biological molecules Flashcards
(103 cards)
1
Q
what is covalent bonding
A
- when atoms share electrons to have a full outermost shell
- is drawn by a single line
- CNOH - goes down by 1
2
Q
what is a condensation reaction
A
occurs when two molecules are joined together with the removal of water
3
Q
what is a hydrolysis reaction
A
occurs when a molecule is split into two smaller molecules with the addition of water
4
Q
what is a hydrogen bond
A
a weak interaction which happens whenever molecules contain a slightly negative charged atom bonded to a slightly positive charged atom
5
Q
whats a monomer
A
the units joined together in a condensation reaction
6
Q
whats a dimer
A
two monomers joined together
7
Q
whats a polymer
A
when lots of monomers join together
8
Q
does water have a low or high viscosity
A
low which means it can flow easily
9
Q
why is water being a liquid at room temperature beneficial
A
- provides habitat
- forms a major component of tissues in living conditions
- provides a reaction medium for chemical reactions
- acts as an effective transport medium
10
Q
is water non-polar or polar
A
polar
11
Q
what is unique about water density
A
- it gets more dense as it gets colder until 4°C
- as it goes from 4°C to freezing point, (as its polar) the water molecules align themselves in a structure that is less dense than water which makes it float
12
Q
why is it beneficial that ice is less dense than water
A
- aquatic organisms have a stable environment to live in through the winter
- bodies of water (such as lakes/ponds) are insulated against extreme cold
13
Q
why is water a good solvent
A
because water clusters around the charged parts of the solutes because of its polarity - which helps seperate them
14
Q
why is it beneficial that water is a good solvent
A
- molecules and ions can move around and react together in water
- molecules and ions can be transported whilst dissolved in water
15
Q
why does a drop of water on a flat surface not spread out
A
because the hydrogen bonding between the molecules pull them together
16
Q
whats surface tension
A
when the surface of water contracts and has the ability to resist force applied to it
17
Q
what is high specific heat capacity
A
- the amount of heat energy required to increase the kinetic energy and temperature of water
- 4.2kJ of energy to raise temp of 1kg of water by 1°C
18
Q
what is the high latent heat of vaporisation
A
the energy used to change state
19
Q
why is latent heat of vaporisation useful
A
because when water evaporates it helps the molecules to break away from eachother to become a gas
20
Q
what do carbohydrates contain
A
- carbon
- hydrogen
- oxygen
21
Q
what is the function of carbohydrates
A
- acts as a source of energy
- acts as a source of energy
- acts as a structural unit
22
Q
what are the three main groups of carbohydrates
A
- monosaccharides (one monomer)
- disaccharides (two monomers)
- polysaccharides
23
Q
key points about monosaccharides
A
- simplest carbohydrate
- important as a source of energy
- are sugars and soluble in water but insoluble in non-polar solvents
- can exist as a straight chain or in ring or cyclic forms
- are the backbone of single-bonded carbon atoms with one double-bond to an oxygen to form a carboxyl group
24
Q
what are the different isomers of glucose
A
α-glucose: H above and OH below
β-glucose: OH above and H below
25
what are the most common dissacharides
* maltose
* lactose
* sucrose
## Footnote
maltose and lactose are reducing sugars whereas sucrose is non-reducing
26
key points about disaccharides
* are sweet and soluble
* are made when two monosaccharides join together
* when they join, a condensation reaction occurs to form a **glycosidic bonds**
-where two hydroxyl groups line up next to each other where a water molecule is removed which leaves an oxygen atom acting as a link
27
whats a polysaccharide
a polymer of a monosaccharide
28
whats a homopolysaccharide and a heteropolysaccharide
**homopolysaccharide** - made solely of one kind of monosaccharide (e.g. starch)
**heteropolysaccharide** - made up of more than one monomer (e.g. hyaluronic acid)
29
why are polysaccharides good energy stores
* the structure of some polysaccharides help
* are less soluble in water than monosaccharides because of their size
30
why is glycogen in animals and starch in plants (made from amylose and amylopectin) good stores of monosaccharides
* they are compact
* hold glucose molecules in chains which means it can easily be 'snipped off' the chain by hydrolysis
