C3- Biological molecules Flashcards
What is hydrophilic?
A molecule which is attracted to water.
What is hydrophobic
A molecule that repels water.
Why is water a polar molecule
An unequal distribution of charge between the covalent bond. Electrons have stronger forces of attraction tot h oxygen atom.
What is a dipolar molecule
A molecule with 2 charged regions
What holds water molecules together
hydrogen bonds
6 properties of water
- Cohesion
- Adhesion
- solvent
- High surface tension
- ice is less dense than water
- transparent
What is water cohesion
How water molecules are attracted to other water molecules by hydrogen bonds, which allows water to be pulled as one continuous column.
What is water adhesion
Water molecules stick to the sides of walls of xylem due to forces of attraction, this aids the transpiration stream
How does water act as a solvent
Water dissociates ions and causes the ions to move to the either of the polar ends of the water molecule
then surrounds ions in solution
Is a soluble substance hydrophilic or hydrophobic
hydrophilic
Why do metabolic reactions take place in solvents
Substances dissolve in water and are free to move, this increases the chances of collisions and therefore reactions
Thermal properties of water
High latent heat of vaporisation, high heat capacity
Why does water have high heat capacity
Hydrogen bonding. It will absorb or loose a large amount of energy before its temperature changes. Temperature ‘buffer’
Why is waters density important
Ice floats, provides habitat and insulation
Why is waters constant temperature important
Maintains enzyme function, due to its narrow range of temperatures for optimum
Uses of waters high latent heat of vaporisation (2)
Sweating. Cooling effect as water evaporates from skin as energy is used up
Same effect but for transpiration
Water metabolite reactions (3)
Hydrolysis reactions- Large Molecules are broken down into smaller ones using water
Condensation reactions- water is produced when smaller molecules join together
Photosynthesis
Why is the fact that water is a solvent useful
Most biological reactions take place in a solution
Dissolved substances can be transported around the body
Hydroxyl Group
OH
Polar functional group
-> when added to a molecule it helps it mix with water
3 functions of carbohydrates
1- Energy source
-> Sugars
2- Energy store
-> Glycogen and starch
3- Structural
-> Cellulose, Chitin
Alpha glucose Vs Beta Glucose
Both are hexose monosaccharides
C1 OH and H Group are swapped around, OH down on alpha
What bond joins a disaccharide of alpha glucose
1,4 Glycocidic bond
Pointed downwards as OH groups were down`
Isomer
Same molecular formula but a different structural formula
E.g Alpha vs beta Glucose
Ribose Vs Deoxyribose
Both pentose Monosaccharides
-> 5C
C2OH Group on ribose looses oxygen on Deoxyribose
hydrolysis reaction
Large molecules broken down by addition of water
E.g Lactose is hydrolysed into glucose + Galactose
2 types of starch
Amylose
-> Unbranched
Amylopectin
-> Branched
Amylose (5)
Storage of glucose in plants
Alpha glucose monomers
1,4 Glycocidic bonds ONLY
Helical ( due to H bonds)
Not branched
Amylopectin (5)
More efficient store of glucose for plants
Alpha glucose monomers
1,4 AND 1,6 Glycocidic bonds
Helical
Quite branched
-> every 20 monomers
Glycogen (5)
Store of Glucose in Animals
Alpha glucose monomers
1,4 AND 1,6 Glycocidic Bonds
Helical
Very branched
-> Every 10 monomers
Explain how the structure of glycogen makes it a suitable storage molecule
highly Branched
Compact
-> Can store a lot of energy
Many terminal glucose molecules
-> Hydrolysed quickly
Glycogen is more branched than starch
What’s the significance of this for animals?
