Topic 1: Biological Molecules Flashcards
Packs 1, most of 4 and some of 5
1
Q
What does common biochemistry indicate about evolution? Why?
A
- Shows a common ancestry between living organisms
- All organisms derived from a common beginning
2
Q
What is a polymer?
A
A long chain of monomers joined together
3
Q
What is a monomer?
A
Small units from which large molecules (polymers) form
4
Q
Starch is a polymer, what is it’s monomer?
A
Alpha Glucose
5
Q
Glycogen is s polymer, what is it’s monomer?
A
Alpha Glucose
6
Q
Cellulose is a polymer, what is it’s monomer?
A
Beta Glucose
7
Q
Protein is a polymer, what is it’s monomer?
A
Amino Acids
8
Q
What are the monomers of polysaccharides?
A
Monosaccharides; Glucose, Fructose and Galactose
9
Q
What is covalent bonding?
A
Where atoms share electrons
10
Q
What is ionic bonding?
A
- Atoms with opposite charges are attracted to each other
- Weaker than covalent bonds
11
Q
What is Hydrogen bonding?
A
- Electrons are unevenly distributed causing slight differences in charges, a polar molecule
- Individually weak, collectively strong
12
Q
What is the name of a reaction where a water molecule is released?
A
A condensation reaction
13
Q
What is the name of a reaction where a water molecule is added?
A
Hydrolysis
14
Q
What is the molecular formula of Glucose?
A
C6 H12 O6
15
Q
What is the general molecular formula for a monosaccharide?
A
Cn H2n On
16
Q
What is the difference between alpha and beta glucose?
A
- The hydrogen and hydroxide arms on the right hand side are the other way round.
- a glucose has hydrogen at top and hydroxide on bottom at both ends.
17
Q
What is an isomer? Can you name an example?
A
- The same molecule but in a different arrangement/structure giving it different properties
- eg Alpha/Beta glucose
18
Q
What is the food test for reducing sugars? How do you do it?
A
- Use benedict’s test (benedict’s reagent is blue)
- Add 1cm^3 of solution to test tube, heat
- Colour change from blue-red, depends on Concentration.
19
Q
What is making a range of dilutions called?
A
A serial dilution
20
Q
What type of reaction is it when two monosacchrides join together?
A
A condensation reaction
21
Q
Maltose is a disacchride, what are it’s monosacchrides?
A
2 alpha glucose
22
Q
Sucrose is a disacchride, what are it’s monosacchrides?
A
Alpha glucose and fructose
23
Q
Lactose is a disacchride, what are it’s monosacchrides?
A
Alpha glucose and galactose
24
Q
Name 3 disacchrides
A
- Maltose
- Lactose
- Sucrose
25
What type of bond is formed when two monosacchrides join to make a disacchride?
A glycosidic bond
26
What is the main use of disacchrides in living organisms?
In respiration (called respiratory molecules)
27
What is the role of Glycogen?
Energy storage in animals, specifically liver/muscles
28
What is the role of Starch?
Energy storage in plants (seeds)
29
What is the role of Cellulose?
Gives strength to plant cell walls
30
Starch is insoluble. Why is this important?
- A storage molecule, being insoluble prevents excess water entering cells
- No osmotic effect or effect on water potential
31
Why is it important for starch to have a compact structure?
It can fit a lot into a small space
32
What property of starch makes it suitable for enzymes to work on?
It has multiple branches from chains (carbon 1-6 glycosidic bonds
33
What is the test for presence of starch?
- Use iodine in potassium iodide
| - Colour change from red->blue->Black
34
What is the structural difference between Starch and glycogen?
Glycogen has more 1-6 branches
35
What must happen to beta glucose in order to create cellulose?
The individual beta glucose molecules need to be flipped round between every one. (flip-flop)
36
How to some herbivores (eg cows) manage to digest cellulose?