* some chains are branched (glucose and amylopectin) and some are unbranched (amylose) - branched are more compacts and offer the chance for lots of glucose to be snipped off
31
where is cellulose found
in plants, forming cell walls
32
key points of cellulose
* is tough, insoluble and a fibrous substance
* is a **homopolysaccharide** - made from a long chain of up to 15000 β-glucose molecules
* bonded through a condensation reaction forming **glycosic bonds**
* chains are straight and lie side by side
33
what happens to the hydrogen and hydroxyl groups on carbon 1 in cellulose
* are inverted
* every other β-glucose molecule in the chain is rotated by 180° - helps prevent the chain from spiralling
34
what is the bond between the β-glucose molecules in cellulose
* hydrogen bonds which gives extra strength
* hydrogen bonds also form between rotated β-glucose molecules in different chains (hydroxyl group on carbon 2 sticks out enabling H bonds between chains)
35
whats a microfibril
* when 60-70 cellulose chains are bound together
* 10-30nm in diameter
36
whats a macrofibril
* when microfibris bundle together (contains 400 microfibrils)
* embedded in pectins to form plant cell walls
* macrofibrils run in all directions criss-crossing the wall for extra strength
37
what are bacteria cell walls made from
* peptidoglycan
* made from long polysaccharide chains that lie in parallel, criss-crossed by short peptide chains (made from amino acids)
38
what are insect and crustaceans exoskeletons made from
* chitin
* has an **acetylamino group** on carbon 2
* froms cross linkes between parallel chains of acetylglucosamine
39
what are the key feature for the function of plant cell walls
* plants have no rigid skeleton so each cell needs strength to support the plant
* space between macrofibrils for water and mineral ons to pass through (membrane is fully-permeable)
* wall has high tensile strength - prevents turgid cells from bursting and the turgid cells provide support
40
what are lipids
* contains larg amounts of carbon and hydrogen and small amounts of oxygen
* insoluble in water (non-polar) but dissolve in alcohol
41
what are 3 examples of macromolecules
* triglycerides
* phospholipids
* steroids
42
what are triglycerides made from
glycerol and fatty acids
43
whats the structure of glycerol
* has 3 carbon atoms
* is an alcohol
* has 3 -OH groups
44
whats the structure of fatty acids
* have a **carboxyl group** (-COOH) at one end attached to a hydrocarbon tail
* carboxyl group ionises into H+ and -COO- groups
45
what does it mean if a fatty acid is unsaturated or saturated
* **unsaturated** - there is a C=C double bond (means fewer H atoms are bonded)
* **saturated** - no C=C bond in the molecule
* a single C=C bond makes a fatty acid **monosaturated**
* more than one C=C bond makes it **polysaturated**
46
what happens if there is more than one C=C bond in a fatty acid
* it changes the shape of the hydrocarbon - gives a kink where the double bond is
* kink pushes the molecules slightly apart, making it more fluid
47
whats an ester bond
* a condensation reaction happens between the -cooh group of the fatty acid and the -OH groupd of the glycerol
* 3 fatty acids bond to 3 -OH groups
* a water molecule is produces and an ester bond is formed
48
whats the functions of triglyceride
* **energy source** - triglyceride can be broken down in respiration to realease energy and generate ATP
* **energy store** - as they are insoluble in water, they can be stored without affecting the water potential of the cell
* **insulation** - adipose tissue stores lipids in whales, lipids in nerve cells act as an electrical insulator
* **buoyancy** - as fat is less dense than water, used by aquatic mammals to stay afloat
* **protection** - humans have fat around delicate organs to act as a shock absorber
49
whats the structure of a phospholipid
* glycerol, 2 fatty acids and a phosphate group
* a condensation reaction between an OH group on a phosphate acid molecule (H3PO4) and one of the three -OH groups on the glycerol form an ester bond
50
whats a phospholipids behaviour in water
* the phosphate groups are polar whilst the fatty acids are non-polar
* the heads are hydrophilic whilst the tails are hydrophobic whcih makes the phospholipid amphipathic
* may form a layer on surface of water with heads in the water whilst tails stick out
* can form **micelles** (tiny balls with the tails tucked away inside and the heads pointing outwards into the water)
51
whats a phospholipid bilayer
