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Raffles Institution Raffles Programme
Secondary Three Raffles Academy Biology
Unit 3: Chemicals of Life
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) Date: _______
Worksheet 1: Introduction to Biochemistry & Amino Acids
Exercise 1
4. 4
Exercise 2
4. –NH3+
5. No, molecular formula shown.
6. O
7. Yes, structural formula shown
8. The components of organic molecules that are most commonly involved in chemical
reactions. 6
10. phenylalanine, glycine, aspartic acid
11. 14
12. a. enzymes (catalyse chemical reactions); b. transport; c. structural, e.g. collagen
15. C H N O
16. a. molecules that are mirror images of each other
b. carbon bonded to four different groups
c. different enantiomers have different biological effects
d. 2n , n = number of asymmetric carbons
Review Questions
1. Amino acids/proteins
2. Amino acids
3. 20
4. A large number, order and number can vary
Worksheet 2: Proteins
Exercise 1
1. Ionized/dissociated, exist as zwitterions
2. Campbell: non-polar, polar, electrically charged
Biomodel: non-polar aliphatic; polar uncharged, aromatic, basic, acidic
Differentiate between aliphatic (open carbon chains) and aromatic (benzene rings);
acidic and basic
3. Depends on side chain
4. High electronegativity of O or N attached covalently to H
5. Central carbon atom in amino acid/first carbon after carbon attached to functional
group; no, e.g. glycine
6. Peptide bond; amino and carboxyl groups
7. Monomer = molecules that can combine to give polymer; dimer = molecule
consisting of 2 monomers joined together
1
8. Condensation/dehydration synthesis, covalent bond formed with loss of 1 molecule
of water
9. Hydrolysis, break covalent bond with addition of 1 molecule of water
10. Dipeptide = two amino acids bonded together by peptide bond; oligopeptide = a few
(3-40) amino acids bonded together by peptide bonds; peptone = water soluble
compounds formed by partial hydrolysis of proteins; polypeptide = string of amino
acids; protein = 1 or more polypeptides folded together/macromolecule that is the
end product of transcription and translation
11. No, N-terminus and C-terminus, protein synthesis move from N to C direction
12. Sticks out, interact to give conformation
13. Bonds between parts of chain; determines its function (emergent property)
14. Describe complex architecture (superimposed levels)
15. Sequence of amino acids, may change interactions, e.g. sickle cell anemia
16. E.g. α-helix and β-pleated sheet, structure formed due to hydrogen bonds between
atoms of backbone (not side chain); ribbons/arrows
17. Irregular contortions; due to interactions between side chains of amino acids
(hydrogen bonds, disulphide bonds, ionic bonds, hydrophilic interactions, van der
Waal’s interactions)
18. Aggregation of polypeptide subunits
19. Loss of native conformation, biologically inactive
Exercise 2
Comparison
Found in
HIV Protease
HIV
Collagen
Connective tissue, skin
tendon, internal organs, bone
Function
Cuts pre-protein synthesised by
human host into pieces which
assemble to make new HIV
Provides structure, protection
and support; holds us
together, strong and flexible,
provides flexible strength,
underlying structure for
bones and teeth
Structure
Small, dimer of 2 identical
polypeptides (each 99 amino
acids long); assemble to form
long tunnel covered by two
flexible flaps, active site in centre
3 strands of polypeptides
twisted together to form
tropocollagen (~1400 amino
acids long), right-handed
triple helix, repeated proline,
hydroxyproline and glycine
(glycine in centre occupy
minimum space as only
glycine small enough to
pack); Pro and Hpr form
hydrogen bonds; 5
tropocollagen molecules
twisted to form fibre
2
Medical
significance (or how
does understanding
of the structure help
mankind?)
Design HIV protease inhibitor
(e.g. ritonivir) added together with
2 anti-HIV drugs; difficult for HIV
to develop resistance
Rare genetic diseases and
scurvy (vitamin C deficiency)
due to defects in collagen;
need oxygen and vitamin C
to produce hydroxyproline
from proline
Worksheet 3 Lipids
Exercise 1
4. 3: palmitic, oleic, stearic acid
5. 2 (palmitic and stearic); 1 (oleic)
7. saturated – molecule straight, unsaturated – molecule kinked; prevents molecules
from packing together
8. geometric isomers
9. polyunsaturated – many double bonds; monounsaturated – 1 double bond; 2 families
of essential fatty acids (EFAs) with double bond in ω3 and ω6 positions,
respectively; ω3 in fish oils (e.g. α-linolenic acid/ALA 18C, eicosapentaenic
acid/EPA 20C, docosahexaenoic acid/DHA 22C); ω6 in vegetable oils (e.g.
