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Keratin strucure
- rich in cysteine- lots of disulfide bridges form between polypeptide chains
- alongside hydrogen bonding, this makes the molecule very strong
116
Keratin function
- found wherever a body part needs to be hard and strong
- found in fingernails, hair, claws, hoofs, horns, scales, fur and feathers
- provides mechanical protection
- provides impermeable barrier to infection
- waterproof- prevents entry of water-borne pollutants
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Elastin structure
- crosslinking and coiling make structure strong and extensible
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Elastin function
Found in living things where they need to stretch and adapt their shape as part of life processes
- skin- can stretch around our bones and muscles- without it, it wouldn't go back to normal after being pinched
- lungs- allows them to inflate and deflate
- bladder- helps it hold urine
- blood vessels- helps them stretch and recoil as blood is being pumped through them- helps maintain pressure wave of blood as it passes through
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Properties of globular proteins, 3 examples
- relatively spherical shape
- hydrophobic R groups turned inwards and hydrophilic on outside- water-soluble as water molecules can easily cluster around to bind to them
- often have very specific shapes- helps them to take up roles as enzymes, hormones and haemoglobin
- haemoglobin, insulin, pepsin
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Haemoglobin structure
- Quaternary structure made up of 4 polypeptides- 2 alpha-globin chains and 2 beta-globin chains
- each of these has its own tertiary structure, but when fitted together they form 1 haemoglobin molecule
- shep held together by normal bonds
- interactions between the polypeptides gives the molecule a very specific shape
- at one position on the outside of each chain, there is a space in which a haem group is held- called prosthetic groups- essential part of molecule (couldn't function without it), but not made of amino acids
- haem group contains an iron ion
- a protein associated with this kind of group is called a conjugated protein
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Function of haemoglobin
- carries oxygen from the lungs to the tissues
- in the lungs, an oxygen molecule binds to the iron in each of the 4 haem groups in the haemoglobin molecules
- when it binds, haemoglobin turns from a purple-red colour to a bright red
- the oxygen is released by the haemoglobin when it reaches the tissues
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Insulin structure
- made of 2 polypeptide chains
- The A chain begins with a section of alpha-helix, and the B chain ends with a beta-pleat
- both chains fold into a tertiary structure, and are then joined together by disulfide links
- amino acids with hydrophilic R groups are on outside- makes it soluble in water
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Insulin function
Blinds to glycoprotein receptors on the outside of muscle and fat cells to increase the uptake of glucose from the blood, and to increase the rate of consumption of glucose
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Pepsin function
Enzyme that digests protein in the stomach
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Pepsin structure
- made up of single polypeptide chain of 327 amino acids, but it folds into a symmetrical tertiary structure (not quaternary as not 2 or more tertiary)
- very few amino acids with basic R groups (only 4)- but 43 amino acids with acidic R groups
- helps to explain why it is so stable in acidic environment of the stomach- very few basic groups to accept H+ ions, and therefore there can be little effect on the enzymes structure
- the tertiary structure is also held together by hydrogen bonds and 2 disulfide bonds
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How to prepare a food test sample
- grind and squash food
| - mix with small amount of water (or alcohol in lipids)
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How to prepare a food test sample
- grind and squash food
| - mix with small amount of water (or alcohol in lipids)
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Test for starch, how it works, positive result
- add iodine solution to sample
- when dissolved in potassium iodide, the iodine (I2) forms a triiodide ion I3-, which slips into the middle of the amylose helix- causes colour change
- yellow-brown turns to blue-black
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Test for reducing sugars, how it works, positive result
- includes all monosaccharides and some disaccharides
- known as reducing as they can reduce or give electrons to other molecules
- heat with benedicts solution (alkaline copper II sulfate)
- contains Cu2+ ions which are reduced to Cu+ ions- forming orange-red copper (I) oxide (Cu2O)
- called precipitate as it comes out of solution and form solid suspended in reaction mixture
- turns from blue to green to yellow to orange-red
- if you use benedicts solution in excess, the intensity of the colour is proportional to the concentration of sugar
- can also use commercially manufactured strips- match with calibration card- often used for diabetes tests
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Test for non-reducing sugars, how it works, positive result
- test sample for reducing incase some in solution
- take separate sample and boil it with hydrochloric acid to hydrolysed the sucrose into glucose and fructose
- frees up reducing groups
- cool and use sodium hydrogencarbonate to neutralise
- test for reducing sugars again
- positive result (green-yellow-orange-red) indicates a non-reducing sugar (e.g. sucrose) was present in the original sample
- sample may contain both- test for reducing first, if precipitate has more mass in nonreducing test, there is some present
- extract precipitate through filtration or using centrifuge
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Test for lipids, how it works, positive result
Emulsion test:
- mix sample thoroughly with ethanol
- and lipid will go into solution with ethanol (not waterr-soluble)
- filter
- put into water in clean testube
- cloudy white emulsion indicates the presence of lipids
- made up of tiny lipid droplets that come out of solution when mixed with water
-
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Test for proteins, how it works, positive result
Biuret test:
- light blue to lilac
- reagent may be supplied as biuret A (sodium hydroxide- add first), and biuret B (copper sulfate)
- colour formed by complex between the nitrogen atoms in a peptide chain and Cu2+ ions- test really tests for peptide bonds
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Describe the need for computer moddeling of protein structure
- being able to predict shape of a protein molecule from its primary structure can be incredibly useful in biochemistry
- e.g. predicting the occurrence of biologically active binding sites on a protein molecule can help to identify new medicines
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Describe computer modelling for secondary struuctures of proteins
- as they were developed, they were based on the probability of an amino acid, or sequence of amino acids being in a particular secondary structure
- such probabilities derived from 'already-known' protein molecular structures