Animals are metabolically active
-> Need more energy
Glycogen stores more energy and releases it faster
Fatty acid general formula
RCOOH
R= variable number of N C O atoms
What type of reaction takes plac when glycerol reacts with a fatty acid
Condensation
3 H20 molecules produced
Type of reaction when a triglyceride is broken down in digestion
hydrolysis
Cellulose
structure
4
beta glucose monomers
Straight parallel unbranched chains
Hydrogen bonds crosslink chains
Every other beta glucose monomer is inverted
Which functional groups do H bonds form between parallel chains of cellullose
OH
Hydroxyl Group
Beta glucose monomers joined by ____ in cellulose
1,4 Glycosidic bonds
Structural feature that gives cellulose its high tensile strength
Cross linkages of hydrogen Bonds
Cellulose
Function
Structural polymer
Strength + rigidity
Inwards force to prevent bursting maintaining turgor
4 Cellulose properties
Insoluble
flexible
unreactive
high tensile strength
How is cellulose formed
3
Made of beta Glucose
1,4 glycosidic bonds
Formed by condensation polymerisation where every other beta glucose monomer inverts
Fats
5
Solid at RTP
Large macromolecules of C H O
Low mass for molecule size
Energy rich
insoluble
triglyceride
Glycerol + 3 fatty acids -> triglyceride
I—
I—
I—
Fatty acids
COOH - carboxyl group
–> carbocyclic acid
Saturated fatty acid general formula
Cn H2n+1 COOH
Esterification
Type of condensation reaction
Carboxyl group on fatty acid and hydroxyl group on glycerol
alcohol +acid -> ester + water
Ester bond
COO
o I o=c
Reducing sugars
All monosaccharides
some disaccharides
Can donate electrons
–> ability to reduce other molecules
Benedict’s reagent
Cu 2+ ions
Alkaline solution of Cu(II) sulfate
Reducing sugars Chemical test
method
1 place sample to be tested in a boiling tube, if not liquid then grind or blend in water
2 add equal volume benedict’s reagent
3 heat gently in >80c water bath for 5 minutes
benedict reagent
Result
Green to brick red
low to high level of reducing sugars
Cu 2+ ions reduced to red Cu + ions
More reducing sugars= more ions
Non reducing sugars chemical test
E.g. Sucrose
Acid hydrolysis
–> boil with dilute HCl
Sucrose hydrolysed to glucose and fructose
-both reducing sugars
Then use benedict’s Reagent
Saturated fatty acid chain
No double bonds present between carbon atoms
Unsaturated fatty acids
Double bonds between some of carbon atoms
causes molecules to kink
–> less dense at RTP
- cannot pack as closely together
Monounsaturated fatty acids
One double bond
More than one double bond
= polyunsaturated
Phospholipids
structure
Modified triglycerides
–> P C H O
PO4 3- ions
one fatty acid chain replaced with phosphate group
O
II
Phospholipid structure
Non polar tail - fatty acid
polar/charged head - phosphate
Tail= hydrophobic
head= hydrophilic
Surfactant- forms a layer on water surface
O
II
Phospholipid bilayer
Protect from water
Hydrophobic tails point inwards and hydrophilic heads point outwards in a ring
sterols
steroid alcohols- type of lipid
OH group
4 carbon ring
Dual hydrophilic/phobic characteristics
Cholesterol
Sterol - lipid
In cell membrane
–> between phospholipids and OH group
For stability of cell membrane
Roles of lipids
6
Membrane formation
hormone production
electrical insulation- axons
thermal insulation
cushioning of organs
buoyancy
Identification of lipids
test
Emulsion test.