- Cows have 4 stomachs
| - 1 stomach contains a bacteria which produces celluase to digest the cellulose
37
Name 5 Key features of Cellulose structure
1. B glucose linked by glycosidic bond 1:4 (flip/flop)
2. Hydrogen bonds form cross links + microfibrils
3. Provides strength to cells
4. Resists turgor/osmotic pressure
5. 1:4 bonds are difficult to break, resisting digestion
38
What are the 2 groups of lipids?
Triglyerides and phosopolipids
39
How are triglycerides formed?
The condensation reaction of one molecule of glycerol and three molecules of fatty acid
40
What is the general formula for a fatty acid?
HOOC - [CH2}n - CH3
41
What is the bond between a fatty acid and a glycerol called?
A ester bond
42
What is the functional group (at end of repeating hydrocarbon units) on a fatty acid called?
The carboxyl group
43
How does a saturated fat differ from an unsaturated fat?
Saturated fats have no double C=C bonds, unsaturated fats do
44
What is fat used for in biological organisms?
- Water proofing (waxy cuticle)
- Insulation
- Protection
45
What is the difference between a phospholipid and a triglyceride?
Phospholipids have a phosphate group instead of one of the 3 fatty acids in triglycerides
46
What cellular structure contains phospholipids?
Cell membranes
47
Which part of a phospholipid molecule is hydrophilic?
The phosphate group (head)
48
Which part of a phospholipid molecule is hydrophobic?
The fatty acid tails
49
True or false: Phospholipids are polar molecules.
True
50
What does hydrophilic mean?
Attracted to water
51
How would you test for NON-reducing sugars?
- Non reducing sugars are disacchrides
- Add dilute HCl, boil
- Neutralise with Sodium hydroxide
- Use benedicts test
52
What are the two polysacchrides of starch?
1. Amylose; Unbrached chain of a glucose, coiled, good for storage
2. Amylopectin; Branched, allowing for enzymes to break it down and release stored glucose for energy
53
Are triglycerides soluable in water?
No. They are insoluble because the tails are hydrophobic
54
Why are unsaturated fatty acids better insulation for organisms in cold climates?
The C=C double bond causes a kink in the fatty acid chain, irregular shape interrupts conduction
55
Why are triglycerides good storage molecules?
1. Long hydrocarbon tails stores chemical energy
2. Insoluble, causing no effect on water potential, so the cell is unaffected by osmotic effect
3. Low mass
4. Source of water (through hydrolysis)
56
How do you test for lipids?
- Use emulsion test
- Add alcohol, shake
- Add to water
- Milky emulsion/layer will form
57
What is the term used to describe all chemical processes that take place in living organisms?
Metabolism
58
What is a solvent?
A substance which dissolves a solute resulting in a solution.
59
What does a 'high heat capacity' mean? (with water)
- A large increase in temperature will result in a small rise in water temperature
- Water is good at maintaining a persistent temperature despite large fluctuations in the environment
- Buffers temperature changes within living organisms
60
What property of ice is beneficial to aquatic organisms?
When water freezes it becomes less dense, so it forms on the surface of ponds. Other liquids would build up at the bottom. Insulates from the cold.
61
What does cohesion mean?
How water molecules stick together
62
What is surface tension?
The connection (cohesion) of water molecules on the surface because they are more attracted to each other than the air.
63
Where do inorganic ions occur (biologically speaking)?
In the cytoplasm and body fluids of organisms
64
What does pH determine?
- The potential for hydrogen
- High concentration of hydrogen ions = low pH
- Low concentration of hydrogen ions = high pH
65
How many iron ions does one molecule of haemoglobin contain?
4
66
What inorganic ion associates itself with haemoglobin?
Iron ions (Fe2+)
67
How many O2 molecules can join onto a molecule of haemoglobin (with iron)
8
68
What is co-transport
- 2 substances simultaneously transported across a membrane by a protein, a symport
- Na/K pump helps for sodium and glucose to be co transported in epithelial cells of intestines
69
What is important about water cohesion for plants?
