Chapter 2: Biological Molecules Flashcards
How do saturated and unsaturated lipids vary in structure
Sat have C-C only single bonds
Unsat have double bonds
What are 3 types of unsaturated lipids in terms of no. of double bonds
Mono unsat
Di unsat
Poly unsat
Which states are sat and Unsat lipids at room temp, and what are their originsm
Sat - solid, animals
Unsat - liquid, plants
Why are unsat lipids liquid at room temp
Double bonds make them melt more easily because the double bond causes gaps in the tail
What is the formula for formation of an Ester?
(carboxylic) acid+ alcohol —> ester + water
Recall structural formulae equation
How is a triglyceride molecule formed (process and raw materials)
Glycerol+ 3 Fatty acids with hydrocarbon tails
—> By-product water and Triglyceride molecule
—> = Condensation
Recall structural formulae equation
How is a phospholipid formed
When one of the 3 fatty acids in triglyceride is replaced by a phosphate group
What is a dipole
Unequal distribution of charge
Where do dipoles essential occur
Molecules containing -OH, -CO & -NH groups
What is a hydrogen bond (eg in water)
In water negatively charged oxygen of one molecule is attracted to positively charged hydrogen of ANOTHER molecule, the attraction between the 2 is the H bond
Note: the attraction between 2 atoms WITHIN the SAME molecule is the covalent bond
What are polar molecules
Having dipoles
HYDROPHILIC
Why are non polar molecules insoluble
They not have dipoles (uncharged) to attract dipoles of water molecules
HYDROPHOBIC
What is the specialty of H bonds?
Individually weak, but collectively very strong
Which lipids are sol and which are insol
And why
Sol-phospholipid(hydrophilic) : charged phosphate attracts partially +ve hydrogen
Insol-triglyceride(hydrophobic) : no charged groups
Tests (2) for lipids:
- 1cm3 unknown + 1cm3 of alcohol/organic solvent (ethene) —> sample dissolved if lipid is present
- 1cm3 of unknown + 1cm3 of water —> sample will not dissolve if lipid is present(emulsion)
Confirmatory test for lipids:
1cm3 unknown + 1cm3 organic solvent —> lipid will dissolve
Transfer to testtube with water. Milky white ppt formed, lipid is confirmed
Why are lipids significant energy reserves
They are richer in carbon-hydrogen bonds than carbs, which when broken supply hydrogen yo make nadh and fadh2.
A given mass of lipids yields more energy on oxidation than same mass of carb (high caloric value)
How are lipids insulators
Below the dermis of skin, and around the kidneys it prevents heat loss
Lipids can be blubber. What is this
In sea mammals, insulated and provides buoyancy (float)
How are lipids metabolic sources of water
When oxidised in respiration they are converted to CO2 and H2O. It is important for survival in dry habitats
General formula of carbohydrates :
Cx (H2O) y
Carbohydrates aka
Hydrates of carbon
Elements in carbs:
C
H
O
What 3 types of carbs
Monosaccharides (1 sugar unit)
Disaccharides
Polysaccharides
Examples of
Monosaccharides
Disaccharides
Polysaccharides
Mono - glucose, fructose, galactose
Di- maltose, sucrose, lactose
Poly- starch, glycogen, cellulose
General properties of monosaccharides :
- 1 sugar unit
- sweet in taste
- easily soluble in water
- general formula : (CH2O) n
Types of monosaccharides based on n (name, n, formula, eg)
Trioses n=3 C3H603 glyceraldehyde 3 phosphate
Tetroses n=4 C4H8O4 trythulose
Pentoses n=5 C5H10O5 ribose and deoxyribose
Hexoses n=6 C6H12O6 glucose, galactose, fructose
Linear structure of glucose
Recall structure (aldehyde/ketone and carbonyl groups, 6 carbons)
How is ring structure of glucose formed from linear
Long chain of carbon atoms is enough to close up on itself to form stable ring
Recall the ring structure of glucose
lol k
Structural difference between α and β glucose?