Mix sample with ethanol
mix with water and shake
White emulsion formed = positive
Remains clear= negative
Basic structure of an amino acid
H H O-H
N - C- C
H R =O
Which elements are proteins made of
H N C O
S - cysteine only
–> Sulfur in R group
Bond formed between two amino acids
and func groups
Peptide bond
Amine and carboxyl group
Dipeptide
2 Amino acids bonded together
R group on amino acids
On amino acid
Variable
Determines properties
Polypeptides
Primary structure
Peptide bonds
Sequence in which amino acids are formed
Sequence influences how polypeptides form
–> determines function
Polypeptides
Secondary Structure
Repeating structure of amino acids interact
–>not R groups
H bonds form in chain
- Coiled Alpha helix
- Beta pleated sheet
Polypeptides
Quaternary structure
2 or more individual proteins called subunits
same interactions as tertiary except now between whole molecules and not within
subunits may be identical or different
Tertiary structure
Hydrophilic and hydrophobic interactions
Protein folds based on whether the R group is hydrophilic or hydrophobic
Breakdown of peptides
breaking peptide bonds is a hydrolysis reaction that is catalysed by proteases
Polypeptides
Tertiary structure
Section of the secondary structure
–> interactions between R groups
1) Hydrophilic / hydrophobic interactions
2) H bonds ( weak)
3) Ionic bonds ( vulnerable to PH changes)
4) Disulphide bonds/ Bridges ( strong)
Final shape determines function
- specific 3D shape
H Bonds
Heat
H Bonds are overcome
Causes 3D shape of protein to change
–> changing its function
‘denaturing’
Polypeptide
Secondary structure
–> formation
(3)
H bonds
Form between amino acids in polypeptide chain
Causes regions of chain to twist into an alpha helix or fold into a beta pleated sheet
Amino acid
Properties, 3
Soluble
- form polar ions in water
3 bases ( codon) codes for an amino acid
amphoteric
- Can donate or accept protons. Ph buffer
Polypeptides
Primary structure
Sequence in which amino acids are formed
Peptide bonds
Sequence influences how polypeptides formed
–> determines function
Polypeptides
Secondary structure
Repeating structure of amino acids interact
–> not R groups
H bonds form in chain
–> coiled alpha helix
beta pleated sheet
Polypeptides
Quaternary Structure
2 or more individual proteins called subunits
Same interactions as tertiary
–> except now between molecules not within
Subunits may be identical or different
Hydrophilic and hydrophobic interactions
Protein folds based on whether R group is hydrophilic or hydrophobic
Breakdown of peptides
breaking peptide bonds is a hydrolysis reaction catalysed by proteases
Polypeptides
Tertiary structure
Sections of secondary structure interact between R groups
1- hydrophilic/ hydrophobic interactions
2- H bonds ( weak)
3- Ionic Bonds ( vulnerable to Ph changes)
4- Disulphide bonds/ bridges ( strong)
Final shape determines function
–> specific 3D shape
H bonds
Heat
H Bonds overcome
Caused 3D shape of protein to change
Denatured
Polypeptide
secondary structure formation
H bonds
Form between amino acids in polypeptide chain
causes regions of the chain to twist into alpha helix or beta pleated sheet
Amino Acids
Properties
Soluble- form polar ions in water
3 bases ( a codon) codes for amino acids
Amphoteric
–> can donate or accept protons
Ph buffer
Globular proteins
SPADES
s- Compact and spherical
p- functional/ metabolic
a- irregular amino acid sequence
d- more sensitive to changes in pH or temperature
e- enzymes, haemoglobin, immunoglobins, insulin
s- ( generally soluble in water
Conjugated proteins
Simple proteins with a non protein component within its structure called a prosthetic group
Fibrous proteins
SPADES
s- long and narrow
p- structural
a- repetitive amino acid chain
d- less sensitive to pH or temperature changes
e- Collagen, Keratin, elastin
s- (generally) insoluble in water
cross linkages between 3 polypeptides chains
