1
Q
mixture
A
A combination of two or more substances that are not chemically bonded together
2
Q
solvent
A
A substance that dissolves other substances (solutes), to form a solution
3
Q
solute
A
A substance that dissolves in a solvent to create a solution
4
Q
solution
A
A mixture of one or more solutes dissolved in a solvent
5
Q
dipole dipole interactions
A
Electrostatic forces between molecules with permanent dipoles, where the positive end of one molecule is attracted to the negative end of another- Van der Waals
6
Q
chromatography
A
separate mixtures of substances into their components
7
Q
types of chromatography
A
Gas
Liquid
8
Q
chromatography is useful in
A
.Identification of components of a mixture,
.following course of reaction
.analysing purity of compound
.analysing fractions collected during purification
9
Q
thin layer chromatography-stationary phase
A
plate or strip coated with a form of silica gel “the thin layer”
10
Q
thin layer chromatography-mobile phase
A
developing solvent
11
Q
thin layer chromatography (TLC)
A
.TLC is a form of liquid chromatography
.TLC is similar to paper chromatography
.principle of separation is adsorption to stationary phase
12
Q
stationary phase principles
A
.interaction of substance with stationary phase
determines its movement
Silica is common stationary phase:
Dipole-dipole interactions
Polar molecules adhere strongly
13
Q
mobile phase principles (TLC solvent)
A
.Organic solvents of high polarity are more
powerful eluters
.Substances move faster/further if they dissolve in solvent well
14
Q
main principle in TLC
A
.main principle used in TLC is adsorption
.component with more affinity towards stationary phase, adheres more strongly and travels slower
.component with lesser affinity towards stationary phase, adheres weakly travels faster
.components of samples will separate on stationary phase according to:
.How strongly they adsorb on stationary phase v How readily they dissolve in mobile phase
15
Q
Rf (retention or retardation factor)
A
.It is an indication of position of migrated spots on chromatogram
.used to identify components in a sample
16
Q
Rf equation
A
distance of spot on TLC plate/ distance of solvent front
always between 0 and 1
17
Q
Distance of the solute moved is measured by…
A
from centre of spot
18
Q
advantages of TLC
A
.simple AND rapid method
.cost of equipment is low
.Separation of small amounts of substances can be achieved
.MOST types of compounds can be analysed
.Uses small quantity of solvent AND COMPOUND
.Reliable method
.Requires short analysis time
19
Q
steps in TLC
A
- Select a plate with proper sorbent material
- Prepare mobile phase
- Mark plate
- Apply sample
- Develop plate
- Detect analytes
20
Q
running a TLC plate
A
- Using a capillary tube or micropipette to deliver “spot” a small volume of sample
- Place TLC plate into developing chamber containing mobile phase
- Spotting area should not be immersed in mobile phase
- Allow plate to develop, as mobile “solvent” phase rises to top. Mark this level
- Visualize plate
21
Q
visualising plates- 4 different techniques (used if you cant see the components)
A
- Sulfuric acid/heat: destructive, leaves charred blots behind
- Ceric stain: destructive, leaves dark blue blot behind for polar compounds
- Iodine: semi-destructive, iodine absorbs onto spots, not permanent
- UV light: non-destructive, long wavelength (background green, spots dark), short wavelength (plate dark, compounds glow)
22
Q
ninhydrin
A
.reagent produces a blue-purple stain pattern if positive, and can be used to reveal fingerprints
.it reacts with amino acids in oil from fingers
23
Q
applications of TLC
A
Used in food, cosmetic and pharmaceutical industries:
.Check for purity of sample
.Examination of reaction products
.Identification of compounds
In pharmaceutical industry:
.Separation of multi-component pharmaceutical formulations
24
Q
PCR (polymerase chain reaction)
A
.amplification of DNA in vitro (outside) into millions of times to create a large enough DNA sample for extensive analysis
.DNA doubles each time PCR is done
25
components of PCR
.DNA sample
.primers
.nucleotides
.TAQ polymerase
.mix buffer
.PCR tube
26
PCR v DNA replication differences
.no Okazaki fragments in PCR
.have forward and reverse primer-used to amplify target sequence (continuous elongation) in PCR instead of primase
.PCR uses heat v replication uses helicase to break H bonds
27
PCR stages
1. denaturation at 95c- break hydrogen bonds-DNA strands separate
2. annealing at 55c-cooled to allow DNA primers to attach at start of section of target DNA
3. synthesis at 70c- TAQ polymerase (heat tolerant) attaches nucleotides to synthesise complementary strand
28
locating a gene
use DNA probes
29
DNA probe
short single stranded section of DNA complementary to section of target DNA
can be tagged w/fluorescent or radioactive agent
30
using a DNA probe
1. make labelled probe
2. expose probe to DNA
3. isolate labelled DNA
31
uses of DNA probes
1. locating desired gene for genetic engineering
2. identify presence/ absence of allele-useful for screening for heritable diseases
3. determine predisposition to certain diseases
32
why we convert RNA to DNA in PCR
PCR works on DNA-reverse transcriptase is used
33
genetic fingerprinting-restriction enzymes
ability to cut DNA molecules into specific fragments (they're palindromic)
34
genetic fingerprinting-blotting
separate and transfer DNA,RNA or proteins onto membrane for analysis
-southern=DNA
-northern=RNA
-western=proteins
35
genetic fingerprinting-electrophoresis
uses electric current or field to push substance of interest-causes separation of DNA (negative) /RNA and proteins (separated by size)
-small travel faster
36
blunt ends eg.