where two rows of phospholipids form with the tails pointing inwards and the heads pointing outwards
52
key feature of a phospholipid bilayer
* phospholipids are free to move around in their layer but will not expose their tails - gives some stability
* the membrane is selectively permeable
53
what is cholesterol
* a steroid alcohol (sterol)
* consists of 4 carbon-based rings or isoprene units
54
key features of cholesterol
* is small and hydrophobic
* regulatyes the fluidity of the molecule
* made in liver of animals (plants have a cholesterol derivative called stigmasterol)
* the steroid hormones testosterone, oestrogen and vitamin D are all made from cholesterol
55
what are proteins
* large polymers of long chains of amino acids
56
key features of proteins
* form structural components of animals in particular (uscles are made of proteions - actin and myosin)
* have a tendency to adopt specific shapes
* membranes have protein constituents that act as carriers and pores for active transport
57
what is the structure of an amino acid
* contains carbon, hydrogen, oxygen and nitrogen (some contain sulfur)
* there are over 500 different amino acids but only 20 are proteingenic
* each protein chain of amino acids has an **amino group** (-NH2) at one end and a **carboxyl group** (-COOH) at the other
* the R group is different in each amino acid (20 different types)
58
whats the R group in glycine
H
59
whats the only amino acid which contains sulfur
cysteine (CH3S)
60
how are amino acids joined
* through a covalent bone called **peptide bonds**
* making a peptide bond involves a condensation reactin and breaking one involves a hydrolysis reaction
61
what enzyme breaks down peptide bonds
protease enzyme in the intestines (also breaks down protein hormones)
62
whats a dipeptide
two amino acids joined together
63
whats the name for joining a long chain of amino acids together
polypeptide
64
whats a buffer
a substance which helps resist large changed in pH
65
how do amino acids act as buffers
* when dissolved in water, the amino group and carboxyl group can ionise
* the carboxyl group acts as an acid and the amino group acts as a base inn accepting H+ ions
* at low pH (lots of H+ ions) the amino acid will accept H+ ions
* at high pH (few H+ ions) the amino acid will release H+ ions
* by accepting/releasing H+ ions, amino acids are able to regulate changes in pH (buffering)
66
whats the primary structure of proteins
* the sequence of amino acids in a protein chain
* the number and order of the amino acids determine the shape of the protein
* the function of the protein is determined by the structure
67
whats the secondary structure of proteins
* the coiling or folding of an amino acid chain
68
what is an α-helix
* a coil of amino acids - there are 36 amino acids per 10 turns of the helix
* held together by hydrogen bonds between the -NH group of one amino acid and the -CO group of another 4 places ahead
69
what is an β-pleated sheet
* a zig zag structure where the chain of amino acids folds over onto itself
* held by hydrogen bonds
70
whats the tertiary structure of proteins
* the overal three-dimensional shape of a protein molecule
* very precise shape held together by multiple bonds (hydrogen, ionic, disulfide bonds) between amino acids which lie close to each other
* can adopt a supercoiled shape (in fibrous proteins - e.g. colagen) or a more spherical shape (in globular proteins)
71
whats the quaternary structure of proteins
* how multiple peptide chains are arranged to make a complete protein molecule
* may be held together by hydrogen, ionic or disulfide bonds
72
what are the bonds that hold together all the different structures of proteins
* **primary structure** - peptide bonds
* **secondary structure** - hydrogen bonds
* **tertiary and quaternary structure** - hydrogen, ionic and disulfide bonds
73
what are hydrogen bonds
* form between H+ ion with a slight positive charge and other atoms with a slight negative charge
* in amino acids form hydroxyl, carboxyl and amino groups
* can form between polar areas of the R groupds on different amino acids
* the presence of multiple hydrogen bonds gives a lot of strength
74
what are ionic bonds
* form between a carboxyl and amino groups that are part of R groups (these ionise into NH3+ and COO-)
* stronger than a hydrogen bond
75
what are disulfid links/bridges
* form between the R groups of 2 cysteines (as cysteine's R group contains sulfur)
* are strong covalent bonds
76
what is a fibrous protein
