Chapter 2: Biological molecules Flashcards
1
Q
what are the two types of chemical compounds
A
inorganic compounds and organic compounds
2
Q
what are inorganic compounds
A
- from rocks and mineral deposits
- e.g. Na+, K+, Mg2+
3
Q
what are organic compounds
A
- formed by organisms
- C is the basic element
- C, H, O, N, P, S
- C atoms join by covalent bond to form chains or rings
- chains and rings as the C-skeleton of organic molecules
4
Q
what are monomers
A
- relatively simple molecule
- used as a basic building block for the synthesis of a polymer
- n(monomer) joins up polymer usually by condensation reactions (H2O will come out)
5
Q
what are polymers
A
- a giant molecule
- made from many similar repeating subunits (monomers)
- joined together in a chain
- macromolecule = a very large biological molecule such as polysaccharide, protein,nucleic acid
6
Q
what is the basic unit/monomer of carbohydrate
A
monosaccharide
7
Q
whatis the linkage of carbohydrates
A
glycosidic bond
8
Q
what is the macromolecule of carbohydrate
A
polysaccharide
9
Q
what is the basic unit/monomer of lipids
A
fatty acids and glycerol
10
Q
what is the linkage of lipids
A
ester bond
11
Q
what is the macromolecule/polymer of lipids
A
lipids do not reach this level
12
Q
what is the basic unit (monomer) of proteins
A
amino acids
13
Q
what is the linkage of proteins
A
peptide bonds
14
Q
what is the macromolecule/polymer of proteins
A
polypeptides
15
Q
what is the basic unit (monomer) of nucleic acid
A
nucleotide
16
Q
what is the linkage of nucleic acid
A
phosphodiester bond
17
Q
what is the macromolecule (polymer) of nucleotides
A
nucleic acids (DNA, RNA)
18
Q
what are carbohydrates
A
- made of C, H, O where H:O ratio 2:1, same as H20
- general formula= Cx(H2O) y
- hydrate of carbon
- two forms:sugar and polysaccharide
19
Q
what are sugars
A
- in mono and disaccharide form
- sweet and soluble
- triose (made of 3 carbons)
- tetrose (made of 4carbons)
- pentose (made of 5 carbons)
- hexose (made of 6 carbons)
20
Q
what are polysaccharides
A
- not sweet, insoluble
- e.g. starch, glycogen, cellulose
21
Q
what is the structure of a glucose molecule
A
- made up of 6 carbon atoms
- each carbon (C2 to C6) has a -H and -OH attached to it
- C1 is part of the functional group (carbonyl group)
- the carbon atom is numbered starting from #1 for the ‘C’carbon nearest to the functional group
- form2 rings : alpha and beta
22
Q
what is a functional group
A
a specific group of atoms within an organic molecule that gives the molecule its specific property
23
Q
what are the two forms that starch exist in
A
- amylose
- amylopectin
24
Q
what is the structure of amylose molecule
A
- unbranched
- glucose residues linked by a-1,4-glycosidic bond
- amylose chains coil up in 3D form as the glycosidic bonds are not straight/180 deg to each other
25
what is the structure of amylopectin molecule
- branched (branches to main chain glycogen)
- in the main chain, residues are linked by a-1,4-glycosidic bond
- in the branch chain (at the branching point between the branch chain and the main chain) they are linked by a-1,6-glycosidic bond
26
what are glucose residues
once glucose monomers are attached to form a polymer, its calleda glucose residue
27
what are the properties/characteristics of glycogen
- similar to amylopectin but its highly branched
- the chains and branches can fold into compact form (takes up less space)
- glycogen molecules clump together to form granules (liver and muscle cells)
28
what is the function of starch and glycogen
- food and energy storage compound
- starch in plants and seeds
- glycogen in animals and many fungi
29
why is starch and glycogen used for food and energy storage
- they are insoluble in water (prevents lysis by osmosis)
- does not easily react with water soluble compounds in the cell, while glucose is a reactive molecule
- compact and occupies less space
- easily converted back to glucose when needed (7 terminal glucose residues can be removed at a time, one per branch)
30
what is the terminal glucose residue
the last glucose in a chain (1st to be removed) is called the terminal glucose residue
31
what is the structure of cellulose molecules
- made up of Beta glucose subunits
- one beta molecule needs to be rotated 180 deg for the OH groups to line up alongside to form a glycosidic bond
- B-1,4-glycosidic bond
- 10000 glucose residues per chain
- unbranched chain, can stack up parallel to each other bound by intramolecular and intermolecular hydrogen bonds
32
what are the properties/characteristics of cellulose?