Sma1
37
sticky ends
easily reattach to other ends eg. EcoRI
38
plasmids
carry antibiotic resistant genes-used in vivo genetic engineering
39
recombinant DNA
form of DNA that has been artificially created by combining genetic material from multiple sources
40
southern blotting
technique that transfer DNA that has been separated using electrophoresis onto nitrocellulose filter
41
western blotting
process of separating proteins and identifying them in a complex biological sample
42
amino acids
bi-functional organic molecule
proteins=polymers
amino acids= monomers
contain COOH (carboxyl) and NH2 (amine)
43
acid & base defintion
acid-donates protons
base-accept protons
44
amino acid structure
derived from proteins have an a-amino which is carbon
R-group differs & determines properties of proteins
45
properties of amino acids
1. readily ionise
2. more polar in polar solvents
3. at physiological pH (7.4) amino acids are protonated-carboxylic acid is deprotonated
4. they can act as an acid and base
5. molecules which bear charged groups of opposite polarity-zwitterions or dipolar ions
46
amino acid as a zwitterion
zwitterion-compound can exist w/both positively charged (amine) and negatively charged (carboxyl) regions w/no net charge
amino acids accepts H+ and becomes positive and carboxylic group loses H+ and becomes negative
charges cancel out and amino acid carries no net charge
47
effect of pH
1. increase in pH of a solution of an amino acid-adding hydroxide ions-removal of H+ ions from the -NH3 group
2. decrease in pH by addition of acid to a solution of an amino acid-protonation of -COO- group
48
peptide bond formation
bond formed between two amino acids by elimination of a water molecule (condensation reaction) =peptide bond
product formed by linking amino acid molecules through peptide linkages, -CO-NH- =peptide
49
classification of amino acids
1. Structure- Polarity
Side chain characteristics
2. Nutritional requirements
50
peptides
2=dipeptide
3=tripeptide
4=tetrapeptide
5=pentapeptide
linear and unbranched w/each amino acid within chain attached to two neighbouring amino acids
51
structural classification-polarity basis
1. Non-polar amino acids
2. Polar amino acids with no charge
3. Polar amino acids with charge
based on polarity of R group
52
non-polar amino acids
.equal number of amino and carboxyl groups and are therefore neutral
.are hydrophobic and have no charge on ‘R’ group
53
polar amino acids w/no charge
.have either an OH or NH2 group on their R-side chain, when in aqueous solution
.acids are hydrophilic and have no charge on ‘R’ group
.participate in hydrogen bonding of protein structure-help contribution to folding of proteins
.tyrosine is partially hydrophilic
54
polar amino acids w/positive charge
.positive charge on ‘R’ group are placed in this category
.are hydrophilic
.have more amino groups as compared to carboxyl groups making it basic
55
polar amino acids w/negative charge
.negative charge on ‘R’ groups are placed in this category
.are hydrophilic
.have more carboxyl groups than amino groups, making them acidic
56
classification of basis of side chains
1. Aliphatic side chains
2. Aromatic side chains
3. Hydroxyl containing side chains
4. Sulphur-containing side chains
5. Basic side chains
6. Acidic side chains
57
aliphatic side chains
.contain C and H in long straight chains
.long hydrocarbon chains are more hydrophobic
58
aromatic side chains
.all contain aromatic groups (rings)
.hydrophobic
.due to –OH group on Tyrosine, it is hydrophilic
59
hydroxyl containing side chains
.hydroxyl group in their side chain
.hydrophilic
60
sulphur containing side chains
.have sulphur side chain
.presence of -SH makes cysteine hydrophilic
61
basic side chains
.hydrophilic amino acids containing amine groups and are nitrogenous bases
.positively charged at physiological pH
.main component will be in zwitterion state and NH2 group on R-side chain will exist as NH3+
62
nutritional classification
1. Essential amino acids
2. Non-essential amino acids
3. Conditional amino acids
63
acidic side chains
.hydrophilic amino acids contain carboxyl groups on their side chains
.negatively charged at physiological pH
.main component will be in Zwitterion state and COOH group on R-side chain will exist as COO-
64
non-essential amino acids
.synthesised by body from glucose
65
essential amino acids
.amino acids that body cannot make-need to be obtained through diet eg. phenylalanine
66
conditionally essential amino acids
.amino acids that become essential in certain cases (eg. pregnancy, stress and disease)
.some amino acids like arginine have growth promoting factors
.not synthesised in sufficient amounts during growth
.Tyrosine is produced from phenylalanine, so, if diet is deficient in phenylalanine, tyrosine will be required as well
67
phenylketonuria
.rare disorder where patients lack enzyme phenylalanine hydroxylase which is needed to dispose of amino acid phenylalanine
68
why would phenylketonuria be a genetic disorder...
.phenylalanine rapidly builds up in blood stream and becomes toxic to nervous system
.If untreated can lead to brain damage
69
phenylketonuria treatment
.diet low in phenylalanine
.no meat, fish, poultry, eggs, cheese, milk, beans, or peas
.low-protein diet
70
why might it be possible to treat phenylketonuria w/ gene therapy...
Phenylalanine is broken down an enzyme
71
1 difference between PCR and RT-PCR
PCR amplifies DNA
RT-PCR uses RNA strand to form cDNA-can then be used to amplify DNA
72
explain how RT-PCR can be used to show that someone is COVID-19 positive
1. viral RNA used w/reverse transcriptase
2. forms cDNA
3. cDNA is amplified using PCR to form multiple copies
4. presence shows that they are positive
73
residue meaning
amino acids
74
protein uses
uses-membrane transport, structural activity, enzymes, receptors
75
protein structures
they are macromolecules
1. primary- amino acid sequence
2. secondary- peptide backbone orient into a regular pattern (H bonds)
3. tertiary- entire protein molecule coils into an overall three-dimensional shape (H, I, D bonds)
4. different multiple protein molecules come together to yield large aggregate structures
76
is the primary structure of a protein is determined by sequence of bases on DNA..