regular, repetitive sequences of amino acids and usually insoluble in water
77
key feature of collagen
* is a fibrous protein
* function is to provide mechanical strength
78
give some examples of what collagen does
* prevents arteries bursting when withstanding high pressure
* tendons are made from collagen and connect muscle to bones
* bones are made from collagen and are reinforced with calcium phosphate which makes them hard
* cartilage and connective tissue are made from collagen
79
key features of keratin
* is a fibrous protein
* is rich in cysteine (lots of disulfide bridges and hydrogen bonding makes it strong)
* is found where the body needs a part to be hard and strong (fingernails, hair, scales, fur etc)
* provides mechanical strength, is an impermeable barrier to infection and is water which prevents entry of water-borne pollutants)
80
key feature of elastin
* is a fibrous protein
* the cross-linking and coiling makes the structure strong and extensive
* found in living things where they need to stretch or adapt their shape as a part of life processes (found in skin, the lungs and blood vessels)
81
key features of haemoglobin
* is a globular protein
* has a quaternary structure made up of 2 α-globin chains and 2 β-globin chains (each has its own tertiary structure)
* on the outside of each chain there is a space for a **haem group** (contains an iron ion) to be held
* carries 4 O2 molecules as each molecule binds to the 4 iron ions
82
key feature of insulin
* is a globular protein
* made from 2 polypeptide chains
* soluble in water
* the A chain begins with a section of α-helix and the B chain ends with a section of β-pleat
* folds into tertiary structure and joined by disulfide bridges
* binds to glycoprotein receptors to increase their uptake of glucos from the blood
83
key features of pepsin
* globular protein
* an enzyme that digests proteins in the stomach
* made of a single polypeptide chain of 327 amino acids
* folds into a symmetrical tertiary structure
* has 4 amoni acids with basic R groups and 43 with acidic R groups
* held by hydrogen bonds and 2 disulfide bridges
84
what are the two approaches scientists can use to predict tertiary structure
* **ab inito protein modelling** - model built based on physical and electrical properties of the atoms in each amino acid sequence
* **comparitive protein modelling** - protein threading (scans the amino acid sequence against a database of solved structures and produces a set of possible models which would match the sequence
85
# carbohydrate test
how to test for starch
* add iodine solution to a sample
* if starch is present, it will change from **yellow-brown to blue-black**
* when dissolved in potassium iodide, the iodine (I2) forms a triiodide ione I3- which causes the colour change
| iodine test
86
# carbohydrate test
how to test for reducing sugars
* known as reducing sugars because they reucde or give electrons to other molecules
* if you heat a reducing sugar with Benedict's solution, it will go **blue to green to yellow to orange-red**
* the solution contains Cu2+ ions (which are reduced to Cu+ ions) forming orange-red copper (I) oxide (Cu2O) precipitate
* the intensity of the red colour is proportional to the concentration of sugar
| Benedict's test
87
# carbohydrate test
how to test for non-reducing sugars
* hydrolyse the bond first
* take a sample for reducing sugars to check there are none in the first place
* take a seperate sample and boil it with hydrochloric acis to hydrolyse the sucrose into glucose and fructose
* cool the solution and use sodium hydrogencarbonate solution to neutralise it
* test for reducing sugars again
* posititive result (**green to yellow to orange to red**) indicated the non-reducing sugars were present in the original sample
88
how to test for proteins
* if proteins are present, the colour will change from **light blue to lilac**
* colour is formed by a complex between the nitrogen atoms in a peptide chain and Cu2+ ions
| the biuret test
89
how to test for lipids
* take a sample and mix it thoroughly with ethanol
* filter
* pour solution into water in a clean test tube
* a cloudy white emulsion indicates the presence of lipids
| the emulsion test
90
how do you use a colorimeter
- works by shining light through a sample
- use a puppeteer to take the supernatant and place it in a cuvette, which is then placed in a colorimeter
- use a coloured filter and shine the coloured light through the solution
- then detect how much light passes through (percentage transmission)
91