- the most abundant organic molecule because presence in cell wall
- has a slow breakdown rate
- has a high tensile strength = difficult to break by pulling on each end
33
what is delta charge of atoms
slightly charged (+/-) attraction due to uneven electron distribution
34
what are hydrogen bonds
-a relatively weak bond, formed between the delta +H of with any one of the three types of delta - atoms -O, -N, -F
35
what is a dipole?
-the unequal sharing of electrons/distribution of charge between two atoms in a molecule is called a dipole
36
what are the properties o polar molecules
-molecules with dipole are polar
-polar molecules are hydrophillic (water loving) because they attract H2O
molecules to form hydrogen bonds with them
37
why do cellulose fibres have high tensile strength
- because glucose molecules have many intermolecular and intramolecular hydrogen bonds due to the many -OH groups and 1 -O-
- because of the building up/structure of cellulose fibres (specify)
38
what is the building up/structure of cellulose fibres
60-70 cellulose molecules-> join to form microfibril-> join to form cellulose fibre-> join to form cell wall
39
why is the cell wall strong
cellulose fibres are arranged in different orientation in primary wall and secondary wall layers
-this gives the cell wall its rigid property that contributes to its function
40
what are the properties/characteristics of lipids
- a diverse class of organic compounds
- insoluble in H2O but soluble in organic solvents (e.g. chloroform,acetone, ether)
- consists of C, H, O where the ratio of H:O is never 2:1 (never has water molecule)
- includes tryglycerides, phospholipids, steroids etc.
41
what are tryglycerides
- a type of lipid formed when 3 fatty acids combine with a glycerol with an ester bond (-COO-)
- it is produced by a condensation reaction, releasing 3H20 in the process
42
what are fatty acids made up of
fatty acids = acid head +hydrocarbon tail
43
what are the acid heads that fatty acids are made up of
- (-COOH)
- carbonyl group
- acidic group
- hydrophillic
44
what are the hydrocarbon tails fatty acids are made up of
- formula CnH2n+1 (represented by letter 'r')
- fatty acid tail
- variable in length (number of C) but usually 15-17C atoms
- if more than 4C atoms, the tail is hydrophobic
- can be saturated (singlebonds) or unsaturated (double bonds) (see diagram)
45
what is the difference in structure (chains) between saturated fat and unsaturated fat
- saturated fats are straight chains
| - unsaturated fats have a kink/backwards twist at each double bond
46
what are the two types of double bonds
-cis form (hydrogen atom on same side of chain)
-trans form (hydrogen atoms on opposite sides of chain)
(see diagram)
47
what are the properties/characteristics of saturated fatty acid chains
- straight chains
| - highly ordered parallel packing
48
what are the properties/characteristics of unsaturated ftty acid chains
- are between saturated fatty acid chains
- double bonds disrupt the close packing of fatty acids
- this is because of the kinks
49
what are the properties/characteristics of tryglycerides
- come in two forms: oils and fats
- both are non polar (water insouble)
- both float in water as they are less dense than the water
- rich energy source
- lighter storage compound than carbohydrates and proteins for the same amount of energy released on oxidation
50
what is the difference between the two forms of tryglyceride
Oils:
- liquid at rtp
- more unsaturated bonds
- lower melting point
Fats:
- solid at rtp
- more saturated bonds
- higher melting point
51
why are tryglycerides a rich energy source
- higher calorific value than carbohydrates and CHONs (proteins)
- energy of lipids is 2x the energy of carbohydrates per unit mass
- this is because of more C-H bonds/more H:O ratio in the lipids
- -H can be further oxidised to release energy
52
what are the functions of tryglycerides in plants
- energy storage compounds
- found in seed, fruits and chloroplasts (as lipid droplets)
- e.g. olive oil, peanut oil, corn oil
53
where are tryglycerides found in animals
- found in adipose tissue
- made of fat cells
- cels are filled up until nucleus is pushed to the side against the cell membrane