not folded- limited sec or tert structure
SPADES
shape, purpose, acid sequence, durability, examples, solubility
Used to compare proteins
Collagen
High proportion of glycine, so chains can lie close together
High tensile strength, but inelastic
Skin, tendons, ligaments
Structural component of skin
Keratin
Fibrous protein
structural protein
High tensile strength, unreactive, insoluble
hair, skin, nails
Elastin
Fibrous protein
allows stretch in vessels, accommodates blood pressure
Elastic, insoluble, unreactive
Walls of blood vessels, skin, alveoli
Insulin
Globular protein
Soluble
Simple protein
Quaternary protein
Hormone to reduce blood sugar levels
haemoglobin
Globular protein
Soluble
Conjugated- 4 Haem groups
Quaternary protein
Binds to oxygen on RBC
Catalase
Globular protein
Soluble
Conjugated
Quaternary protein
Enzyme that decomposes hydrogen peroxide
Constituents
Lipoproteins
Glycoproteins
Glycoprotein= Protein + carbohydrate
Lipoprotein= Protein + lipid
Nucleotide
Phosphate group- po4 2-
Pentose sugar- 5 carbons
Organic base/ nitrogenous base
Water soluble due to phosphate group and OH group on pentose sugar
Nucleic acids
Large polymers formed from monomers called nucleotides
Pyrimidines
Single ring bases
Thymine
–> Uracil in RNA
Cytosine
Purines
PURAG
Double ring structure
Adenine
Guanine
DNA Chains
2 antiparallel strands of DNA
5’= Phosphate end on C5
3’= Sugar end on C3
Elements in Nucleic acids
C H O N P
Type of bond that joins individual nucleotides
Phosphodiester bond
Risks for TLC practical
TLC= thin layer chromatography
–> used to separate non volatile mixtures
Solvent= irritant and flammable
- Used small volumes of solvent, ventilate room, gloves+ goggles
Ninhydrin 9 dye)= flammable
- Kept away from naked flames
Rf value
Retention factor
Measured form the middle of the spot
Distance travelled by component/ distance travelled by the solvent
TLC method
1 Cut paper, while wearing gloves, hang straight in jar
2- pour small Volume of solvent into the jar
3- Draw a pencil line with 2 points, dot on the amino acid using a cocktail stick then place paper in the jar for 20 minutes
4 remove when solvent front has reached 3/4 the way up the chromatogram
5- Spray chromatogram With ninhydrin to visualise spots and dry using a blow dryer
Amino acid polarity
effect on solubility
Polar= soluble
non polar= insoluble
Strength of polarity determines how soluble an amino acid is
What does how far an amino acid moves during TLC depend on ?
1 Solubility of amino acid in the solvent ( mobile phase)
2 How an amino acid interacts with the paper (stationary phase)
3 the Mr of the Amino acid
DNA helicase
Catalyses reactions that break H bonds
between the complimentary base pairs
Causes a DNA molecule to unwind and the two strands to separate
DNA polymerase
Catalyses the formation of phosphodiester bonds between nucleotides
Always assembles in 5’ to 3’ direction
Semi conservative replication
Half the original DNA molecule is built into each new DNA molecule
One old, one new strand on each DNA molecule
DNA
Sense strand
From 5’ to 3’
Contains sequence of bases that code for proteins to be synthesised
Coding strand
DNA
Antisense strand
3’ to 5’
Contains complimentary copy of sense strand
Non coding for proteins
Template for MRNA
Number of H bonds between bases
A=T
2 H bonds
C///G
3 H bonds
DNA extraction
Why mix crushed fruit with detergent and salt
Detergent:
Degrades phospholipid bilayer, Hence releasing DNA
Salt:
Na+ ions shield PO4- ions that make DNA negatively charged, precipitating the DNA within the solution
DNA extraction
Water bath?
Why cool the ethanol, and the mixture
Water bath at 60c
Denatures DNase, which would otherwise cut the DNA into fragments
Cooling ethanol-
Nucleic acids are insoluble in ethanol, so will precipitate into this layer
Cooling the mixture-
Slows the breakdown of DNA
DNA extraction
Blend?
Protease?