α- anomeric carbon (C1) has H bonds at top and OH at bottom
β- C1 has H bonds at bottom, and OH at top
Recall exact structures of α & β glucose
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Where is anomeric carbon derived from
Carbon of ketone/aldehyde functional group of the open chain form of carbohydrate
What is anomerization
Process of interconversion of one anomer to another
3 roles of monosaccharides
2f acts as building block (glucose: starch glycogen, cellulose)
Nucleic acid (RNA & DNA, each have basic functional unit ie nucleotide, which is made of PO3-, nitrogenous base- A, G, T, C, U, pentosugar)
Many C-H bonds broken to release energy which is transferred to help make ATP
What are sucrose, lactose, maltose made of?
Sucrose= glucose + fructose ( transport form in plants, sold sugar) Lactose= glucose + galactose (milk sugar) Maltose= glucose + glucose (malt sugar)
Difference between reducing and non reducing sugars?
Red- free anomeric carbon (c1)
Non red- free anomeric (c1) carbon absent
Examples of red and non red sugars
Red- maltose, lactose
Nonred- sucrose
Bonds involved in monosaccharides and in disaccharide maltose and process. Also recall structural formulation of maltose
α glucose + α glucose —> α1,4 glycosidic bond (C-O-C) by condensation
Bonds involved in monosaccharides and in disaccharide sucrose and process. Also recall structural formulation
α glucose + β fructose —> β1,2 glycosidic linkage by condensation
State the test for reducing sugars and the mechanism
1cm3 of sugar+ 1cm3 of benedicts (CuSO4) reagent (excess to react all sugar) —> brick red ppt (confirms)
Reducing sugar+ Cu(II) blue —> brick red ppt(Cu+) + oxidised sugar
Cu2+ reduced to Cu+ by reducing sugar
Steps for testing for a non reducing sugar:
1) Convert it to reducing sugars
2cm3 of non red sugar + 1cm3 HCl —mix and heat 2min, break glycosidic bond—> α glucose + β fructose
2) Neutralise HCl
Add 1ml of NAOH OR NAHCO3 until fizzing stops (benedicts works best under alkaline condition)
3) Perform benedicts.
To above + 2ml benedicts –heat–cool–> brick red ppt (confirms presence of non red sugar). If no color change still no sugar
Why use excess benedicts ?
Ensure all reducing sugar has reacted
This helps in calculating exact concentration of sugar in solution using a colorometer
How does color of ppt change for benedicts with concentration of sugar
Intensity
Blue, green, yellow orange red, brick red
Outline how benedicts test can be used to estimate concentration of a reducing sugar
Add benedicts. Heat in water bath. Will turn gradually from green, yellow, orange, red as insol Cu(i) oxide forms a ppt.
Use color standards made by comparing color against colors obtained with reducing sugar tests of known concentrations.
Or use colorimeter to measure more precisely (graph of conc plotted against colorimeter reading)
Why are they called reducing sugars?
Can carry out reduction, by themselves getting oxidised in the process. (lose electrons, to make other reactant ion less positively charged)
How can a benedicts test tell you if both reducing and non reducing sugars are present
Ppt obtained in non reducing test will be heavier than benedicts normal test
What are Polysaccharides
Made up of more than 2 sugar units
What is starch
A Polysaccharide, storage form in glucose in plants, in chloroplasts.
What is starch made up of
Amylose and amylopectin
Structure of Amylose
Polymer of α glucose
α 1,4 glycosidic bond
Structure of amylopectin
Polymer of α glucose
α 1,4 and α 1,6 glycosidic bonds
Branched
Structure of glycogen :
Polymer of α glucose
α 1,4 and α 1,6 glycosidic bond
More branching than in amylopectin
Function of glycogen
Storage form of glucose in animals. Stored in muscle and liver cells
Why can glucose not be stored as such in cells
It is very reactive and will affect cell chemistry badly.
It will dissolve the cytoplasm and make it too concentrated that will further sensitively affect osmotic properties of the cell
Why is glucose stored as glycogen
It is inert (unreactive)
Needs less space
Insoluble doesn’t affect osmotic properties of cell
Most abundant organic molecule in plant ?