YES
77
primary structure of proteins
determines eventual shape of protein, hence its function
determined by sequence of bases in gene (read as codons)
78
secondary structure of proteins
.R group impacts where H bonds are formed but don't get involved
.a-helixes and b-sheets are regular secondary structures
.form loops and turns
79
secondary structure-alpha helixes
.stabilized by hydrogen bonds
.several hydrogen bonds stabilize each turn of α-helix
.side chain groups point outwards from helix
.typically amphiphilic (hydrophobic and hydrophilic regions)
80
secondary structure-beta sheets
.in a β-sheet, carbonyl oxygens and amides form hydrogen bonds
.side chains point alternately above and below plane of beta-sheet
.can be either anti-parallel (more stable) or parallel
81
secondary structure-beta turns
.allow protein backbone to make abrupt turns
.such reverse turns or bends almost always occur at protein surfaces
.found mainly linking and turning β-sheets
.stabilised by hydrogen bonds-more stable than a-helixes eg. proline and glycine
82
secondary structure-omega loops
.compact globular entities where their side chains (R-groups) tend to fill in their internal cavities
.located on protein surfaces
.important in biological recognition processes
.usually hydrophilic-body is made up of H20
83
tertiary structure
.more bonds form due to interactions between R-groups of polypeptide chain
.side chains that define the tertiary interactions
84
influence of amino acids properties on tertiary structure
.Charged and polar R-groups tend to map to surface of 3D protein surfaces
.Non-polar R-groups tend to be buried in cores of proteins
85
bonds in protein structure
Ionic bonds between charged R groups
Hydrogen bonds between polar R groups-WEAK
Van der Waals forces between non-polar R groups-WEAK
Disulphide bridges between sulphur containing R-groups-STRONG
86
ionic bonds between charged R groups
.bonds results from neutralisation of an acid and amine on side chains
.resulting ionic interaction is ionic between positive amino group and the negative acid group
.R-group that is involved in ionic bond
87
van de Waals between non-polar R-groups
.non-polar groups mutually repel water and other polar groups and results in net attraction of non-polar groups for each other
.forces set up would be enough to contribute to holding folded structure together
.Water excluded from these hydrophobic side chains helps keep side chains together
88
hydrogen bonds between polar R-groups
.Hydrogen bonding occurs between carboxyl and amide groups in secondary protein structures
.also occurs between side R-chains giving in variety of amino acid combinations
89
sulphur/disulphide bridges
.involves amino acid cysteine, which has a free –SH on its R-side chain
.If two cysteine amino acid residues end up next to each other they can react to form a sulfur bridge
.contribute to stability of protein’s tertiary structure
.Disulfide bonds are only found in proteins that function outside of cell
90
quaternary structure
.proteins with molecular masses >100kD, consist of several polypeptide chain or subunits held together by bonds
.biological function of some molecules is determined by multiple polypeptide chains – multimeric proteins
.chains can be either e.g. homodimer or heterodimer
91
haemoglobin
.made of four polypeptide chains bonded together in quaternary structure
.quaternary structure determines final 3D structure and its biological activity
.curled up so that hydrophilic side chains face outwards and hydrophobic side chains face inwards
.makes Hb soluble and good for transport in blood
92
quaternary structure-prosthetic group
.non-amino acid derived groups for biological activity
.can be formed from metal ions, sugars, vitamins, methyl groups, phosphate groups
93
globular proteins
coiled into compact, roughly spherical shapes, easily soluble-hydrophilic
.chemical function in living organisms and take part in specific reactions eg. enzymes, Hb
94
fibrous proteins
.polypeptide chains arranged side by side in long filaments
.insoluble in water and have structural role eg. actin and myosin
.fibres form a triple-helix of polypeptide chains-chains are held together by hydrogen bonds
95
denaturation of proteins
.peptide bonds are not usually affected
.primary structure of protein is unchanged by denaturing
.hydrogen bonds, disulfide bonds, ionic bonds and non – polar interactions can all be disrupted
96
lipids
.fats, oils and waxes
.insoluble in water “hydrophobic”
.good source of energy (37kJ/gm)
.poor conductors of heat and often act as insulation
.Most fats exist as triglycerides, made from fatty acids and glycerol
.contain C, O, H
97
Fats are used as an energy store because...
contain more carbon atoms per gramme than glucose
98
functions of lipids
1. Protection of vital organs
2. insulate body against variations in temperature
3. form myelin sheath around some neurones
4. major component of cell membranes
5. used for energy storage by organisms
6. act as signalling molecules
99
saturated fatty acids
1. Carbon chain is straight, with no bends
2. Mainly found in animal fats from meat and dairy products
3. Triglycerides consisting of saturated fatty acids can pack together to form solid fat at room temperature
100
groups of lipids
Fats
Phospholipids
Steroids
101
unsaturated fatty acid
1. Double bonds introduce a definite ‘kink’ in carbon atom chain
2. more double bonds more kinks there will be
Mainly found in vegetable oils, nuts and fish
3. Triglycerides consisting of ‘ kinky’ unsaturated fatty acids do not pack together easily and form liquid oils at room temperature
102
trans fatty acids
1. produced by hydrogenation of oils
2. Sometimes more saturated than natural vegetable oils
3. Able to pack together more tightly
4. Usually solid at room temperature
5. Behave more like saturated fatty acid
103
hydrogenation
1. makes oils more manageable at room temp
2. Unsaturated fatty acids may be converted to saturated fatty acids by relatively simple hydrogenation reaction
104
phospholipids
.one of fatty acids is replaced w/phosphate group- found in cell membrane
Common phospholipids include:
lecithins
cephalins
.head charge on molecule is unevenly distributed- polar and hydrophilic
.hydrocarbon tails do not have an uneven charge distribution- uncharged, non-polar and hydrophobic
105
phospholipid bilayer
aqueous environment phospholipids will arrange themselves in a double layer-forms bilayer
106
triglycerides
.three fatty acid molecules joined to a glycerol
.Each fatty acid consists of an acid (-COOH group) joined to long hydrocarbon chain consisting of C & H
.if 3 fatty acids are identical then it is simple if not it is mixed
107
synthesis of triglycerides
.formed by condensation reaction- glycerol and fatty acids-ester bond
.enzyme involved is Diacylglycerol Acyltransferase (DGAT)
108
properties of triglycerides
.insoluble in water
.soluble in some organic solvents, e.g. ether or ethanol
.non-polar
.Hydrophobic
109
functions of triglycerides
.Energy reserve
.Insulator against heat loss
.Buoyancy
.Protection (vital organs)
.Metabolic source of water
110
steroids/sterol
.found in most living organisms
.Some of most important sterols in humans are: bile, sex hormones, Vitamin D
.Cholesterol is starting material for these sterols
111
cholesterol
.only found in food derived from animals and biological membranes and steroid hormones
.small molecule made from 4 carbon based rings
.made in liver from carbohydrates, protein, fat
.small, narrow and hydrophobic- ideal to sit in between hydrophobic tails of phospholipid bilayer
.helps to regulate fluidity and strength of membrane
112
problem with excess cholesterol
.Form gallstones in bile
.Cause atherosclerosis in blood vessels
113
health benefits of essential fatty acids
.Monounsaturated and polyunsaturated fats
lower possibility of heart disease
.Omega-3 fats
Lowers triglyceride levels, prevents atherosclerosis - protects against blood clots, irregular heart beats and lowers blood pressure
.Omega -6 fats
Stimulate skin and hair growth, maintain bone health, regulate metabolism.