54
what are the functions of tryglycerides in animals
- energy storage for hibernation
- thermal and electrical insulation
- blubber
- H2O source
- protection of internal organs
55
what is the function of blubber
help sea mammals to float (buoyancy)and provide thermal insulation
56
how does H2O source help animals
fat stored in desert kangaroo rat and humps of camel an be oxidised in respiration to form H2O
57
what is the benedict's test
the test for reducing sugars (eg. glucose, maltose, fructose)
58
why/how does benedicts solution indicate the presence of reducing sugars
the functional group Aldehyde (RCOH) can reduce Cu2+ to Cu+
59
what is the procedure of the benedict's test
1. solution starts out blue as sample is added
2. volume of sample must be equal to volume of benedicts solution
3. heated in a water bath, water level just above solution level (submerged)
4. heat for 2-5 mins, make sure water bath is boiling before placing test tube in
60
what color and opacity solutions may benedict's test produce
- green opaque
- orange opaque
- brick red opaque
61
why doesnt benedicts test work for non reducing sugars (i.e. sucrose)
- functional groups of both glucose residue and fructose residue are attached to each other by glycosidic bond (A-1,2-glycosidic bond)
- cannot reduce Cu2+ to Cu+
- must hydrolyse first
62
what is protection (provided by tryglycerides) in animals
fats around internal organs protect them from damage caused by impact
63
what are phospholipids
- lipid containing a phosphate group
| - main molecule that forms plasma membrane
64
what do phospholipids consist of
glycerol and phosphoric acid (fatty acid tails)
65
how are phospholipids formed
glycerol joins up with fatty acid tails via condensation (remove H2O)
66
which part of the phospholipid molecule is polar/hydrophillic
phosphate head
67
which part of the phospholipid molecule is nonpolar/hydrophobic
the fatty acid tails
68
which part of the phospholipid molecule is the ester bon
O-C=O
69
which part of the phospholipid molecule is the phosphoester bond
O-P=O
70
what are amino acids
- the monomer for protein
| - there are 20 different types of amino acids
71
what determines a protein's shape and function
The sequence, type and number of the amino acids within a protein determines its shape and therefore its function
72
what are the functions of proteins
```
Enzymes
Cell membrane proteins (eg. carrier)
Hormones
Immunoproteins (eg. immunoglobulins)
Transport proteins (eg. haemoglobin)
Structural proteins (eg. keratin, collagen)
Contractile proteins (eg. myosin)
```
73
what is the general structure of all amino acids
The general structure of all amino acids is a central carbon atom bonded to:
An amine group -NH2
A carboxylic acid group -COOH
A hydrogen atom
An R group (which is how each amino acid differs and why amino acid properties differ e.g. whether they are acidic or basic or whether they are polar or non-polar)
74
what is a zwitterion (properties)
- electrically neutral
- but carries + and - charges on different atoms
- dipolar and soluble in water
75
how is a zwitterion formed
- acid (+H^+) is added to amino acid so H2N forms H3N^+
| - base (-OH) is added to amino acid so (-COOH +OH- -> -COO^- + H2O)
76
what can amino acids be
- a buffer
| - an ion
77
what is a buffer
a solution that resists the change of pH upon the addition of small amounts of acid or base, upon dilution
78
what are R groups
- variable groups
- determines the identity of an amino acid
- has 4 major groups
79
what are the 4 major R groups
- neutral and nonpolar (hydrophobic)
- neutral and polar (hydrophillic) (not charged but unequal distribution of charge)
- basic/can be charged (hydrophillic)
- acidic/can be charged (hydrophillic)
80
which neutral and nonpolar r group molecule is the smallest r group
Glycine (one H)
| -short form Gly
81
which neutral nonpolar r group molecule has SH
cysteine
| short form Cys
82
what is the base of the basic positive r group molecules
NH
83
what is the base of the acidic negative charge r group molecules
COOH (H released)
84
how is a peptide bond formed