Water is cohesive, allowing it to flow up xylem in transpiration
70
What is ATP?
- Adenosine triphosphate
- A nucleotide base adenine, a ribose sugar and three phosphate groups
- An energy source for cells, made from glucose
71
How does ATP become ADP?
When one of the phosphate ions is hydrolysed, releasing a phosphate ion (Pi)
72
What are the monomers of proteins?
Amino Acids
73
Which 4 elements are always present in proteins?
Carbon, Hydrogen, Nitrogen + Oxygen
74
What is the Amine group of proteins?
NH2 on the left hand side
75
What is the Carboxyl group of proteins?
COOH on right hand side
76
What is the Variable group of proteins?
'R' group on the top (20 different types)
77
What is the primary structure of proteins?
The number and sequence of amino acids joined by peptides bonds.
78
What bond joins two amino acids? How is it formed?
A peptide bond formed by condensation reactions and broken by hydrolysis
79
What causes chains of amino acids to fold?
+ve and -ve charges of the R groups attract to opposite charges.
80
What are extra features of some R groups?
- Positive and negative charges
- Second carboxyl and anime groups
- Disuphide bond
- Hydrophobic/phillic
81
How can some properties of R groups of amino acids help separate them out?
- Chromatography can separate amino acids by size and polarity whist suspended within an organic solvent
82
How do you calculate the Retardation factor (Rf value)?
Distance moved by spot / distance moved by solvent
83
What is the secondary structure of proteins?
The folding of proteins due to H bonds forming between amino acids
84
What are the two different arrangements of secondary structures of proteins?
1. Alpha helix
- H bonds between each peptide link
- Strong, fibrous proteins
2. Beta pleating
- Sheets with H bonds, flexible
85
What is the tertiary structure of proteins?
- Further folded to form a 3D structure
| - Includes H, disulfide and ionic bonds
86
What are dislufide bonds (protein)?
Strong bonds which occur between sulphur atoms in R groups
87
What are ionic bonds (protein)?
- Form between carboxyl groups and amino groups not used in peptide bonds
- Easily broken by changes in pH
88
What are hydrogen bonds (protein)?
- Bonds between Hydrogen atoms in Amino acids and R groups
| - Weak alone but strong in numbers
89
Why is having Hydrophobic and hydrophillic side chains on amino acids useful?
- Hydrophillic sides will face outwards on cell membranes
- Hydrophobic sides face inside, away from water
- Helps to arrange proteins in the phospholipid bilayer
90
What is the quaternary structure of proteins?
Proteins with more than one polypeptide chain, sometimes includes a non-protein prosthetic group
eg Haemoglobin
91
What is a globular protein?
Tertiary structure is a round 3D shape and small and soluble. Eg enzymes
92
What are the 8 functions of proteins?
1. Anti bodies (immune response
2. Muscle proteins (contraction)
3. Enzymes (metabolism)
4. Structural proteins
5. Transport proteins (haemoglobin)
6. Protein synthesis (ribosome proteins)
7. Membrane proteins (receptor/transport proteins)
8. Hormones
93
What is the test for proteins? What would a positive result loom like?
The biuret test
- Add sodium hydroxide
- Add 1% copper sulfate
- Positive result = Purple
- Negative (no change = blue)
94
Is the biuret test quantitative?
No, it is qualitative because only positive/negative
95
What is anabolic metabolism?
Building up i.e. A+B -> AB
96
What is catabolic metabolism?
Breaking down AB -> A+B
97
What is meant by activation energy?
The energy needed for a reaction to start/proceed
98
What is an enzyme
An organic catalyst which speeds up the rate of a reaction whilst remaining unchanged
99
How does an enzyme-substrate complex (ESC) form?
Enzyme (E) combines with the reactant (Substrate S)
100
Why do reactions occur faster with enzymes?