114
obesity negative risks
.involve release pro-inflammatory chemical signals adipokines/cytokines
.reduce sensitivity of body cells to insulin
.Pancreatic beta-cells compensate by over production of insulin “hyperinsulinemia”
.Chronic problems involve failure to produce insulin
115
essential fatty acids
.body can synthesize most of the fats it needs from diet except two:
linoleic acid/omega-6
found in vegetable oils and meats
linolenic acid/omega-3
fatty fish
116
sources of lipids
1. in diet
2. stored in adipocytes
3. produced by liver
117
dietary lipids
1. Lipids in diet are emulsified by bile salts produced in liver
2. Renders them soluble in water environment
3. lipids are then digested in small intestine
4. Lipase helps to break down triglycerides to free fatty acids and monoglycerides
5. products are then absorbed into body
6. Glycerol and free fatty acids transported in blood bound to albumin
118
stored triglycerides in adipocytes
1. Dietary triglyceride are transported to liver or adipose tissue for storage
2. Triglycerides are made in a process called “lipogenesis”
3. Fatty acids are made in cytoplasm and form triglycerides w/glycerol in ER of liver and adipose tissue
119
breakdown of stored triglycerides in adipocytes
1. Lipolysis is process of lipid mobilization
2. Triglycerides stored in adipose tissue can be rapidly mobilized by hydrolytic action of lipases of adipocyte
3. occurs in response to an increase in epinephrine, in process-sympathetic
4. involves cell signalling, where cell responds to an extracellular signal “epinephrine”
120
excess carbs and fatty acid synthesis
1. Fat cells and Liver cells can convert glucose to fatty acids for storage
2. Insulin promotes FA accumulation in 2 ways:
.Inhibits lipase which converts Triglycerides to Fatty acids
.Stimulates fatty acid synthesis in liver and adipose cells
121
lipid metabolism
.hydrolysis to fatty acids and glycerol -LIPOLYSIS-takes place in cytoplasm of cell
.fatty acids -> B-oxidation -> Acetyl CoA
.glycerol -> glucose -> glycolysis -> Acetyl CoA
122
lipoproteins
.Cholesterol and triglycerides are insoluble and are carried in blood attached to lipoproteins
.allow lipids to be transported in circulatory system
.mainly lipids surrounded by proteins
123
endogenous lipids
.produced in SER of liver cells
.lipids are then transported to tissues that need them
.main challenge for this transport is that lipids are hydrophobic, while blood is aqueous
124
types of lipoproteins
1. Chylomicrons
2. Very-low-density lipoproteins (VLDL)
3. Low-density lipoproteins (LDL)
4. High-density lipoproteins (HDL)
.classified according to their physical properties and their function
125
chylomicrons functions
1. gather up proteins and cholesterols and triglycerides from intestines/lymphatic system
2. transport triglycerides and cholesterols obtained from diet to skeletal, cardiac and adipose tissue
3. chylomicrons arrive at target tissue, triglycerides are hydrolysed by lipoprotein lipase
4. free fatty acids produced can then be absorbed by tissue
5. leftovers are taken to liver where they are taken up by endocytosis
126
chylomicrons structure
.largest lipoproteins
.least dense lipoproteins because they contain large amounts of triglycerides
.Inside chylomicron is high in triglycerides w/small amounts of cholesterol
.Outside chylomicron is made up of phospholipids and apolipoprotein- makes it soluble in water
127
very-low-density lipoproteins (VLDL) structure
.Endogenous lipids are produced in liver
.VLDL transport endogenous lipids to target tissue-mainly carry triglycerides
.synthesised when there is an excess energy consumption
.Excess carbohydrate are converted to triglycerides
128
very-low-density lipoproteins (VLDL) function
1. target tissues are muscular tissue and adipose tissue
2. muscles, free fatty acid can be used to produce energy
3. In adipose tissue fatty acids are stored as triglycerides- can lead to obesity
4. excess glycerol is taken to liver and leftover of VLDL is called an Intermediate-Density Lipoprotein (IDL)
129
low density lipoprotein (LDL) structure
.leftovers of IDL
.formed in blood and contain large amounts of cholesterol
.main function is to transport cholesterol to peripheral tissues
.referred as “bad” cholesterol, because high levels of LDL lead to build-up of cholesterol in your arteries
130
low density lipoprotein (LDL) function
1. LDL can be taken up by liver or peripheral tissue
2. Liposomal lipase release cholesterol at target tissues
3. If in excess, macrophages take up LDL and this causes them to turn into Foam cells, which contribute to formation of atherosclerotic plaques
131
high density lipoproteins (HDL) structure
.smallest lipoprotein and is most dense lipoprotein
.produced in blood using ‘leftovers’ from degradation of other lipoproteins
.referred to as “good cholesterol”- in liver, excess cholesterol can be broken down safely
.HDL are very useful in lowering formation of atherosclerotic plaques in vascular tissue because of its function
132
high density lipoproteins (HDL) functions
.transport excess cholesterol from tissues to liver
133
carbohydrates
.large group of organic compounds w/carbon, hydrogen, and oxygen
.energy and to build body structures
.synthesized from carbon dioxide and water through photosynthesis, (CH2O)n, or Cn(H2O)n-1
