Unit 3.1 - biological molecules Flashcards
1
Q
what are monomers?
A
they are the smaller units from which larger molecules are made
2
Q
what are polymers?
A
they are molecules from a large number of monomers joined together
3
Q
what are carbohydrates made up of?
A
hydrogen, oxygen and carbon. they have a general formula of (CH2O)n
4
Q
what are carbohydrates?
A
they are polymers whose monomers are simple sugars
5
Q
what are monosaccharides?
A
they are the monomers from which larger carbohydrates are are. glucose, galactose and fructose are common examples
6
Q
what is a condensation reaction?
A
it joins the two molecules together with the formation of a chemical bond and involves the elimination of a molecule of water
7
Q
what does a condensation reaction between two monosaccharides form?
A
a glycosidic bond
8
Q
how are disaccharides formed?
A
by the condensation of two monosaccharides
9
Q
what is maltose?
A
its a disaccharides formed by condensation of two glucose monomers
10
Q
what is sucrose?
A
its a disaccharides formed by condensation of a glucose molecule and a fructose molecule
11
Q
what is lactose?
A
its a disaccharides formed by condensation of a glucose molecule and a galactose molecule
12
Q
what are glucoses two isomers?
A
a glucose and b glucose
13
Q
what categories do monosaccharides fall into?
A
- 3 carbons triose
- 4 carbons tetrose
- 5 carbons pentose
- 6 carbons hexase
14
Q
why is the reaction between two monosaccharides a condensation one?
A
when 2 glucose monomers are joined by one oxygen atom, the two hydrogens and single oxygen atom are lost which form water
15
Q
what happens during a condensation reaction?
A
the reaction joins two molecules (monosaccharides) together with the formation of glycosidic bond and involves the elimination of a molecule of water
16
Q
what is a hydrolysis reaction?
A
it breaks a chemical bond between two molecules and involves the use of a water molecule
17
Q
what are the polysaccharides?
A
starch, glycogen and cellulose
18
Q
how are glycogen and starch formed?
A
by the condensation of alpha glucose
19
Q
how is cellulose formed?
A
the condensation of beta glucose
20
Q
what is the structure of starch?
A
its a mixture of two polysaccharides of alpha glucose - amylopectin and amylose
21
Q
what is amylopectin?
A
a long, branched chain of alpha glucose, its side branches allow the enzymes that break down the molecule to get at the glycosidic bonds easily so glucose can be released quickly
22
Q
what is the amylose like?
A
a long unbranched chain of alpha glucose, the angles of glycosidic bonds give it a coiled structure, like a cylinder. this makes it compact, so its good for storage as you can fit more into a small space
23
Q
what is starch used as and for?
A
- a storage molecule, its compact (amylose) to fit into small spaces
- it can be broken down quickly to release glucose (amylopectin)
- its large and insoluble so has no impact on osmosis
24
Q
what is glycogen?
A
its a polysaccharide of alpha glucose. its structure is similar to amylopectin but is shorter and has more side branches, which means stored glucose can be released quickly which is important for energy release in animals.
- also very compact and insoluble
25
what is cellulose?
its found in plant cell walls, its not an energy store it has a structural purpose.
26
what is the structure of cellulose like?
made of lomg, unbranched chains of beta glucose.
- when beta glucose molecules bond they from straight cellulose chains
- the chains are linked together by hydrogen bonds to form strong microfibrils which means cellulose provides structural support
27
how do the polymers lie in cellulose?
they lie close to one another and cross linkages form from hydrogen bonds between them. this makes cellulose strong and stable, which is what makes the cell strong
28
What is a water molecule made up of?
Two atoms of hydrogen and one of oxygen, it has no overall charge and has both slight negative and positive poles and is dipolar
29
How do hydrogen and water bond?
The positive pole of one water molecule will be attracted to the negative pole of another water molecule. The attractive force is the hydrogen bond
30
What are hydrogen bonds like?
Each bond is fairly weak (tenth as strong as a covalent bond), many of them together form important forces that cause the molecules to stick together
31
What happens due to water molecules sticking together?