In order to form a peptide bond a hydroxyl (-OH) is lost from a carboxylic group of one amino acid and a hydrogen atom is lost from an amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid
This is a condensation reaction so water is released. The resulting molecule is a dipeptide
85
what is a polypeptide
When many amino acids are bonded together by peptide bonds the molecule formed is called a polypeptide. A protein may have only one polypeptide chain or it may have multiple chains interacting with each other
86
what is hydrolysis of polypeptides
During hydrolysis reactions polypeptides are broken down to amino acids when the addition of water breaks the peptide bonds
87
which part of a dipeptide/polypeptide is a peptide bond
H-N-C=O
88
what is a n terminus/n terminal
the NH end of a polpeptide chain
89
what is the C terminus/C terminal
the C=O end of a polypeptide chain
90
how many amino acid residues can a polypeptide have
100-1000 amino acid residues
91
how many polypeptide chains make up a protein
1 or more polypeptide chains can make up 1 protein
92
what does conformation mean
a 3D structure or shape
93
what are the 4 levels of protein structure
- primary
- secondary
- tertiary
- quaternary
94
what is the primary structure of a protein
the sequence of amino acids from the N terminal to the C terminal in a polypeptide chain
95
what is the secondary structure of a protein
the spatial arrangement of a polypeptide chain due to its regular coiling (a-helix) or regular folding (b-pleated sheet)
96
what are the 2 types of secondary protein structures
alpha helix and beta pleated sheet
97
how is a alpha helix formed
- the electronegative O of the carbonyl group (C=O group) of each amino acid residue forms a hydrogen bond with the electropositive H of the amino group (-NH group) located 4 amino acid residues ahead in the linear sequence
- both C=O group and -NH group are part of peptide bond
98
what are the properties and characteristics of alphahelix
- due to the extensive hydrogen bonds, alpha helix is very stable, rigid and rod like
- has a small R group
- 1 turn/singular coil has 36 aa residues
- insoluble in water
- makes up keratin
99
why do alpha helixes have a small R group
-if the R group is big, it may interfere with the Hydrogen bonds and the alpha helix cant be formed
100
how are Beta pleated sheets formed
- adjacent polypeptide chains arrange parallel in the same or opposite direction (which causes folding)
- chains are held by H bonds between the electronegative O of the carbonyl group (C=O group) of an amino acid residue with the electropositive H of the amino group (-NH group) of an a residue in the adjacent chain
101
what are the properties/characteristics of beta pleated sheets
- double folded on itself
| - due to extensive Hydrogen bonding, Beta pleated sheet is very stable and rigid (strong)
102
what is the tertiary structure of proteins
myoglobin - consists entirely of 8 a-helix which form a pocket that encloses a haem group
103
what are the properties and characteristics of the tertiary protein structure
- a precise and compact 'globular' chape formed from extensive bending and folding/coiling of a polypeptide chain
- water soluble
104
how are myoglobins water soluble
- hydrophillic R group will face the aqueous surrounding
- hydrophobic R group will form R group interactions among themselves in the internal surface to be shield away from the aqueous surrounding
105
why do polypeptide chains bend and fold into tertiary structure
- either bondswill form between molecules in the chain that have NH3+ and COO- which folds toward each other
- or the polypeptide chains bend because the hydrophobic R group will bend away from the water (point inwards) while the hydrophobic R group points outwards to bend with water
106
what are crosslinks
- the precise and exact shape of the tertiary structure is maintained by 4 types of bonds between R groups
- the folding is very precise to the location of attracted molecule
107
what are the 4 types of crosslinks in R groups
- Disulphide bridges
- Hydrophobic interactions
- Ionic bonds
- Hydrogen bonds
108
what is the disulphide bridges crosslink
covalent bond between R groups of cysteine amino acids
109
what are hydrophobic interactions crosslink