134
types of carbohydrates
1. Monosaccharides
2. Disaccharides
3. Oligosaccharides
4. Polysaccharides
135
monosaccharides
.simple sugars that cannot be converted into smaller group eg. glucose, fructose and galactose
.divided into aldoses and ketoses:
Aldoses have the carbonyl group on carbon-1 eg. glucose, galactose
ketoses have their carbonyl group on carbon-2 eg. fructose
CnH2nOn-formula
136
monosaccharides characteristics
.white crystalline solids
.dissolve in water to form sweet tasting solutions-soluble
137
ribose function
protein synthesis
138
glucose
.hexose sugar- source of energy
.starting point for glycolysis
.produced commercially via the enzymatic hydrolysis of starch
.can exist as either a straight open-chain or as a cyclical ring structure
139
disaccharides
eg. sucrose=glucose + fructose
eg. lactose=galactose + glucose-through β - (1,4) glycosidic linkage
eg. maltose=glucose + glucose
Cn (H20) n -1-formula
140
polysaccharides
.very large, often branched, molecules
.tend to be amorphous, insoluble in water, and have no sweet taste
eg. storage polysaccharides- starch and structural polysaccharides- chitin
C6xH10xO5x-formula
141
monomer
individual monosaccharides which join to form polysaccharide
142
polymerisation
.process of bonding many MONOMERS by condensation reactions to form one large molecule
143
starch structure
.a-glucose + 1-4,1-6 glycosidic bonds
.helical structure, which makes it good for storage
.insoluble due to its structure-main plant storage sugar
144
amylose
.a-glucose
. has 1,4 glycosidic bonds
.Spiral structure (α helix)
. 20% of starch
145
amylose function
.Helical structure takes up less space and is more stable
.Amylose is used for energy storage
146
amylopectin
.a-glucose
.1,4 and some 1,6 glycosidic bonds
.presence of 1,6 glycosidic bonds produces branched structure
. 80% of starch
147
amylopectin function
.Highly branched and hydrolysed more quickly than amylose
.Plants store it then hydrolyse it when they need a supply of energy
148
cellulose structure
.b-glucose + 1-4 glycosidic bonds
.Alternate β-glucose molecules are rotated through 180o- inverted
.very long straight unbranched chain
.hydroxyl (-OH) groups project from both sides of chain
.Forms chains which run parallel with hydrogen bonds between chains to form microfibrils
.Microfibrils are strong
.Being fibrous, cellulose is structurally important in plant cell walls
149
cellulose function
.Main structural sugar in plants
.Structural component of plant cell walls
.Very strong
.permeable to numerous substances
.About 33% of plant matter
.Most common organic compound on Earth
150
glycogen structure
.a-glucose + 1-4,1-6 glycosidic bonds
.same subunits as amylopectin but much more branched
.insoluble compact store of glucose
151
glycogen function
.storage sugar found in animals
.made mostly by liver & muscles
.stored as granules in cytoplasm of cells
.can be quickly hydrolysed when energy supply is needed
152
oligosaccharides
.short chains of monosaccharides joined together by glycosidic bonds
.some oligosaccharides are joined to proteins- glycoproteins
.Some oligosaccharides are also joined to lipids-glycolipids
153
types of oligosaccharides-glycoproteins
O-linked oligosaccharides
N-linked oligosaccharides
154
O-linked oligosaccharide
.attach to proteins by O-glycosidic bond
155
N--linked oligosaccharide
attach to protein by N-glycosidic bond
156
carbohydrate function
.substrates for respiration
.form intermediates in cellular respiration
.Energy stores: starch, glycogen
.Structural: cellulose
.Transport
.Involved in recognition of molecules outside of a cell
.Constituent of RNA and DNA
157
lactose intolerant
.when person cant produce lactase
158
carbohydrate disorders eg.
Lactose intolerance
Diabetes (Type I and type II)
Hypoglycemia
159
diabetes mellitus
.characterised by hyperglycaemia
.can be caused when insulin are either too low/deficient or if it is less efficient at producing a cell response
.impairs insulin-stimulated glucose entry into cells
.Starves cells of glucose/energy -> muscle weakness -> high blood glucose levels -> damage to peripheral tissue
.leads to ketosis or high levels of ketone bodies in blood
.leads to excessive thirst symptom of diabetes and life-threatening decrease in blood volume
160
type 1 diabetes
.pancreas produces no insulin at all
161
type 2 diabetes
.resistant to insulin or pancreas is unable to produce enough insulin
162
hypocalcaemia
.blood glucose decrease below normal level- more likely in diabetic patients taking insulin in type 1
163
hyperglycaemia
.blood glucose increases above normal level-higher likely in diabetic patients in type 1
164
enzymes
.proteins made of amino acids-coded in DNA
.all chemical reactions controlled by enzymes-increase rate
.don't get used up-only need small amount
165
enzyme functions
1. catalyse metabolic reactions
2. involved in cell communication
3. neurotransmission
4. muscle contraction
166
why do we have enzymes
reduce need for very high temperature
167
structure of enzymes
.has its own amino acid sequence- has same bonds as protein
168
characteristics of enzymes
.specific
.unique 3D shape
.decreases activation energy by forming enzyme substrate complex
.only change rate of reaction
.very efficient and have high turnover no.