It takes more energy (heat) to separate them than would be needed, so the boiling point of water is higher than expected
- without hydrogen bonding, water would be a gas
32
Why does water have a high specific heat capacity?
the hydrogen bonds between water can absorb a lot of energy, so it has a high SHC. its useful in living organisms as it means that water doesn't experience rapid temperature changes, this makes water a good habitat as the temp under water is likely to be more stable than on land
- also remain stable inside organisms helping them to maintain a constant body temp
33
What is the latent heat of vaporisation?
it takes a lot of energy to break the hydrogen bonds between water molecules, so water has a high LHofV as a lot of energy is used up when water evaporates
34
what is cohesion in water?
the tendancy of molecules to stick together is known as cohesion; with its hydrogen bonding, water has large cohesive forces & these allow it to be pulled up through a tube eg xylem vessel AKA capillary pressure in plants.
35
what happens when water molecules meet air?
they tend to be pulled back into the body of water rather than escaping from it. this force is cohesion tensions and means that the water surface acts like a skin and is strong enough to support small organisms due to the flat surface as it reduces pressure.
36
how is water used in metabolism?
- water is used to break down many complex molecules by hydrolysis eg proteins into amino acids
- its also produced in condensation reactions- chemical reactions take place in an aqueous medium and is a major raw material in PHs
37
What does water readily dissolve?
- gases eg oxygen and carbon dioxide
- waste eg ammonia and urea
- inorganic ions and small hydrophilic molecules (water loving) eg amino acids, ATP and monosaccharides
- enzymes, whose reactions take place in solution
38
what are the other important features of water?
- its evaporation cools organisms and allows them to control their temperature
- its not easily compressed and therefore provides support
- its transparent so aquatic plants can photosynthesis and light rays can penetrate the jelly like fluid that fills the eye
39
what's the test for reducing sugars?
1. add benedicts solution and heat in a water bath (at least 85 degrees) almost boiling point
2. red/orange/yellow colour means reducing sugar is present
40
what's the test for non reducing sugars?
1. a negative test at first with benedicts
2. boil the sugar with HCL for 5mins
3. neutralise with sodium carbonate
4. re-test with benedicts
5. = positive test
41
what are lipids like?
- they are made up of carbon, oxygen and hydrogen
- they have less oxygen than carbohydrates
- they are insoluble in water -> hydrophobic
- they are soluble in alcohol and acetone (organic solvents)
42
what do lipids do?
1. cell membrane - phospholipids provide flexibility and control movement of substances
2. protection - fat is around delicate organs
3. insulation - fats are slow conductors of heat so a layer of this in the body preserves heat, they also insulate neurones (myelin sheath)
4. energy - when oxidised fats release x2 energy of carbohydrates whilst releasing water
5. waterproofing - plants/insects rely on waxy cuticles to make them waterproof eg mammals release an oily secretion
43
what are triglycerides?
they are formed by the condensation of one molecule of glycerol and three molecules of fatty acids
44
what are the ester links?
the ester bonds are formed from a condensation reaction between glycerol and a fatty acid, they can be broken down by hydrolysis.
- the 3 fatty acids are bound to the glycerol via ester linkages.
45
what is produced/released when a triglycerides are formed?
A total of 3 molecules are produced when a triglyceride form, one water molecule if removed from each ester bond
46
why are triglyceride's non polar?
they are unable to form hydrogen bonds with water
47
what is a saturated triglyceride/fatty acid?
a fatty acid where all the carbon-carbon bonds in the hydrogen chain are single bonds
48
what is a unsaturated fatty acid?
a fatty acid where there are double bonds between some carbons so potentially more hydrogen could bind
49
what is a monounsaturated fatty acid?
a fatty acid where one of the carbon-carbon bond is a double bond
50
what is a polyunsaturated fatty acid?
a fatty acid where more than one carbon-carbon bond is a double bond
51
what are phospholipids?
they are based on glycerol but only two fatty acid molecules are bonded to the glycerol, the third is replaced by a phosphate group
52
what is the structure of phospholipid?
the phosphate group is iconic and the hydrogen chains of the two fatty acids are covalently bonded, there are two regions
1. hydrophilic phosphate 'head'
2. hydrophobic 'tails' which HATES water
53
what happens when phospholipids are placed in water?
phospholipids become organised into a bilayer, in which the hydrophilic head faces outwards into the water and the hydrophobic tails face inwards, away from the water.