how to use quantitative testing for reducing sugars
- use colorimetry
- use a centrifuge to separate the precipitate and excess Benedict’s solution (supernatant)
- use a pipette to take the supernatant and place it into a cuvette, which is then placed in a colorimeter
- use a red filter, shine the red light through the solution and detect how much passes through (percentage transmission)
- the solution will reflect blue light but absorb red light
- if there is a lot of unreacted copper sulfate, the supernatant will be quite blue, absorption of red light is high and percentage transmission is low
92
how do you create a calibration curve
1. take a series of known concentrations of reducing sugar
2. using a sample of each, carry out Benedict’s test
3. use a colorimeter to record the percentage transmission of light through each supernatant
4. plot a graph to show ‘transmission of light’ against conc. of reducing sugar
93
how do biosensors work
- they take a biological or chemical variable which cannot be easily measured and convert it into an electrical signal
- the molecules to be measured are bonded at the binding site (where the receptor is attached to the biological layer)
- at the transducer surface the attachment energy is converted into an electrical signal
- the electrical signal then passes to the signal conditioner (electronics) where it is amplified to a bigger output
94
what are some applications of biosensors
- to detect contaminants in water, pathogens and toxins in food
- to detect airborne bacteria
95
what’s the aim of chromatography
to separate a mixture into its constituents
96
what’s the stationary phase in chromatography
- either the chromatography paper or a thin-layer chromatography (TLC) plate
- paper is made of cellulose
- TLC plate is often a sheet of plastic, coated with a thin layer of silica gel or aluminium hydroxide
- in each case free -OH groups point outwards
97
what’s the mobile phase in chromatography
- is the solvent for the biological molecules
- at simple level, water (for polar molecules) or ethanol (non-polar molecules) can be used
- the mobile phase flows through and across the stationary phase
98
what’s the chromatography practical
- wear eye protection
- draw the line in pencil and put a tiny dot on the line to show you where to place you solution mixture
- spot the solution mixture onto the pencil dot several times by using capillary tubing. Wait for the spot to dry before putting on the next spot and try to make the spot as thin as possible. When it’s completely dry, lower it into the solvent (level of solvent below the pencil line)
- cover the beaker with a watch glass or glass plate
- let the apparatus ‘run’ until the solvent has reached a point just underneath the top of the paper/TLC plate
- remove from solvent and let dry
99
what happens during chromatography
- as the solvents travel up the paper, the components of the mixture travel with it
- mixtures will travel at different speeds
100
how can you identify the pigments in chromatography
- use the relative distance travelled
- calculate the Rf value by measuring the distance from the pencil line to the centre of a spot of pigment (x) and the distance from the pencil like to the solvent front (y)
Rf = x/y
101
how can you identify where colourless molecules finish in chromatography
- **ultraviolet light** - TLC plates have a chemical which fluoresces under UV light. If you look at the plate under UV, most of it will glow, except the places where the spots have travelled to
- **Ninhydrin** - to see amino acids, allow the plate to dry, and then spray with ninhydrin. This binds to the amino acids which are then visible as brown or purple spots
- **Iodine** - allow plate to dry and place in enclosed container with a few iodine crystals. The iodine forms a gas which then binds to the molecules in each of the spots
102
how does chromatography work
- the speed the molecules move along the paper depends on their solubility in the solvent and their polarity (sometimes size as well)
- exposed -OH groups make the surface of the paper or plate very polar and allow it to form hydrogen bonds with the molecules
- a highly polar solute will tend to stick to the surface (adsorbed) and move more slowly
- a non-polar solute will travel very quickly up the plate
103
how is chromatography used
- TLC is commonly used to monitor the progress of reactions
- urine testing of athletes for illegal drugs
- analysing drug purity of components
- analysis of foods to determine presence of contaminants