The activation energy is less than the alternative without the enzyme
101
What was the old theory for enzyme action?
The lock and key theory
102
What kind of protein structure are enzymes?
A tertiary structure with ionic, disulfide and hydrogen bonds
103
Enzyme active sites and the substrates are said to have a ? shape
A complementary shape
104
What was wrong with the old lock and key model for enzyme action?
Lock and key did not explain how other molecules (inhibitors) could fit to other parts of enzymes
105
What is the induced fit model for enzyme action?
- Substrates combine with enzymes
- Active site of enzyme changes shape slightly
- Strain exerted on substrate, distorting bonds and lowing the activation energy needed
106
What is meant by "turn over number"?
The number of substrate molecules converted into products each minute. Enzymes work VERY quickly
107
Name 4 key properties of enzymes.
1. Work very quickly
2. Unchanged by reactions
3. Work in both directions (depending on conc)
4. Specific to substrates
108
What factors affect enzymes?
- Temperature
- pH
- Substrate concentration
- Enzyme concentration
- Inhibitors
109
What is the rate of reaction for all enzymes at 0 degrees C? Why is this?
- The rate is 0
| - There are no collisions between enzymes and substrates because there is no kinetic energy
110
What happens to the rate of enzyme action as temperature increases (UP TO OPTIMUM)? Why?
- Rate increases as temperature increases
- Due to more kinetic energy
- Substrates move more and collide with enzymes more regularly
- Reduces activation energy
- More ESCs
111
What happens to the rate of enzyme action as temperature increases (BEYOND OPTIMUM)? Why?
- H and ionic bonds within the tertiary structure break due to too much heat and thus kinetic energy
- Tertiary structure is lost
- Enzyme denatures, active site changes shape and less ESCs form
- Disulfide bond do not break
112
What happens once the tertiary structure of an enzyme is lost?
It is permanently damaged and stops working indefinitely
113
What similarities and differences are there regarding "effect of pH on enzyme rate" graphs for different pHs?
- The graph shape is always the same for all enzymes
| - The optimum pH varies depending on enzymes
114
What is the effect of a low pH on enzymes?
- At low pH lots of H+ ions present
- Ionic and H bonds break
- Enzyme denatures because the tertiary structure is lost and the active site changes shape
- Less ESCs form
115
What is the effect of a high pH on enzymes?
- Many OH- ions present
- Ionic and H bonds break
- Enzyme denatures because the tertiary structure is lost and the active site changes shape
- Less ESCs form
116
As substrate concentration increases and enzymes concentration is constant, what is the limiting factor?
- Initially the substrate concentration
| - Once substrate concentration exceeds enzyme concentration, enzymes concentration becomes the limiting factor
117
Name the 2 types of inhibitor to enzymes.
Competitive and non-competitive inhibitors
118
What do competitive inhibitors do?
Compete with the substrate for the enzymes active site, temporarily inhibiting enzymes action
119
Name 4 key features of competitive inhibitors.
1. Substrate and inhibitors have SIMILAR SHAPES
2. COMPLEMENTARY to shape of enzyme active site
3. If inhibitor goes into active site the substrate is unable to bind
4. No ESCs are made
120
True or false; Competitive inhibitors have the same shape as substrates
FALSE
| They have a SIMILAR shape
121
What happens to the amount of competitive inhibition when you add more substrate?
Less competitive inhibition
122
Do non-competitive inhibitors have a similar shape to substrates.
No, non-competitive inhibitors bind to receptor sites elsewhere on the enzyme
123
How do non-competitive inhibitors inhibit enzymes?
- Bind to receptor sites on enzymes
- Changes shape of enzyme
- Substrates cannot bind to active sites
- No longer complementary
- No ESCs form
124
What do cells need to do in order to efficiently regulate metabolism?
Needs to inhibit reactions
125
How do cells effectively inhibit reactions
With metabolic reactions/pathways and inhibition
126
Which organelle makes enzymes?