- the phospholipid bilayers are the bases of plasma membranes
54
What are inorganic ions?
They are found in organisms where they occur in solution (dissolve easily) in the cytoplasm of cells and in bodily fluids as well as part of larger molecules
55
What may inorganic ions be in?
Concentrations that range from very high to low
56
What do inorganic ions perform?
A range of functions due to their size and functiona, the specific function a ion performs is related to its properties
57
What do iron ions do?
They're found in haemoglobin where they play a role in the transport of oxygen
58
What do phosphate ions do?
They perform a structural role in the structure of DNA molecules and a role in storing energy in ATP molecules
59
What do hydrogen ions do?
They're important in determining the pH of solutions and therefore the functioning of enzymes
60
What are sodium ions?
They're important in the transport of glucose and amino acids across plasma membranes
61
what is ATP made from?
adenine - a organic base containing nitrogen
ribose - a sugar molecule with a 5-carbon ring structure (pentose)
phosphates - three phosphate groups are attached
62
what are organic bases?
they are compounds that act as proton accepters, they usually contain nitrogen
63
how do you form AMP and Adenosine?
- adenine + ribose + 1 phosphate = Adenosine monophosphate (AMP)
- adenine + ribose = adenosine
64
what is ATP classed as?
a nucleotide derative with three phosphate groups, the bonds between the 3 phosphate is where is the energy is released; each bond is unstable and has a low activation energy which means its easily broken
65
what is a nucleotide derative?
its a molecule made from a sugar, phosphate group and nitrogen- containing base
66
what is the reaction of ATP being hydrolysed?
its an exothermic reaction and is catalysed by an enzyme called ATP hydrolase, which is also called ATPase.
- ATP + H20 --> ADP + Pi + E
usually in living cells its only the terminal phosphate end that's removed which produces ADP
67
how can ATP be synthesised?
its done by adding an inorganic phosphate group to ADP, water is then produced and therefore its an exothermic reaction. its catalysed by ATP Synthase.
ADP + Pi + E --> ATP + H20
68
when does the synthesis of ATP from ADP + P occur?
1. photosynthesis - during a process called photophosphorylation
2. respiration - during a process called oxidative phosphorylation
3. in plant/animal cells when phosphate groups are donated to ADP from other molecules (substrate level phosphorylation)
69
where is ATP synthesised?
in the mitochondria, cells that nee to produce a lot of ATP will have many mitochondria
70
what do the unstable bonds in ATP do?
they make it a goof energy producer and a bad long term energy store, its therefore the immediate energy store while fats and carbs are used for long term storage
71
why can cells use a large quantity of ATP?
its reformed quickly once its used, therefore a little ATP can make a large amount of energy
72
what are the first 4 uses of ATP?
1. metabolic processes - eg making larger molecules from smaller molecules (anabolic reactions)
2. active transport
3. movement - ATP is used to move muscle fillaments past each other to allow it to contract
4. secretion - ATP is used to make lysosomes that are necessary for cells to secrete/ release molecules
73
how is ATP used in activating molecules?
when ATP is hydrolysed, the inorganic phosphate released Is used to make other compounds more reactive. this lowers the activation energy of enzyme-catalysed reactions
74
what is DNA?
- deoxyribonucleic acid is an important information carrying-molecules, it holds all genetic information
75
what is DNA made up of?
its a polymer made up of monomers called nucleotides.
76
what are nucleotides made up of?
its made of a deoxyribose, a phosphate group and one of the organic bases adanine, guanine, thymine and cytosine
77
how are the components of nucleotide joined?
Base + sugar + phosphate group joined via a condensation reaction
78
what is a nucleotide also called?
a mononucleotide
| - 2 mononucleotides can join together via a condensation reaction to form a dinucleotide
79
what's the bond between the mononucleotides formed between?
forms between the sugar of one and the phosphate group of another during a condensation reaction
- the bond is called a phosphodiester bond
80
what do many mononucleotides form?
a polynucleotide via a condensation reaction
81
what are the pairs?