169
activation energy
amount of energy needed for reaction to occur
170
2 types of enzymes-QUESTION ASKED ON EXAM
breaker enzymes-reactions where larger molecules are broken into smaller enzymes-catabolism
builder enzymes-reactions where small molecules are built into more complex molecules anabolism
171
lock and key theory
.enzyme=lock
.substrate=key
.substrate attaches to active site of enzyme to form enzyme substrate complexes- perfectly complementary
.activation energy reduced
172
induced fit model
enzyme and substrate forms enzyme substrate complexes-not perfectly complementary-used hexokinase to find it out
173
factors that effect enzyme activity
.temperature
.pH
.substate concentration
.enzyme concentration
174
how temperature affects enzyme activity
BELL SHAPED CURVE GRAPH
.increase in temp-molecules have greater kinetic energy increase molecules colliding-increasing rate of reaction
.once it reaches optimum temperature-it will decrease and enzyme denatures
.hydrogen bonds break -> change secondary and tertiary structure -> changes shape of active site -> decreases rate of reaction
175
enzymes at low and high temperatures
low-inactive but hasn't denatured-no kinetic energy
high-denatures and is permanent
176
how pH affects enzyme activity
BELL SHAPED GRAPH
.optimum pH= 8-when enzyme work most efficiently
.denatures at too low or too high temperatures
.have small reversible changes and can change rate of reaction
.changes charge-affects formation of H and I bonds in proteins and affects shape
177
how substrate concentration affects enzyme activity
INCREASES AND THEN PLATEUS AFTER POINT OF SATURATION GRAPH
.if amount of enzyme is constant-rate of reaction will increase as substrate increases
.enzymes active sites are full- become saturated
178
how enzyme concentration affects enzyme activity
DIRECTIONAL PROPRTIONAL GRAPH
.increase in enzyme conc. will increase enzyme reaction
.excess substrate increase in rate is linearly related to enzyme conc.
179
activators
.switch enzymes on
.either co-factors or co-enzymes
.inactive enzyme- apoenzyme
.apoenzyme and cofactor/enzyme =active enzyme-holoenzyme
180
coenzymes
.non-proteins that help enzymes function
.associated with active site of enzymes
.organic
181
cofactor
inorganic compounds eg. Mg 2+
182
inhibitors
.switch enzymes off-stop form enzyme substrate complex
183
competitive inhibitors
.structurally similar to substrate
.inhibitor has a shape that lets it fit into active site-they will compete w/substrate for active site of enzyme
184
competitive inhibitors properties
.if substrate conc. increases it will reduce effect of inhibitor
.substrate molecules present greater chance of them finding active sites
.fewer occupied by inhibitor and maximum rate is unchanged
185
non competitive inhibitors
.bind to site away from active site
.alters overall shape enzyme-active site can no longer accommodate substate
.does not compete
186
non competitive inhibitors properties
.rate of reaction unaffected by substate concentration
.not dependant on substrate eg. cyanide
187
allosteric regulation
.change in kinetic properties of an enzyme caused by binding of another molecule eg. non competitive inhibitor
.binding site is remote from active site
.activity can be changed by molecules other than substrate
.binding of a small molecule to enzyme alters its conformation and this affects active site
.can either increase or decrease enzyme activity
188
feedback inhibition
.end-product inhibits an earlier reaction in sequence
.end-product in pathway accumulates as metabolic demand for it declines
.end-product in turn binds to allosteric regulatory site of enzyme at start of pathway and decreases its activity
.greater end-product levels greater inhibition of enzyme activity
189
quorum sequencing-unicellular signalling
.bacterium produce signalling molecule A
.At low density of bacteria, low concentration of signal ”auto-inducer”
.Increase in population increases concentration of A
Enable cell to sense changes in population density- bacteria emit light which is an advantage
190
why we need feedback inhibition
Prevents cellular depletion/waste
Prevents dangerous build-up
191
types of multicellular cell signalling
1. DIRECT CELL
2. AUTOCRINE
3. PARACINE
4. ENDOCRINE
192
direct cell signalling
.Direct signalling with cells that make physical contact
.Connection is through gap junctions
.No signal-ligand produced
eg. between neighbouring heart cells
193
autocrine (self-signalling) signalling
.involves chemical signal that binds to receptors on same cell
.Results in change in same cell
.important to help cells take on and reinforce their correct identities
eg. monocytes
194
paracrine signalling
chemical signal that binds to receptors on a different but nearby cell eg. neuromuscular junction
195
endocrine signalling
.when endocrine cells release hormones
.hormones travel in blood to distant target cells in body eg. adrenaline
196
requirements for signalling
A ligand
A specific signalling molecule forms extracellular signal and acts as “key”
A Receptor Protein
A specific protein, normally found on cell surface acts as the “lock”
The Intracellular Signal
A relay chain consisting of intracellular signalling molecules and proteins that form an Intracellular Signalling Pathway
Effector proteins
Protein targets inside cell that change their properties in response to signalling protein cascade
197
extracellular signal molecules
.referred to as LIGAND
.can be local between neighbouring cells or long distance
.Target Cells have “Receptor Proteins” specific to
Signal Molecule
.Receptors are usually on cells surface membrane but not always
.Most cells produce and receive signals, so communication is a 2-way process
198
general principle for cell signalling
1. Binding of Ligand to the Receptor Protein, activates Intracellular Signalling Proteins
2. then change properties of target proteins
199
ligand
.small molecules and include proteins, peptides, amino acids, nucleotides, steroids, dissolved gases
.referred to as “first or primary messenger” eg. acetylcholine, GABA, adrenaline, insulin
200
extracellular receptors
.present on surface of Target Cell
.acts as a signal transducer
.Converts extracellular ligand-binding into an intracellular signal
201
intracellular receptor
.associated with nucleus
.Bind small hydrophobic molecules able to cross plasma membrane
.signal molecule is hydrophobic and able to cross lipid bilayer
.form hormone-receptor complexes in the cells, which increases gene transcription
.acts on transcription factors leading to increase gene transcription eg. steroid hormones
202
types of extracellular receptors
1. Ion-Channel-Coupled
2. G-Protein-Coupled
3. Enzyme-Coupled
203
ion channel coupled receptor
.Involved in rapid synaptic transmission and bind neurotransmitters eg. acetylcholine