Ribosomes - enzymes are proteins
127
Where to intracellular enzymes act?
Inside cells
128
Where to extracellular enzymes act?
Outside cells
129
What is digestion?
- The chemical digestion and physical breakdown of foods
| - Large molecules are hydrolysed by enzymes to produce smaller molecules to be absorbed and assimilated
130
Why do enzymes only catalyse one reaction?
Because only one complementary substrate will fit into the active site
131
Does increasing the concentration of substrates reduce competitive inhibition?
Yes. There is a higher chance that the substrates will get to active site + form ECS before the inhibitor
132
Does increasing the concentration of substrates reduce NON-competitive inhibition?
No. The tertiary structure is changed, enzyme changes shape so no enzymes will bind to active site and form ESCs
133
What are two methods of measuring the rate of an enzyme controlled reaction?
1. Measure how fast the product is made
| 2. Measure how fast the substrate is broken down
134
How can you calculate the rate of reaction from a graph?
By drawing tangent then dy/dx
135
What is the genereic structure of all nucleotides?
- A phosphate group
- A pentose sugar (5 Carbon atoms)
- Nitrogen - containing organ base
136
What are the four bases found in DNA?
Adenine, THYMINE (DNA only), Guanine and Cytosine
137
What are the four bases found in RNA?
URACIL (RNA only), Adenine, Guanine and Cytosine
138
How do the three components of DNA join up?
By condensation reactions
139
Where does the phosphate group and the nitrogenous base join the pentose sugar?
Phosphate group to C4
| Base to C1
140
How does a phosphodiester bond form?
Two mononucleotides join together by a condensation reaction from C3 to the phosphate group
141
What is a long chain of nucleotides called?
A polynucleotide
142
What did scientists use to believe stored hereditary material (before DNA)? Why?
They used to believe that proteins stored genetic material because they are very diverse (20 amnino acids compared to 4 nucleotides)
143
Who worked out the structure of DNA?
Franklin, Watson and Crick
144
What is the pentose sugar in DNA?
Deoxyribose
145
What is meant by double stranded DNA?
DNA (always) has two polynucleotide stands
146
How are the two stands of DNA held together?
Hydrogen bonds between complementary base pairs
147
How many hydrogen bonds are there between Adenine and Thymine?
2
148
How many hydrogen bonds are there between Cytosine and guanine?
3
149
Why are the strands in DNA said to be 'anti-parallel'?
The nucleotide stands run in opposite directions to each other
150
Why is the sugar-phosphate backbone important for DNA?
- Stability and strength
| - Backbone protects bases on inside form chemical/physical damage
151
DNA is a stable molecule. Why is this important?
- Does not change
| - Info can be passed on accurately
152
Why is the double helix of DNA useful?
Compact
153
Why is the base sequence important?
Codes for polypeptides (unique codes)
154
By what method does DNA replicate?
Semi-conservatively
155
Why is complementary DNA base paring important?
Ensures accurate replication takes place
156
Why does DNA have weak hydrogen bonds between complementary base pairs?
Allows for the 2 strands to be separated easily by DNA helicase (Enzyme)
157
What were the two theories behind DNA replication?
Conservative and semi-conservative replication
158
What was involved in conservative DNA replication?
The old strand of DNA did not 'unzip' but instead was retained along with a new strand
159
Who conducted an experiment to prove that DNA replicated semi-conservatively?
Meselsohn and Stahl
160
What was done to prove that DNA replicated semi-conservatively?
- E. coli fed on two isotopes of nitrogen (14N and 15N)
- 'Heavy' DNA built up at bottom
- Repeated for next generations in 14N only, 'heavy' DNA drained out by semi-conservative replication
161
What enzyme breaks the hydrogen bonds between bases in DNA?
DNA Helicase
162
What enzyme joins 2 new nucleotides together after replication?
DNA Polymerase
163
What does the enzyme DNA helicase do?