- adenine and thymine
- guanine and cytosine
- the quantities of A & T are equal in a dna molecule, therefore the quantities of C & G must also equal. the ratio of the bases will vary between species
82
what is the backbone of DNA like?
the two strands that coil around one another to form a double helix. its made of a deoxyribose sugar and phosphate groups bound together by condensation reactions
83
how are the two strands held?
together in a twist by hydrogen bonds that form between two base pairs.
- two hydrogen bonds form between A & T and three between C & G, therefore the more c & G there are the more stable it is
84
what are adenine and guanine and thymine and cytosine like?
- A and T are purines as they're longer due to having 2 carbon-nitrogen rings
- C & G are pyrimidines are shorter bases as they only have 1 carbon-nitrogen ring
- a purine base bonds with a pyrimidine base means that the DNA molecule is the same width throughout
85
why is DNA stable?
1) . the hydrogen bonds between the bases
2) . the coiling of the DNA keeps the chemically reactive bases inside the helix protected
3) . further forces between the bases help, its called base stacking where bonds form between adjacent bonds
86
what is on carbon 3 and 5 of a pentose sugar?
carbon 3 has a hydroxyl (OH) and carbon 5 is attached to the phosphate group. they're often called the 3-prime and 5-prime carbons
87
what are the other features of DNA?
- its huge and carries a lot of info
- base pairing rules allows dna to be copied accurately each time its needed and can be transferred
- coiling of the DNA into a helix protects bases from chemicals or physical forces outside
88
why wasn't DNA believed to hold the code for life when it was first discovered?
there are only four bases and so the structure of dna seemed too simple to code for something so complicated
89
what are proteins? and functional proteins?
- they are large molecules that always contain the elements carbon, hydrogen, oxygen and nitrogen
- functional proteins may contain one or more polypeptides
90
what are amino acids?
they are the monomers from which proteins are made
91
what are amino acids made from?
a NH4 which represents an amino group, a COOH which represents a carboxyl group and 'R' shows a side chain
92
how many amino acids are there?
there are 20, and they all only differ in their side group
93
how is a polypeptide formed?
via a condensation reaction between two amino acids
94
how are dipeptides and polypeptides formed?
- polypeptides by the condensation of many amino acids
| - dipeptides by the condensation of two amino acids
95
what is a primary structure?
the sequence of amino acids in a polypeptide chain
96
what is a secondary structure?
the shape formed when the polypeptide chain becomes folded and coiled. hydrogen bonds form between the amino acids in the chain, which makes it automatically coil into an structures alpha helix (spiral shape) or fold into a Beta pleated sheet
97
what is the tertiary structure?
the coiled or folded chain of amino acids often fold/ coil further. more bonds form between different parts of the polypeptide chain
98
what are the new bonds formed within the tertiary structure?
2. disulphide bridges whenever two molecules of the amino aids cysteine come close together, the sulfur in one cysteine bonds to the same in another
3. ionic bonds and hydrogen bonds between amino acids with positively & negatively charged parts of the molecule
99
what is the quaternary structure?
occurs when the protein has more than one polypeptide chain
100
what are globular proteins?
they have a tertiary structure that resembles a globule or ball and are shape specific. they usually have a chemical function eg enzymes, such as insulin and haemoglobin
101
what are fibrous proteins?
they are usually long, thin molecules and have a structural function eg collagen and keratin
102
how is the shape of globular and fibrous proteins maintained?
globular by relatively weak forces eg hydrogen bonds and ionic bonds and fibrous rely more on strong disulphide bridges
103
what is RNA?
ribonucleic acid is a polymer that's made from nucleotides also
- its single stranded and quite short
104
what is RNA made up of?
- the sugar is pentose ad is ribose, the bases are A, T, C and U (uracil)
- there are two types of RNA called mrna and trna
105
what is mRNA, tRNA and rRNA?