Blend:
breaks down cellulose cell wall, permitting the release of DNA, only needed for plant cell walls
Protease:
Partially degrades proteins in preparation, Uncoils DNA removing histones
Gene
Sequence of bases in DNA that codes for a sequence of amino acids in a polypeptide
Genetic code
Triplet code
Each sequence of 3 bases on a DNA molecule is called a codon
This codes for a particular amino acid
This is a triplet code
Genetic code
Degenerate code
Different combinations of bases (different codons) can code for the same amino acid
in nature : a mutation is less likely to have an effect
Genetic code
Universal code
Genetic code is the same in all organisms
Genetic code
Non overlapping
Each 3 bases can only ever be a part of one codon
DNA transcription
Semi conservative replication process
Section of DNA containing the gene unwind and the two strands separate- this is catalysed by the enzyme DNA helicase
This exposes the nucleotides on Antisense strand which acts as a template for the synthesis of mRNA
Free RNA nucleotides form complimentary base pairs with the exposed DNA nucleotides
This is catalysed by RNA polymerase which catalyses the phosphodiester bonds being formed between RNA nucleotides
2 identical DNA molecules formed
What do cells require energy for
synthesis
e.g. protein synthesis
transport
Movement
e.g. muscle contraction or spindle fibres
ATP
function
Energy carrier in all living cells
Provides energy needed to drive metabolic processes
How does ATP release energy
Energy is needed to break the weak bonds between phosphate groups
These bonds have a low activation energy so are broken easily
Large amounts of energy released when liberated phosphate undergoes other reactions
ATP structure
3 phosphate groups on carbon 5
Ribose sugar
Adenine base on Carbon 1
Hydrolysis of ATP
equation
Catalysed by ATP hydrolase
ATP + H2O –> Pi +ADP +energy
ATP= adenosine triphosphate
ADP= Adenosine diphosphate
–> two phosphate groups not 3
Pi= inorganic phosphate
Rection form ADP to ATP
catalyses by ATP synthase
condensation reaction
Phosphorylation reaction
Why is energy released so quickly form ATP
Single step reaction involving only on enzyme
Unlike respiration
Properties of ATP
4
Small- moves easily into within and out of cells
Water soluble- energy requiring processes take place in aqueous environments
easily regenerated
releases energy in small quantities
Biuret test
Blue black results
When added to starch
Why add ethanol or propanone to a lipid in the first stage of lipid testing
to dissolve the lipid
Non essential amino acids
can be synthesised from essential amino acids
DNA translation
Protein synthesis
The mRNA binds to a ribosome, at its start codon on the small subunit
a tRNA molecule with an anticodon that is complementary to the first mRNA codon binds to the mRNA
The tRNA delivers the correct amino acid to the ribosome, as specified by mRNA codon
working along the mRNA in a 5’ to 3’ direction each codon is translated in this way and the amino acids are joined by peptide bonds, forming the polypeptide chain
the final polypeptide chain is modified and folded in the golgi apparatus
DNA Transcription
Protein synthesis
The section of DNA containing the gene unwinds and the two DNA strands separate, catalysed by DNA helicase
This exposes nucleotides on the antisense strand which acts as a template for the synthesis of mRNA,
Free RNA nucleotides form complimentary base pairs with the exposed DNA nucleotides
adenine bonds with uracil not thymine on RNA strand
The mRNA nucleotides are joined by phosphodiester bonds in a reaction catalysed by RNA polymerase
Before the mRNA leaves the nucleus, introns are removed and exons are joined together- splicing
The newly formed mRNA detaches from DNA and leaves the nucleus
Exons vs introns
Introns = non-coding and intervening (non-functional)
Exons are expressed sections of DNA
Reason for the presence of introns
Originally functional genes
Mutated
Base sequence changed
No longer code for amino acids
mRNA
tRNA
rRNA
mRNA= Messenger RNA, copies DNA from gene and transports to the ribosome
tRNA= brings amino acid to ribosome
rRNA= component of Ribosomes
Anticodon
The anticodon is a sequence of 3 bases which are complementary to a codon (3 bases) on the mRNA molecule.
Why use a stain for TLC
Ninhydrin
Visualise spots