Unzips the double helix, breaks hydrogen bonds between the base pairs
164
How do new nucleotides join unzipped DNA in replication?
- Unzipped DNA strands act as templates
| - Free nucleotides attracted to exposed base pairs
165
What happens once the free nucleotides become attracted to exposed base pairs in DNA replication?
Hydrogen bonds form between the complementary base pairs
166
What enzyme joins new nucleotides in the last stage of DNA replication?
DNA polymerase
167
Which base of DNA pairs with thymine?
Adenine
168
Which base of DNA pairs with cytosine?
Guanine
169
What type of reaction joins two nucleotides with DNA polymerase?
A condensation reation
170
What bond joins two nucleotides in a strand?
Phosphodiester bonds
171
Is RNA double stranded?
No. It is a single polynucleotide
172
What is the sugar in RNA?
Ribose
173
What base does RNA have instead of Thymine?
Uracil
174
What are the 3 main types of RNA?
Messenger (mRNA)
Ribosomal (rRNA)
Transfer (tRNA)
175
What is the role of messenger RNA (mRNA)?
Transfers info from DNA to ribosomes
176
What is the role of ribosomal RNA (rRNA)?
Associated with proteins, rRNA makes up ribosomes
177
What is the role of transfer RNA (tRNA)?
Carries specific amino acids to ribosmomes during protein synthesis
178
Is DNA a 'long molecule'?
Yes, much longer than RNA
179
Does RNA have hydrogen bonds like DNA?
Sometimes. tRNA has hydrogen bonds in loops of the SINGLE STRAND
180
What is the role of DNA?
- Codes for polypeptides
| - Holds genetic info
181
What is the initial source of energy for all living organisms?
The sun
182
What is the word equation for photosynthesis?
Carbon dioxide + water -> Glucose + oxygen
183
How is ATP made?
Glucose is oxidised to make adenosine triphosphate
184
What are the 3 parts of ATP?
- Adinine
- Ribose sugar
- 3 phosphate groups
185
Why does ATP have a low activation energy?
3 phosphate groups have unstable bonds between them, easily broken
186
How is one of the phosphate groups in ATP removed?
Water is added (hydrolysis) and enzyme ATP hydrolase
187
What enzyme is involved in forming ATP from ADP?
ATP synthase (water also added, condensation reaction)
188
Under what circumstances is ATP synthesized (made from ADP + Pi)?
1. Photosynthesis (in chlorophyll)
| 2. During respiration
189
What is the process called whereby ATP is synthesized in photosynthesis?
Photophosphorylation
190
Why can't ATP be stored?
Because of instability of the phosphate bonds
191
ATP cannot be used as a long-term energy source - so what can?
Fats and carbohydrates
192
Why is ATP often useful in Cells?
Provides an immediate energy source
193
Is ATP soluble?
Yes. In cytoplasm
194
Does ATP leave cells?
NO. Stays within the cell it was made
195
Why is ATP better than glucose as an immediate energy source?
- Glucose is difficult to break down -takes time
| - Less energy is released by hydrolyzing ATP, but more manageable and instant
196
For what processes is ATP used for within cells?
- metabolic processes
- Movement
- Active transport
- Secretion
- Activation of molecules
197
How is ATP used in metabolic processes?
Builds molecules from small molecules
| eg Proteins, DNA, glycogen and starch
198
How is ATP used in movement?
Muscle contraction
199
How is ATP used in active transport?
Changes the shape of carrier proteins so that molecules or ions can move against the concentration gradient
200
How is ATP used in secretion?
Formation of lysosomes/vesicles for exocytosis
201
How is ATP used in activation molecules?
Pi released from APT can be hydrolyzed to make other compounds more reactive, lowering activation energy
202
What is translation?
When RNA is read in Ribosomes to make polypeptides (proteins)
203
What is a phosphodiester bond?
- A bond joining 2 nucleotides
| - Contains 2 ester bonds and the phosphate group