between non-polar R groups such as those on the amino acids tyrosine and valine
110
what are ionic bonds crosslinks
between NH+and COO- ions on basic amino acids such as asparagine and acid ones such as aspartic acid
111
what are hydrogen bonds crosslinks
between electronegative oxygen atoms on CO groups and electropositive H atoms on NH groups
112
what is the order in strength of crosslinks bonds
disulfide>ionic>hydrogen>hydrophobic interactions
113
what is the tertiary structure of the protein maintained by
it is maintained by the 4 types of bonds between R groups
114
what is denaturation
the process where CHONs (proteins) loses their specific 3D shape (proteins function is based on their complementary shape) so the protein cannot form its normal biological function
-the change may be temporary or permanent
115
what may denaturation be caused by
- heat
- acid/base/pH change and high salts
- heavy metals (cations)
- organic solvents and detergents
- reducing agents
116
why does heat cause denaturation
atoms gain kinetic energy and vibrate violently, breaking hydrogen bonds and then ionic bonds
117
why does pH change cause denaturation
break ionic bonds (and then hydrogen bonds)
118
why do heavy metals/cations cause denaturation
break ionic bonds
119
why do organic solvents and detergents cause denaturation
disrupts hydrophobic interactions, form bonds with hydrophobic R groups
120
why do reducing agents cause denaturation
break disulphide bridges
121
what is renaturation
a process whereby a denatured protein spontaneously (by chance) refold into its original specific 3D shape after denaturation, when there is a suitable condition
122
what is the quaternary structure
The 3D arrangement of a complex CHON structure made up of 1 polypeptide chain that are held together by disulphide bridges, ionic bonds, H bonds and hydrophobic interactions or sometimes including a non-CHON component (prosthethic group) (which sits in the pockets of subunits) to form a specific configuration/3D-shape
-each polypeptide chain has its own tertiary structure
123
what are simple proteins
proteins purely made up of amino acids
124
what are conjugated proteins
- globular protein contains non protein components (prosthetic group) permanently in it
- eg. carbo - carboprotein, lipid - lipoprotein, pigment - chromoprotein, nucleic acid - nucleoprotein
125
what are fibrous proteins
- long parallel chains
- physically tough
- insoluble in H2O (fibrous)
- structural CHON
- metabolically inactive
- e.g. collagen, keratin, silk
126
what are globular proteins
- ball shape
- compact
- easily soluble
- functional CHON
- e.g. enzymes
127
what are intermediate proteins
-fibrous but soluble
128
what is an example of a globular protein
haemoglobin
- the red pigment in red blood cells
- transports O2
129
what is an example of fibrous proteins
collagen
- the most abundant protein in our body (1/3 of all proteins)
- the main structural CHON of animals
- holds the body together
- found in skin, tendons, ligaments, cartilage, bones, teeth, walls of blood vessels, organs and connective tissue
- flexible with high tensile strength
130
why is collagen a triple helix
- triple= 3 polypeptide chains twisted around each other in a rope-like formation
- helix= each polypeptide chain is a helix (not as tightly wound as alpha helix)
- strong with high tensile strength
131
what is the primary structure of collagen polypeptide chain and molecule
- every 3rd a.a. is glysine (allows tight coil)
- covalent bonds between collagen molecules
- H bonds and covalent bonds between polypeptide chains (hold chains together)
- staggered ends of molecules overlap
- molecules arrange parallel to form a fibril
- bigger than cellulose molecule
132
what is the order of formation in collagen
a helical polypeptide -> a collagen triple helix -> a fibril
133
why does collagen have high tensile strength
- staggered gaps between molecules (seen in dark lines)
- fibres orientated to the forces they must withstand
- tendons are parallel
- skin placed in different directions in different layers to resist pulling forces from many directions
134
what are examples of structural proteins function
tendons, cartilage, hair, nails
135
