Biological molecules Flashcards
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
Q
Different types of monosaccharides, differences between them
A
- 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
Q
What can glucose exist as
A
- 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
27
Q
Disaccharide properties
A
- sweet
- soluble in water
28
Q
When are disaccharides made
A
- when 2 monosaccharides are joined togetehr
29
Q
2 types of disaccharides, examples
A
- maltose and lactose- reducing sugars
- sucrose- non-reducing
30
Q
Examples of disaccharides and their components
A
A (alpha) glucose + A glucose = maltose
A glucose + fructose = sucrose
B (beta) glucose + A glucose = lactose
B glucose + B glucose = cellobiose
31
Q
Formation of disaccharides
A
- 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
32
Q
Breaking down of disaccharides
A
- 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
33
Q
A glucose- displayed and molecular formula, role in the body, type of sugar
A
- C6H12O6
- energy source, component of starch and glycogen which act as energy stores
- hexose
34
Q
B glucose- displayed and molecular formula, role in the body, type of sugar
A
- C6H12O6
- energy source, component of cellulose which provides structural support in plant cell walls
- hexose
35
Q
Difference between A and B glucose
A
Isomers- hydroxyl group on C1 below the plane of ring in A, above in B
36
Q
ribose- displayed and molecular formula, role in the body, type of sugar
A
- C5H10O5
- component of ribonucleic acid (RNA), ATP and NAD
- pentose
37
Q
deoxyribose- displayed and molecular formula, role in the body, type of sugar
A
- C5H10O4
- component of DNA
- Pentose
38
Q
2 types of polysaccharides, example
A
- homopolysaccharide- made out of 1 type of monomer- starch
- heteropolysaccharide- more than one- hyaluronic acid in connective tissue
39
Q
Energy source vs store
A
- source- glucose- reactant in respiration
- store- starch/glycogen- many joined together
40
Q
Solubility of polysaccharides
A
- 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
41
Q
2 types of starch
A
- amylose
- amylopectin
42
Q
Starch- where is it found
A
Starch granules in plant cells
43
Q
Amylose- structure
A
- 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
Q
Amylopectin structure
A
- 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
Q
Starch function
A
Acts as an energy store- g; glucose for respiration
46
Q
How starch’s structure is important for its function
A
- 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
Q
How is starch broken down
A
- enzyme amylase- hydrolyses 1-4 glycosidic linkages
- enzyme glucosidase- 1-6 glycosidic linkages (amylopectin)
48
Q
Amylose vs amylopectin displayed formula
A
49
Q
Where is glycogen found
A
Dense granules in animals
50
Q
Glycogen structure
A
- 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
Q
Glycogen function
A
energy store- glucose for respiration
52
Q
How glycogens structure is important for its function
A
- 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
Q
glycogen displayed structure
A
54
Q
Where is cellulose found
A
- cell walls of plants
55
Q
What type of polysaccharide is starch, describe it
A
tough, insoluble, fibrous homopolysaccharide
56
Q
Structure of cellulose
A
- 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
Q
How the structure of cellulose supports its function
A
- 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
58
Q
Structure for function of cell wall as a whole
A
- 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.
59
Q
How has cellulose been used by humans
A
- 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
65
Q
Structure (with displayed formula) of glycerol
A
- alcholol so has free -OH groups (hydroxyl)
- three -OH groups
66
Q
Fatty acid structure (with displayed formula)
A
- 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
67
Q
2 types of fatty acids- describe, implications of this
A
- 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
68
Q
Formation of a triglyceride (with displayed formula)
A
- 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
69
Q
triglyceride displayed formula
A
72
Q
Structure of phospholipids
A
- 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
73
Q
Behaviour of phospholipids in water
A
- 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
74
Q
Describe the use of phospholipids in membranes (and why they act as good ones)
A
- 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
76
Q
Cholesterol structure
A
- consists of 4 carbon-based rings (isoprene units)
90
Q
Describe the structure of amino acids, give 3 examples, displayed formula
A
- 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
95
Q
Describe formation of dipeptide/joining of amino acids
A
- 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
Q
describe breaking of multiple amino acids
A
- hydrolysis reaction
- water molecule added
- peptide bond broken
- enzyme used
101
Q
secondary structure of proteins
A
- 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
Q
Tertiary structure of proteins
A
- 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
103
Q
Quaternary structure of proteins
A
- multiple polypeptide chains arranged to make complete protein molecules
- may also be held together with same types of bond that hold the tertiary structure
105
Q
Describe disulphide links in proteins
A
- 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
108
Q
levels of protein structure picture
A
109
Q
tertiary protein structre diagram
A
113
Q
Collagen structure
A
- 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
115
Q
Keratin strucure
A
- rich in cysteine- lots of disulfide bridges form between polypeptide chains
- alongside hydrogen bonding, this makes the molecule very strong
117
Q
Elastin structure
A
- crosslinking and coiling make structure strong and extensible
120
Q
Haemoglobin structure
A
- 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
122
Q
Insulin structure
A
- 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
125
Q
Pepsin structure
A
- 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