.Binding of Ligand Can Open or close channel when bound to neurotransmitter
204
enzyme coupled receptor
.majority are Protein Kinases
.phosphorylates and activates other proteins eg. Insulin receptor
205
G-protein coupled receptor
.Binding of ligand activates an intracellular target protein
.involves special binding protein called GTP-binding protein
.Target proteins that are enzymes produce small signalling molecules eg. Adrenaline, Oxytocin
206
insulin as an enzyme coupled receptor
Associated with a Kinase Enzyme, which phosphorylates and activate other proteins
207
intracellular signalling molecules
.Amplifies original signal
.Enzymes are triggered which produce large amount of second messengers “signal amplification”
.often referred to as Second Messengers
208
types of second messengers
Cyclic Adenosine Monophosphate (cAMP)
Inositol Tri-Phosphate (IP3)
209
cAMP
1. GTP binds to active G protein
2. activate Adenylyl cyclase
3. ATP coverts to cAMP
210
IP3
1. GPT binds to active G protein
2. activate Phospholipase-C
3. IP3 produced
4. IP3 gated Ca2+ channels release calcium
211
effector proteins
Calcium channels- Increase muscle contraction, neurotransmitter release
Internal Calcium stores -Increase contraction strength
Smooth muscle contractile proteins/Ca-release channels- Decrease or increase contraction
Glucose transporters- Increase glucose transport
212
G protein couple receptor
.Binding of ligand activates an G protein-using GTP
.activated G protein activates and enzyme – this enzyme produces second messengers e.g. cAMP
213
heart rate and contraction strength during exercise
1. increase in heart rate and contraction strength
2. Increase in sympathetic activity
3. Circulating adrenaline
4. Neurotransmitter release, noradrenaline
214
cardiac output equation
HR x SV-heart rate x stroke volume
heart rate is determined in the SAN
215
sympathetic stimulation on force of contraction-ventricles
noradrenaline -> B1 receptor -> adenylate cyclase -> cAMP (2nd messenger) -> kinase A -> change in effector proteins have ca channels and sarcoplasmic reticulum-force of contraction
.from adenylate cyclase to kinase is called intracellular signal
216
sympathetic stimulation on heart rate-SAN
noradrenaline -> B1 receptor -> adenylate cyclase -> cAMP (2nd messenger) -> kinase A -> Phosphorylates Calcium channels
Increase calcium influx -> SAN -> increase in heart rate
217
beta 2 adrenergic receptors airways smooth muscle
.Activation of β2 adrenergic receptors leads to relaxation of smooth muscle in lung, and dilation and opening of airways
.Beta2 –Adrenergic receptors on smooth muscle bind circulating adrenaline (epinephrine)
.β2 adrenergic receptors are coupled to a stimulatory G protein of adenylyl cyclase and increases cAMP
.in smooth muscle cells-leads to relaxation, which opens the airways
218
beta 2 adrenergic receptors airways smooth muscle pathway
adrenaline -> B1 receptor -> adenylate cyclase -> cAMP (2nd messenger) -> kinase A -> inhibits contraction of smooth muscle -> open airways and reduces resistance to flow
219
insulin and blood glucose
1. Glucose enters cells through special protein carrier molecules (GLUT4 transporters)
2. Glucose is low in cells, as glucose is metabolized in cell
3. concentration gradient into the cell exists
4. Increase in blood glucose stimulates cells in pancreas to release insulin
5. Insulin binds to its enzyme coupled receptor which causes vesicles containing GLUT4 to move to cell membrane
6. Glucose moves into cells and blood glucose falls
220
opioids and pain relief
. Opioids attach to receptors in brain
.Normally these opioids are endogenous- created naturally in body
.send signals to brain of "opioid effect" which blocks pain, slows breathing, and has calming and anti-depressing effect
.Opioid drugs bind to opioid receptors in brain, spinal cord, and other areas of the body- tell your brain you're not in pain
221
heroine and morphine and the opiate receptors
.GABA release reduces Dopamine release
Opiates inhibit release of GABA, which increases dopamine release
222
function of opiate receptors (G coupled receptors)
.Causes activation of potassium channel and deactivation of calcium channel
.decreases activity of nerve terminal, reducing release of GABA
223
receptor pharmacology QUESTION ON THIS
study of interactions of receptors w/ pharmaceuticals
receptors can be activated by either:
.endogenous agonists eg adrenaline
.exogenous agonists
224
agonist
.chemical that binds to receptor and activates receptor to produce a biological response
.signalling molecule is an agonist
.may be manufactured pharmaceuticals designed to mimic normal function of body
.Useful if body does not make enough or response needs boosting
225
antagonist
.binds to receptor and blocks action of agonist
.may be naturally occurring substances-endorphins and natural pain relief
.may be pharmaceuticals designed to block normal function of body
PAIN RELIEF
CARDIOVASCULAR PROBLEMS IN HIGH BLOOD PRESSURE
226
competitive antagonist (reversible)
.binds to same site as agonist but does not activate it, thus blocks agonist's action
.Emax is not affected, EC50 increases
227
cellular response and dose graph QUESTION ON THIS
.EC50 is concentration of drug that gives half-maximal response (bottom part)
.Emax is maximal response rate (top part)
.Increasing concentration of ligand will not increase Emax
228
non-competitive antagonist (irreversible)
.binds to an allosteric (non-agonist) site on receptor to prevent activation of receptor
.reduce Emax, EC50 is not affected
229
primary messengers
hormones or neurotransmitters
230
cellular respiration
.chemical energy of "food" molecules is released and partially captured in form of ATP
.energy in glucose is transferred to ATP
.glucose + oxygen -> C02 and water
231
glycolysis
.“splitting of sugar”
.occurs in cytoplasm of cells in all living organisms
.does not require O2, and can therefore function anaerobically
.process converts ONE molecule of glucose into TWO molecules of pyruvate
232
stages of glycolysis
cytoplasm and anaerobic
Phosphorylation of glucose using ATP
oxidation of Triose phosphate to pyruvate
net gain of ATP
reduced NAD
.Net gain from 1 x glucose:
2 x ATP
2 x reduced NAD
2 x Pyruvate
233
net yield for ATP in glycolysis
2 for each glucose molecule
2 molecules are used to activate glucose
4 molecules are produced
234
triglyceride and glycerol
.1 molecules of glycerol + 3 fatty acids
.involves hydrolytic actions of lipase
.glycerol is converted to glucose
.occurs by gluconeogenesis
.converted to glycerol-3-phosphate
235
regulation of glycolysis
.Recall product feedback inhibition mechanism
.Involves allosteric regulation of earlier enzyme phosphofructokinase (PFK)
.involves ATP and citrate
236
How many useable molecules of ATP are made directly by glycolysis from 2 molecules of triglyceride?