Cellulose
Structure of cellulose:
Polymer of β glucose with β 1,4 glycosidic bond
In the β isomer the -OH group on C1 is above ring. In order to form a glycosidic bond with C4 where -OH group is below ring, one glucose must be upside down (180°) relative to the successive one
How do cellulose fibres provide strength to cell wall
- Adjacent cellulose molecules are held by hydrogen bonds between +H and -O
- Individual H bonds are weak, collectively strong
- Many cellulose form microfibrils, many of these form fibres
- Cell wall has several fibres running in different directions to provide strength
How do cellulose molecules form fibres?
60-70 molecules are tightly cross linked to form bundles called microfibrils. These are held together in bundles called fibres by hydrogen bonding
Why are cellulose fibres so strong
Arrangement of β glucose molecules in such a way that hydrogen bonds existing between the large no. of -OH groups collectively provide huge strength
Enzymes are which organic molecule
Proteins
Proteins are components of _ and function as _
Cell membrane
Receptors and signallers
Examples of protein hormones
Insulin
Glucagon
Size of mirofibril
10nm diameter
Size of cellulose fibre
50nm
Which oxygen carrying pigments are proteins
Haemoglobin in RBC
Myoglobin in muscle cell
What other component of blood apart of haemoglobin and Myoglobin is protein
Antibodies
Collagen is made of _ and adds _ to animal _
Protein
Strength
Tissues
What do hair nails and layers of skin contain
Protein keratin
Which proteins are responsible for muscle contraction
Actin
Myosin
Casein in milk and ovalbumin in egg white are _ proteins
Storagwb
Functional unit of protein
Amino acid
How many essential and non essential amino acids and define
E- 9 body can’t make, rely on external source
Non E- 11 body can make
General structure of amino acid:
Recall structure
Amine group -NH2
Alkyl group -R (CH3 methyl, C2H5 ethyl, C3H7 propyl)
C-H
Carboxylic acid -COOH
What makes the 20 amino acids different
The R group
How do 2 amino acids link
Loss of water molecule by condensation to form peptide bond and hence a dipeptide molecule
What’s a peptide bonds structure
C=O
|
N-H
How is condensation done between amino acids
One loses -OH from COOH while other loses H from NH2
This leaves carbon of first amino acid to bond with Nitrogen of second
Types of protein based on no of amino acids
Dipeptide -2
Tripeptide- 3
Polypeptide- many
Which organelles help in protein synthesis
Ribosomes join amino acids
Where in digestive system is protein digestion done
Stomach (acidic pH, enzyme pepsin)
and small intestine
What is primary structure of proteins
Linear sequence of amino acids in a polypeptide chain
What are 2 ends of Polypeptide chain called
NH2 terminal
COOH terminal
What is secondary structure
Regular coding folding of amino acid chain
What is secondary coding
α helix
Due to hydrogen bonding between oxygen of CO on one amino acid and NH of an amino acid four places ahead
What is folding secondary structure
β pleated sheet
NH group in backbone of one fully extended strand establishes hydrogen bond with C=O group in backbone of adjacent fully extended strand
2 orientations of adjacent Polypeptide chains
Recall diagrams
1) same direction OR parallel
2) opp direction OR antiparallel
How can hydrogen bonds in β pleated sheets be broken even though are strong enough
High temp
pH changes
What is tertiary structure
3d coiling of already folded SINGLE chain of amino acids, of both α helix and β sheet
Which 2 enzymes have tertiary structure and what’s their function
Hyzozyme - in tears, hydrolyses bacteria by breaking peptidoglycan chain in cell wall to lyse/burst the cell
Myoglobin - 02 carting pigment in muscle
Test for proteins