linoleic acid, arachidonic acid)
10. convert liquid oil into solid, prevent rapid rancidity; produces trans fat, artificial,
cannot be metabolized, linked with cancer, diabetes, heart disease, low birth
rate, obesity
Exercise 2
2. fat – solid at room temperature; oil – liquid at RT; triglyceride = triacylglycerol =
glycerol + 3 fatty acids
3. ester bond; COOH and OH; condensation
5. non-polar; consists of non-polar C-H bonds in hydrocarbon chain of the fatty acids
6. insoluble because non-polar, water molecules hydrogen bond to each other and
exclude the fats
Exercise 3
1. Triglyceride = glycerol + 3 fatty acids; phospholipid = glycerol + 2 fatty acids + 1
phosphate/choline
2. Hydrophilic = substance with affinity for water; hydrophobic = substance without
affinity for water
3. Form major components of all membranes
Exercise 4
3. point to double bond
5. 3
6. point at OH group; wedged between phospholipid molecules, reduces membrane
fluidity at moderate temperature by reducing phospholipid movement; hinders
solidification at low temperatures by disrupting regular packing of phospholipids
3
Worksheet 4 Carbohydrates
Exercise 1
2. yes
5. yes, -OH, C=O due to difference of electronegativity between O and H/C
6. C H O
8. a. both have carbonyl group, aldoses have aldehyde group, ketoses have ketone
group
b. pyranose = 6-membered ring; furanose = 5-membered ring
c. triose – 3C, pentose – 5 C, hexose – 6 C
9. structural isomers
10. enantiomers
11. anomeric carbon = new asymmetric carbon formed by formation of ring structure
a. α-glucose has OH group attached to anomeric carbon (C1) pointed down from
plane of ring; β-glucose has OH group pointed up from plane of ring
b. position of OH on asymmetric carbon farthest from aldehyde/ketone groups
different
12. most commonly D sugars and L amino acids
15. condensation/dehydration synthesis, glycosidic bond
16. glucose + galactose
17. α(14) = glycosidic bond between α-anomeric C1 carbon of 1 glucose with C4 of
second glucose
Α(12) = glycosidic bond between α-anomeric C1 carbon of glucose with C2 of
fructose
18. reducing sugars = sugars with aldehyde groups that can be oxidized to carboxylic
acid groups, and reducing e.g. Cu2+ to Cu+
a. Both reducing, fructose is ketose but ketone group can isomerise to aldehyde
group (tautomeric)
b. Maltose reducing with free aldehyde group; sucrose non-reducing because
aldehyde group used in glycosidic bond formation
Exercise 2
1. Oligosaccharides = few monosaccharides joined together; polysaccharides = many
monosaccharides joined together
2. Small changes in structure result in large difference in function (emergent properties)
3.
Polysaccharide Monomer Type of
Relate structure to property and
glycosidic bond function
Starch α-glucose α(14)
Helical, unbranched, compact
Amylose
Starch –
α-glucose α(14)
Helical, branched, packed into
Amylopectin
α(16) at
granules
branches
Glycogen
α-glucose α(14)
More extensively branched,
α(16) at
dense clusters of granules
more branches
Cellulose
β-glucose β(14)
Straight, unbranched, hydroxyl
4
group free to form hydrogen
bonds with other cellulose
molecules lying parallel forming
microfibrils
Worksheet 5 Cytology/Cell Biology
Cell
ultrastructure /
organelle
Rough
endoplasmic
reticulum
Smooth
endoplasmic
reticulum
Golgi body
Structure
Function
Role of biochemicals
in relation to function
Network of membranous
sacs and tubes studded
with ribosomes,
membrane separates
lumen from cytosol,
continuous with nuclear
envelope
Network of membranous
sacs and tubes not
studded with ribosomes,
membrane separates
lumen from cytosol,
continuous with nuclear
envelope
Stacks of flattened
membranous sacs; has
polarity (cis and trans
faces)
Aids in synthesis of
secretory and other
proteins from bound
ribosomes; adds
carbohydrates to
glycoproteins, produces
new membranes
Synthesis of lipids,
metabolism of
carbohydrates, Ca2+
storage, detoxification of
drugs and poisons
Phospholipids form
membranes
compartmentalizing
protein synthesis for
export out of cell.
Modifications of proteins,
adds carbohydrates on
proteins and
phospholipids; synthesis
of many polysaccharides;
sorting of Golgi products,
which are then released
in vesicles
Cellular respiration
Phospholipids form
membranes which
compartmentalizes
metabolic reactions
and forms vesicles
which contain
metabolites
Mitochondria
Bounded by double
membrane; inner
membrane has infoldings
(cristae)
Ribosomes
Two subunits made of
ribosomal RNA and
proteins; can be free in
cytosol or bound to ER
Typically two membranes
around fluid stroma, which
contains membranous
Chloroplasts
Protein synthesis
Photosynthesis
5
Phospohlipids form
membranes
compartmentalizing
lipid synthesis from
cytosol
Phospholipids form
membranes for
compartmentalizing
respiratory metabolic
reactions, as well as
barrier for ATPase to
work
RNA folded into
conformation to carry
out translation
Phospholipids
compartmentise
organelle separating
thylakoids stacked into
grana
Cell surface
membrane
Phospholipid bilayer with
Form external barrier of
cholesterol molecules;
cell; control entry and exit
integral proteins and
of materials
peripheral proteins within
bilayer; carbohydrate side
chains project from protein
or lipid molecules
Nuclear
envelope
Double membrane with
associated proteins,
surrounding nucleus,
continuous with ER
Centrioles
A pair of nine sets of triplet Found in centrosomes
microtubules arranged in
which serves as a
ring
microtubule-organising
centre, with a role in
spindle formation in cell
division
Nucleus
DNA organized as
chromosomes/chromatin
Carry genes
Nucleolus
Mass of densely stained
granules and fibres
Site where rRNA is
synthesised and where
proteins imported from
cytoplasm is assembled
into ribosomes
Separates chromosomes
and nuclear enzymes
from cytosol
6
light and dark
reaction, holds
photosystem
molecules in place
Phospholipid form
barrier, cholesterol
determine fluidity of
membrane, proteins
serve as transport,
receptor or carrier
molecules,
carbohydrates for cell
signaling or
recognition
Phospholipids
separate
chromosomes from
cytosol;
compartmentalizes
DNA and RNA
synthesis from rest of
cell; proteins form
pore complex which
regulates entry and
exit of proteins and
RNA
Microtubules formed
from globular protein
tubulin (dimer of α and
β-tubulin), assembled
and disassembled to
shape and support
cell, serve as tracks
for motor proteins to
move.
DNA contain
hereditary information
to direct protein
synthesis through
transcription
DNA serve as
template for
transcription of rRNA