- mrna transfers genetic info from dna in the nucleus to the ribosomes
- trna is involved in protein synthesis, its a single strand that's folded to form a clover leaf shape structure
- rRNA makes up ribosomes with protein
106
what does DNA do?
- protein synthesis
- cell division
- passing on genetic info
107
what is DNA replication?
it involves copying the sequence of organic bases to sequence the code for a second time
108
what is the process of DNA replication?
1. the enzyme dna helicase breaks the hydrogen bonds between the bases on the two polynucleotide DNA strands, which makes the helix unwind
2. each original single strand acts as a template for a new strand, complementary base pairing means the free-floating DNA nucleotides are attracted to their complementary exposed bases on each original template strand
3. condensation reactions join the nucleotides of the new strands together, catalysed by the enzyme dna polymerase. hydrogen bonds form between the bases on the original and new strands
4. each new dna molecule contains one strand from the original dna molecule and one new strand
109
what is the active site of dna polymerase complementary to?
the 3' end of the newly forming dna strand, so the enzyme can only add nucleotides to the new strand at the 3' end
110
what direction is the new strand made in?
in a 5' to 3' direction as DNA polymerase moves down the template strand in a 3' to 5' direction. this is because the strands in the double helix are antiparallel, the DNA polymerase working on one of the template strands moves in the opposite direction to the dna polymerase working on the other template strand
111
what did Watson and crick do?
they determined the structure of DNA and they also came up with the theory of semi conservative DNA replication
112
what did Medelson and Stahl's experiment do?
it wasn't until their work, the theory was validated. people before that didnt know if DNA was conservative or semi-conservative.
- if it was conservative it meant the original DNA strands would stay together and the new DNA molecules would contain two new strands
113
what was the first step in the semi conservative theory experiment?
- two samples of bacteria were grown, one in a nutrient broth containing light nitrogen and one in a broth containing heavy nitrogen. as the bacteria reproduced, they took up the nitrogen from the broth to help make nucleotides for the new DNA. so the nitrogen gradually became a part of the bacteria's DNA
114
what was the second step in the semi conservative theory experiment?
- a sample of DNA was taken from each batch of bacteria and spun in a centrifuge. the DNA from heavy nitrogen settled lower down the centrifuge tube than the DNA from the light nitrogen bacteria as its heavier
115
what was the third step in the semi conservative theory experiment?
- then the bacteria grown in the heavy nitrogen broth were taken out & put in a broth containing only light nitrogen. the bacteria, were left for one round of DNA replication and then another DNA sample was taken out and spun in the centrifuge
116
what was the fourth step in the semi conservative theory experiment?
- if the replication was conservative, the original DNA which would've still been together and settles at the bottom. the new light DNA would settle at the top
117
what was the fifth step in the semi conservative theory experiment?
if replication was semi conservative, the new bacteria DNA molecules would contain one strand of the old DNA containing heavy nitrogen and one strand of new DNA containing light nitrogen. so the DNA would settle out between where the light nitrogen DNA settled out and where the heavy nitrogen DNA settled out.
118
what was the sixth step in the semi conservative theory experiment?
- as it turned out the DNA settled out in the middle showing that DNA molecules contained a mixture of heavy and light nitrogen. the bacterial dna had replicated semi-conservatively in the light nitrogen
119
what are enzymes?
they are biological catalysts and catalyse metabolic reactions both at a cellular level and for the organism as a whole
120
what can enzymes affect?
they can affect structures in an organism
- they can be intracellular and extracellular
- they are proteins and highly specific
121
what is needed in a chemical reaction?
a certain amount of energy is needed to start the reaction (usually heat), known as the activation energy
122
what do enzymes do to the activation energy?
they lower the activation energy that's needed, often making reactions happen at lower temps which speeds up the rate of reaction
- if two molecules need to be joined, being attached to the enzyme holds them closer together, reducing any repulsion between the molecules so they can bond more easily
123
what happens when an enzyme is catalysing a breakdown reaction?
fitting into the active site puts a strain on bonds in the substrate, so the substrate molecule breaks up more easily
124
what is the lock and key model?
early scientists studying the action of ezymes came up with the model, where he substrate fits into the enzyme in the active site
125
what did scientists soon realise from the lock and key model?
although the enzyme and substrate do have to fit together in the first place, new evidence showed that the enzyme-substrate complex changed shape slightly to complete the fit. they modified the model and called the induced fit model
126
what does the induced model say?
it helps explain why enzymes are so specific and only bond to one particular substrate. the enzyme is flexible and moulds around the substrate. as it changes shape, it puts a strain on the substrate which distorts a bond in it, consequently lowers the Ea needed to break the bond.