1cm3 of sample + 1cm3 biuret reagent (CUSO4 in KOH/NaOH alkaline medium) —> Purple color (not blue) confirms presence of protein
What extra reagent can be added to biuret to avoid ppt formation
CUSO4 mixed with KOH or NaOH by adding sodium potassium tartrate or sodium citrate
Mechanism of biuret test
Cu + N - copper of biuret forms complex with N of peptide bond to result in purple color
Structure of Myoglobin
α helix linked by polypeptide chains. Haem group attached contained Fe2+ and porphyrin ring
Which 4 bonds stabilise tertiary and quarternery structure
Hydrogen
Covalent (disulfide)
Ionic
Weak hydrophobic interactions
Where do H bonds form
Between strongly polar groups
NH, CO, OH
Howis H bond represented
Where do disulfide bonds form
Between cysteine molecules (an amino acid)
How can disulfide bonds be broken
By reducing agents
Recall diagram of disulfide reaction
2S-H (sulphydryl group) (-2H oxidation) –> S-S disulfide bond
Wher3 in proteins are ionic bonds formed
Ionised Amine (NH3+) and ionised carboxylic acid (COO-)
How can ionic bonds be broken
pH changes
Where do weak hydrophobic interactions occur, and how do they stay together though weak
Between non polar R groups
Repelled by watery environment around them
What is the order of strength of bonds
covalent(disulfide)>ionic>hydrogen>hydrophobic interaction
What is quarternery structure
3d arrangement of 2 or more Polypeptides, or of a Polypeptide and a non protein component
Structure of haemoglobin
2 α globin Polypeptide chains
2 β globin Polypeptide chains
Each chain has a heam group, which is non protein or prosthetic group
Each haem has an Fe atom to bind with a molecule of O2
Each iron atom can _ bind with _ oxygen atoms
Reversibly
8
Where are oxy and deoxy haemoglobin found and what are their colors
Oxy -lung, red
Deoxy -tissue, purple
What maintain the shape and solubility of haemoglobin
Shape - interactions between hydrophobic R groups inside the molecule
Sol - onward pointing hydrophilic R groups on surface of molecule
What is sickle cell anaemia
A genetic disorder
Happens at position 6 of amino acid of β polypeptide chain
At 6, glutamic acid (hydrophilic) is replaced with valine (hydrophobic) responsible for sickle shape RBC
What is cooperative binding
1) each haemoglobin molecule can bind to 4O2
2) haemoglobin exhibits cooperative binding. As O2 binds to iron of any one polypeptide subunit increases the rate (affinity) of other subunits TI bind with O2 in a sequential manner
3) increased affinity is caused by a confirmational change or a structural change in haemoglobin-each of subunits
3 differences between globular and fibrous protein
G- ball shaped or globular F- long strand or fibre
G- soluble because hydrophobic amino acids towards centre and hydrophilic to peripheral
F- insol, mostly hydrophobic amino acids
G- takes part in metabolic reaction
F- takes part to maintain structural parts ie tendon ligaments
Examples of globular and fibrous protein
G - enzyme (lysosome), haemoglobin, myoglobin
F - structural protein like collagen, keratin
What are the 2 types of metabolic reaction
Annabolic - making
Catabolic - breaking
What is nature of collagen
Insoluble fibrous protein
Locations of collagen
Skin Tendons Cartilage Bones Teeth Blood vessel walls
Structure of collagen
- 3 polypeptide chains, wound around each other in shape of triple helix.
- The 3 strands are held together by hydrogen bonds and some covalent.
•Every 3rd amino acid is glycine, smallest amino acid. It is found on insides of strands and it’s small size allows the 3 strands to lie close together and form a tight coil. Other amino acids too large
- Many of these triple helices lie side by side, linked by covalent cross links between side chains of amino acids near ends of polypeptides to form fibrils.