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Describe computer modelling for tertiary struuctures of proteins
- usually, the tertiary structure contributes directly to its bioactive function
2 Types:
- ab initio protein modelling- model built based on the physical and electrical properties of the atoms in each AA in the sequence- can be multiple solutions to same AA sequence- sometimes need other methods to reduce the number of solutions
- comparative protein modelling-one approach is protein threading- scans the amino acid sequence against a database of solved structures- produces a set of possible models that would match that sequence
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Describe quantitive testing for reducing sugar
- benedicts reagent
- if more sugar, the amount of precipitate will increase and the amount of copper (II) ions will decrease
- quantify the concentration. 2 variables above of sample using colourimetry- compared to known glucose concentrations using calibration curve
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Desceribe how to use a colorimeter, how it works, and how you wpuld use it to test concntration of a reducing sugar
- works by shining light through a sample
- in RS test, would use a centrifuge to separate the precipitate and any excess benedicts solution (the supernatant)
- using pipette, take supernatant and place in cuvette (small vial made of glass or plastic)- placed into colourieter
- don't get fingerprints (greasy) on the cuvette as could affect light transmission
- colour filers often used for accuracy- use red for benedicts
- detect how much passes through (percentage transmission) - solution reflects blue light but absorbs red light
- zero between each reading by placing blank sample to reset the 100% transmission/absorption- in this case, blank would be water
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Describe the kind of colorimeter results you would expect to see in highh/low reducing sugar concentraions
- high RS concentration- little unreacted copper sulfate- supernatant less blue- absorption of red light low- percentage transmission high
- Low RS concentration- still quite blue- absorption of red light high - percentage transmission low
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Describe how to draw/use a calibration curve after colorimeter
- using colorimeter gives semi-quantitive results- can compare, but need calibration curve to find exact amounts
- carry out benedicts on series of known glucose concentrations, as well as unknown substance, use colorimeter to measure percentage transmission of light
- plot graph of transmission light against concentration of reducing sugar
- provides calibration curve
- can then draw known number for unknown substance (colorimeter value on Y-axis) down to concentration on X- this is the concentration of the solution
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how would you measure a biological/chemical variable that isn't easily measured, describe how it works, and example uses
Biosensor
- Convert hard to measure variable and convert it to an electrical signal
- Binding event- receptors attached to biological layer pick up substance
- transducer sends an electronic signal to signal conditioner phase- electronics- output
- uses- can detect contaminants in water, pathogens and toxins in food, airborne bacteria (e.g. in counter-bioterrorism programmes)
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Aim of chromatography
- to separate a mixture into its constituents
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2 phases of chromatography- explain
Stationary:
- chromatography paper- paper made out of cellulose
- or thin-layer chromatography (TLC) plat- often sheet of plastic, coated with a thin layer of silica gel or aluminium hydroxide
- in each, there are free -OH groups pointing outwards, in contact with the mobile phase
Mobile phase:
- solvent
- water (for polar molecules)
- Ethanol (for non-polar molecules)
- mobile phase flows through and across the stationary phase- carrying the biological molecules with it
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How to set up chromatography
- Draw line in pencil (pigments in pen would travel up with mobile phase)
- spot solution mixture onto pencil line using capillary tubing
- wait for spot to dry before putting on next spot, make spot as thin as possible
- when completely dry, lower into solvent
- level of solvent start must be below pencil line
- cover beaker with watch glass or glass plate
- let the apparatus 'run' until solvent has reached point just underneath top of paper/TLC plate
- remove from solvent, place on white tile to dry
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Describe what happens in chromatography and how this works
- as solvent travels up paper/plate, the components of the solution mixture travel with it
- separate pigments/components of the ink/bio molecule travel at different speeds- by the time solvent reaches top, some are travelling slow and some are travelling fast- different positions on paper/plate
- speed at which molecules move along TLC/paper depends on their solubility in the solvent and their polarity (in paper, may also depend on size)
- exposed -OH groups make the surface of the plate/paper very polar- allow it to form hydrogen bonds with the molecule, alongside other dipole interactions
- a highly polar solute will tend t stick to the surface (It's absorbed), and hence move more slowly
- a non-polar solute will travel very quickly up the plate
- if 2 molecules travel at the exact same speed, it will be hard to separate them- could try using a different solvent or changing the pH
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Name of the value calculated by chromatography
Rf - relative distance travelled
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How to calculate Rf value (chromatography), how to use this
distance from pencil line to centre of spot of pigment (x)/ distance from pencil line to solvent front (y)
- need to measure y before solvent dries so you can see it
- if you repeat the investigation under the same conditions, each pigment will always have the same Rf value- if you know the Rf values of particular pigments under these conditions, this allows you to identify them- same wot biological molecules
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What is an issue that sometimes happens with chromatography, how to overcome this
Sometimes with colourless molecules, you can't see where they finish- can use these solutions with THIN-LAYER CHROMATOGRAPHY:
- Ultraviolet light- TLC plates have a chemical which fluoresces under UV light- if you loom at plate under UV light, most of it will glow- except those places where the spots have travelled to- mask the plate from the UV light
- Ninhydrin- to see amino acids, allow plate to dry and spray wit with ningydrin- binds to the amino acids which are then visible as brown/purple spots
- iodine- allow the plate to dry, and place in an enclosed container with a few iodine crystals- the iodine forms a gas which then binds to the molecules in each of the spots
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How is chromatograohy used
- Thin layer chromatography often used to monitor the progress of reactions as it works relatively quickly
- also used for urine testing of athletes for illegal drugs, analysing drugs for purity of components, and analysis of foods to determine the presence of contaminants
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