127
why are enzymes so specific?
they usually only catalyse one reaction, this is because only one complementary substrate will fit into the active site
128
what determines the active site's shape?
the enzymes tertiary structure which is determined by the enzymes primary structure
- each enzyme has a different tertiary structure and so a different active site. if the substrate shape doesn't match, an enzyme-substrate complex won't be formed and the reaction wont be catalysed
129
what happens if the enzymes tertiary structure is altered?
the shape of the active site will change which means the substrate wont fit into the active site therefore the enzyme-substrate complex wont be formed. it will then no longer be able to carry out its function
130
what is the primary structure of a protein determined by?
by a gene, if a mutation occurs in that gene it could change the tertiary structure of the enzyme produced
131
when does the rate of an enzyme-controlled reaction increase?
when the temperature's increased. more heat means more KE, so molecules move faster. this makes the enzymes more likely to collide with the substrate molecules. the energy of these collisions also increases which minas its more likely to result in a reaction
132
what happens to the enzyme when there's a rise in temperature?
- a rise makes the enzyme's molecules vibrate more
- if the temp goes above a certain level, this vibration breaks some of the bonds that hold the enzyme in shape
- the active site changes shape and the enzyme and substrate no longer fit together. the enzyme is denatured
133
what is the affect of pH on enzymes?
- all enzymes have an optimum pH in humans its 7 (neutral)
- above and below optimum pH, the H+ and OH- ions found in acids and alkalis can mess up the ionic and hydrogen bonds that hold the enzyme's tertiary structure in place. this makes the active site change shape, so it denatures
134
what happens when the enzyme concentration increases?
the more enzyme molecules there are in solution, the more likely a substrate molecule is to collide with one and form an enzyme-substrate complex, therefore increasing the rate if reaction
135
what happens if the amount of substrate is limited?
there comes a point when there's more than enough enzyme molecules to deal with all the available substrate, so adding more enzyme has no further effect
136
what does it mean if there are more substrate molecules?
the more there are means a collision between the substrate and enzyme is more likely and so more active sites will be used. this is only true up until a saturation point, after that there are so many substrate molecules that the enzymes have as much as they can and adding more makes no difference
137
when does substrate concentration decrease?
it decreases with time during a reaction (unless more substrate is added), so if no other variables are changed, the rate of reaction will decrease over time too. this makes the initial rate of reaction, the highest rate of reaction
138
Give two ways in which the properties of ATP make it a suitable source of energy in biological processes
- energy is released in small amounts
| - its soluble
139
ATP is an energy source used in many cell processes. Give two ways in which ATP is a suitable energy source for cells to use.
- releases a small amount of energy
| - can be rapidly re-synthesised
140
what are competitive inhibitors?
the molecules have a similar shape to that of the substrate molecules, they compete with the substrate molecules to bind to the active site; but no reaction takes place
- they block the active site, so no substrate molecules can fit in it
141
what does it mean if there's a high concentration of 1. inhibitor? and 2. substrate?
1 - the inhibitors will take up nearly all the active sites and hardly any of the substrate will get to the enzyme
2- a higher conc of substrates, means their chances of getting to an active site before the inhibitor increaser, so increasing the conc of substrates will increase the rate of reaction up to a point
142
what is a non-competitive inhibitor?
the molecules binds to the enzyme away from its active site, this causes the active site to change shape so the substrate molecules can no longer binds to it
- they don't compete with the substrate as they're a different shape. increasing the conc of substrate wont make a difference to the reaction rate as they enzyme activity will be inhibited