- The ends of parallel molecules are out of step/staggered preventing a weak spot running across the fibril and hence making collagen stronger
•Many fibrils lie alongside eachother forming strong bundles called fibres
5 differences between triple helix and α helix
1) T has 3 chains, α has 1
2) T has glycine every 3rd position, α amino acids are linked by peptide bonds to form coils
3) T has H and covalent bonds to stabilise structure, α has H bonds to stabilise the structure between CO and NH of amino acid 4 placed ahead
4) Collagen is in skin etc, α is secondary structure
5) T has 3 amino acids per turn, α has 3.6 amino acid residues
Dipole in water molecule
Small Δ- on oxygen atom
Small Δ+ on hydrogen atoms
What makes water molecules difficult to separate
Hydrogen bonding
Why is it difficult to convert water from l to g
A lot of energy needed to break hydrogen bonds
Why is hydrogen disulfide gas at normal air temperature
Lacks hydrogen bonds
Examples of systems using water as a transport medium
Blood circulation Lymph Digestive system Excretory Xyle/phloem
What is specific heat capacity
Amount of heat energy needed by a given mass of a substance- 1kg to raise it’s temperature by 1°C
The higher the _ the higher the energy needed TI raise _
Kinetic energy (due to molecule speed) Temperature
Why do large water bodies not change temp as easily as air
More mass
Hence more energy needed to raise temp even by a bit
Role of water in photosynthesis
Reagent
Photosynthesis equation
sunlight
6CO2+6H2O—————-> 6CO2+C6H1206
chlorophyll
Water has a role in _ opp of condensation
Hydrolysis
What is cohesion
Ability of water molecules to stick to each other because of hydrogen bonds
What is surface tension
Property of water to attain minimum surface area by keeping water molecules close together by Hydrogen bonds
How do organisms exploit surface of water as habitat
High cohesion and surface tension of water due to hydrogen bonds
What in plants uses cohesion and surface tension of water to it’s advantage
Tranpirational pull of water through xylem
Test for starch
1cm3 of sample+Iodine (I2) dissolved in potassium iodide —-> blue black color, because (recall structure) I2 fits into middle hole of starchs helical coil
What is a macromolecule
Large biological molecule (no repeat unit)
Eg protein, polysaccharide
What is a monomer
Simple molecule, uses to basic building block for polymer synthesis, many monomers are joined ie by condensation reactions
Eg monosaccharides, nucleotides
What’s a polymer
Giant molecule made from many similar repeating subunits/functional groups joined together, which are smaller and simpler ie monomers
Eg polysaccharides, nucleic acids
What makes water a good solvent
Dipoles
What happens when NACL dissolves in water
Na+ and Cl- separate and spread between water molecules
Na+ is attracted to -ve charge of O, and Cl- TI +ve charge of H
Where and how do dipoles occur
Molecules with OH, CO, NH groups
Hydrogen bonds form between the partially oppositepy charged parts
Molecules with dipoles are said to be
Polar
Why are polar molecules called so?
Have dipoles
Attracted to water molecules as they also have dipoles
Hydrophilic, sol in water
Molecules without dipoles are
Non polar
Non polar molecules are _ in water they are _
Insoluble
Hydrophobic
What is latent heat of vaporization
Measure of heat energy needed to vaporise a liquid to gas/vapor
Why does water have high latent heat of vaporization
High specific heat capacity
Hydrogen bonding makes molecules stick to eachother
How does high latent heat of vaporization of water help animals and plants (organismally)
When water evaporates it absorbs a lot of heat from it’s surrounding
Animal- sweat evaporates from skin ie cooling effect
Plant- transpiration from leaves
Why is it less likely for water bodies to freeze
Water should change from liquid to solid right
So in this case it must lose a lot of energy, that’s why it’s hard to freeze
Hence advantage to aquatic animals
What is the peculiarity of ice and what’s the reason behind it
In solid form, ice is less dense and doesn’t sink when submerged
Reason: crystalline structure of ice
Which direction does water freeze
Top to bottom
When water cools what happens? What happens further to become ice?
Temp decreases
Density increases
Because molecules lose kinetic energy and get closer below 4°C.
This trend is reversed when water approaches freezing point 0°C, when water forms a lattice and stretches by forming elastic hydrogen bonds.
Density decreases lower than at 4°C and ice floats
How does the water below ice stay as water? How is this good?
Layer of ice acts as an insulator, slowing down heat loss from water beneath which remains at 4°C and liquid
This allows organisms to live even when air temps are below freezing point
What makes water circulate nutrients
Changes in density of water with temperature cause currents which circulate nutrients in oceans
7 properties of water:
- Solvent
- Tranport medium
- High specific heat capacity
- High latent heat of vaporization
- Density (freezing point)
- Reagent
- High cohesion and surface tension
Location of glycogen
Live and muscle cells