0
237
fermentation
.Without oxygen, cellular respiration can not occur because oxygen serves as final electron acceptor in electron transport system
.electron transport system would therefore not be available so pyruvate is electron acceptor
.Glycolysis can occur without oxygen
.glycolysis does not require oxygen, it does require NAD+
NADH is oxidised and donates H atoms to pyruvate
.NAD+ is then free to become reduced again
.Glycolysis can continue
.ATP can continue being made
238
anaerobic respiration
.no oxygen, glycolysis is main source of ATP production
.For glycolysis to occur we need NAD+
2 ways to re-oxidise NADH:
We need to convert nadh back into nad+
Animals – lactate fermentation
Fungi/yeast – ethanol fermentation
.Lactate is carried from muscles to Liver
.converted back to pyruvate when more 02 is available
eg. in running/vigorous exercise
239
aerobic respiration
.mitochondria= site of aerobic respiration
.requires O2 in order to generate ATP
.16 times more efficient than anaerobic respiration, which yields 2 molecules of ATP per 1 molecule of glucose
240
anaerobic exercise
builds up in the muscles leading to pain and fatigue and it is toxic
241
yeast
. can live with or without alcohol
.Glucose -> alcohol + carbon dioxide
C6H12O6 -> 2C2H5OH + 2CO2
Also called fermentation of alcohol
242
commercial uses of yeast
.brewing
.bread making
both use fermentation of yeast
243
enzymes in cellular respiration
. its a redox reaction
.Enzymes alone are no good at redox reactions
.Co-enzymes are ‘helpers’ that ensure enzymes are more effective
.Co-enzymes carry chemical groups or ions around the cells
244
pathway for aerobic respiration
glycolysis -> link reaction -> Krebs cycle -> oxidative phosphorylation
245
link reaction
.Dehydrogenation: Pyruvate is actively transported to mitochondria from cytoplasm and is oxidised as hydrogen is removed and transferred to NAD which is reduced to form reduced NAD
.It is also decarboxylated CO2 is removed to form acetate
.Acetate then combined w/CoA to form Acetyl CoA
.Net gain from 1 x glucose:
2 x reduced NAD
2 x Acetyl Coenzyme A
in the Matrix
246
function of acetyl-CoA
.carry acetate to Krebs cycle
.No ATP is produced during link reaction but NADH is made to make ATP
247
purpose of Krebs cycle
generate NADH and FADH2
248
Kerbs cycle stages
.2C Acetyl CoA enters the cycle and acetyl is accepted by 4C acid to form 6C acid regenerating CoA for link reaction
.Cycle turns twice for each original glucose molecule
.2C acetate fragment is completely broken down and 4C acid is regenerated via 6C and 5C intermediates in series of oxidation-reduction reactions
.1 x ATP is produced directly by substrate level phosphorylation of ADP
.2 x C atoms are released in 2 x CO2 molecules by decarboxylase
.3 x reduced NAD and 1 x reduced FAD are produced as 4 pairs of H atoms are removed to these hydrogen carriers by dehydrogenase
.Net gain from 1 x glucose:
6 x reduced NAD
2 x reduced FAD
4X carbon dioxide
2X ATP
249
oxidative phosphorylation
.occurs in mitochondrial cristae and starts w/Electron Transport System (ETS)
.ETS is found in mitochondrion of eukaryotes and in plasma membrane of prokaryotes
.electron transport chain consists of a series of molecules, mostly proteins, embedded in Inner Mitochondrial Membrane
.molecules pass electrons from a high-energy compound to a final low-energy electron acceptor
250
electron transfer chain (ETC)
.Energy is released during these oxidation-reduction reactions to produce ATP
.Occurs= mitochondria of eukaryotes
NADH or FADH2 bring electrons to ETS in mitochondria
.system contains membrane-bound electron carriers that pass electrons from one to another
release stored in reduced NAD+ (NADH) and reduced FAD (FADH2)
Each NADH molecule makes 2.5 ATP molecules
Each FADH2 molecule makes 1.5 ATP molecules
251
electron transfer
.Oxygen is final electron acceptor
.Electrons lose energy which is used to pump protons against their concentration gradient
.low-energy electrons that emerge from electron transport system are taken up by O2
.negatively charged oxygen molecules take up protons from medium and form water
2H+ + 2e- + 1/2 O2 -> H2O
UNI BIOLOGY
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