what is an example of contractile proteins function
muscle
136
what is an example of transport proteins function
haemoglobin
137
what is an example of storage of energy proteins function
milk
138
what are examples of hormonal proteins function
insulin, growth hormone
139
what are enzyme proteins for
catalyzing reactions in cells
140
how do proteins aid in protection
immune response
141
what are the properties of water
- solvent
- small molecule
- high specific heat capacity
- high latent heat of vaporization
- molecular mobility
- cohesion and surface tension
- density and freezing
- colloid formation
142
which properties of water are due to hydrogen bonds
- high specific heat capacity
- high latent heat of vaporisation
- molecular mobility
- cohesion and surface tension
- density and freezing
- colloid formation
143
why does water have solvent properties
-water is polar because it has a dipole between delta+ H and delta- O
144
how does salt (polar. uncharged) dissolve in water
- electronegative oxygen of water molecules are attracted to cations (+)
- electropositive hydrogen of water molecules are attracted to anions (-)
- a few water molecules surround the cations and anions to form hydration shell
- therefore cations and anions are seperated by water molecules and become hydrated (surrounded by water molecules) in aqueous solution
- as water moves, these ions will be transported together (e.g. mineral ions)
145
how does glucose (polar, uncharged) dissolve in water
- due to formation of H bonds between electropositive H of -OH group of glucose molecule with electronegative O of water molecule
- glucose is a polyol = many alcohol = many
- OH groups (therefore can form H bonds with many water molecules)
- as water moves, these molecules will be transported together (e.g. sucrose in plants//glucose in animals)
146
what happens when lipids (nonpolar) are added to water
- lipid molecules are nonpolar/hydrophobic
- it cannot form H bonds with water molecules
- the water molecules form H bonds with each other, but not with the nonpolar molecule, therefore lipid does not dissolve in water
- lipid molecules will clump together and become spherical-shaped to minimize surface area being exposed to water
147
why is water a small molecule (function)
- less than 1 nanometer
| - so that it can diffuse across the partially permeable cell membrane freely
148
why do water molecules have the ability to form hydrogen bonds with each other (function)
- called cohesion
- results in high specific heat capacity, high latent heat of vaporisation, molecular mobility, cohesion and surface tension, density and freezing properties, colloid formation
149
what is a hydrogen bond
a bond formed between the H of -OH, -NH and -FH with either one of the delta negative atoms of -O, -N or -F
150
what does heat do to water
- breaks the hydrogen bonds between water molecules to set them free to move
- raises the kinetic energy of the water molecules (move further apart and faster)
151
what is specific heat capacity
the amount of heat (J) required to raise 1kg of water through 1C
152
how does water have a high specific heat capacity
H2O molecules will absorb a lot of heat to break the H bonds between them and gain kinetic energy to move faster, leading to a raise in temperature
153
why is the specific heat capacity of water important for the survival of organisms
- maintain body temperature (because 70%-90% of body is made up of water)
- maintain temperature of water body (e.g. lake, sea) to minimize temperature fluctuation
154
what is latent heat of vaporisation
the amount of heat needed to break the H bonds between water molecules and set them free to move and raise the kinetic energy of the water molecules so they move faster and further away and vaporise
155
why is water's high latent heat of vaporisation important for the survival of organisms
- when H2O evaporates, it absorbs lots of heat and cools down the body
- water body will not dry out easily on a hot day so aquatic organisms can survive
156
what is molecular mobility
- individual H bonds are weak bonds
- they can be easily broken and be formed again, allowing the water molecules to move
- hence water is in liquid state
