C3 - Biological molecules Flashcards
What elements are living things primarily made of?
Carbon
Hydrogen
Oxygen
Nitrogen
(Sulfur and Phosphorus)
What is a covalent bond?
Electrostatic force of attraction between shared pair of electrons and the nuclei of the bonded atoms
What are ionic bonds
Electrostatic force of attraction between positive and negative ions
What are calcium ions necessary for?
Ca2+
Nerve impulse transmission
Muscle contraction
What are sodium ions necessary for?
Na+
Nerve impulse transmission
Kidney function
What are potassium ions necessary for?
K+
Nerve impulse transmission
Stomatal opening
What are hydrogen ions necessary for?
H+
Catalysis of reactions
pH determination
What are ammonium ions necessary for?
NH4 +
Production of nitrate ions by bacteria
What are nitrate ions necessary for?
NO3 -
Nitrogen supply to plants for amino acid and protein formation
What are hydrogen carbonate ions necessary for?
HCO3 -
Maintenance of blood pH
What are chloride ions necessary for?
Cl-
Balance positive charge of sodium and potassium ions in cells
What are phosphate ions necessary for?
PO4 3-
Cell membrane formation
Nucleic acid and ATP formation
What are hydroxide ions necessary for?
OH-
Catalysis of reactions
pH determination
What elements do carbohydrates contain?
C, H, O
Cx(H2O)y
What elements do lipids contain?
C, H, O
What elements do proteins contain?
C, H, O, N, S
What elements do nucleic acids contain?
C, H, O, N, P
What are polymers
Long chain molecules composed of multiple individual molecules bonded in a repeating pattern
What are monomers
Individual molecules that make up a polymer
What is polar?
Uneven charge distribution
Electrons closer to one atom
Forming slight positive and negative dipoles
What’s a hydrogen bond?
Bond between NOF and hydrogen
What are the unique characteristics of water
-High boiling point
-Ice is less dense than water
-Cohesive
-Adhesive
-High surface tension
What is cohesion
Molecules attracted to each other
What is adhesion
Molecules attracted to other materials
Is water more cohesive or adhesive
Cohesive
What are key roles of water?
-Solvent: Polar hydrogen bonds, site for chemical reactions
-Transport medium: Cohesion and adhesions:
-Coolant: Large amounts of energy required to overcome H bonds helps maintain constant temp
-Habitat: due to stability
What are carbohydrates?
Organic polymers composed of elements C, H, O
Usually in ratio Cx(H2O)y
Saccharides
What is a monosaccharide
Single sugar molecule
What’s a polysaccharide
Polymer made up of multiple saccharides
Examples of monosaccharides
Glucose
Fructose
Ribose
Examples of polysaccharides
Glycogen
Cellulose
Starch
What is a hexose monosaccharide
Monosaccharide composed of 6 carbons
What’s glucose
Hexose monosaccharide with chemical formula C6H12O6
Product of photosynthesis in plants
Structure of alpha glucose
Structure beta glucose
Are glucose molecules soluble in water?
Yes, due to H bonds
What is a condensation reaction
Reaction between two molecules resulting in formation of a larger molecule and release of water molecule
What do two alpha glucose molecules form
Maltose
Condensation reaction - removing water molecule
Form 1,4 glycosidic C-O-C bond where to OH groups were
What is lactose made up of
Glucose
Galactose
What is sucrose made up of
Fructose and glucose
What is maltose made up of
Two alpha glucose
What is a pentose monosaccharide
Monosaccharide composed of 5 carbons
Examples of pentose monosaccharides
Ribose in RNA
Deoxyribose in DNA
Structure of ribose
What is starch?
Polysaccharide formed from alpha glucose molecules, joined to form amylose or amylopectin
What is the structure of amylose
Alpha glucose joined by 1,4 glycosidic bonds
Glucose twists to form helix, further stabilised by H bonding
Makes it more compact, less soluble (glucose)
What is the structure of amylopectin
Alpha glucose joined by 1,4 and 1,6 glycosidic bonds
Branched structure
Highly soluble
Glycogen compared to amylopectin
Forms more branches
More compact
Less space needed to store it
(glycogen has a similar structure to amylopectin)
What features does coiling/branching give polysaccharides
Compact - good for storage
Many free ends where glucose can be added or removed speeding up rate of reaction
What is a hydrolysis reaction
Breakdown of a molecule into two smaller molecules requiring the addition of water molecule
How does beta glucose join
Alternate beta glucose molecules are rotated 180 degrees
Forming cellulose
What are features of cellulose
Form H bonds with each other, forming microfibrils, which join to make macrofibrils, which join to make fibres
Fibres are strong and insoluble and used for cell wall
What does a Benedict’s test identify
Reducing sugars
What is a reducing sugar?
Saccharides that donate electrons resulting in the reduction of another molecule
How is a Benedict’s test carried out?
Alkaline solution of copper(II) sulfate
1) Place sample into boiling tube
2) Add equal volume of Alkaline solution of copper(II) sulfate
3) Heat gently in water bath for 5 mins
What are the results of a Benedict’s test
Reducing sugars react with Cu2+ ions in reagent
Blue Cu2+ reduced turning them brick red
The more reducing sugar present, the more red precipitate formed
How do you use a Benedict’s test to test for non reducing sugars
Non reducing sugars do not react with Benedict’s solution
1) Boiled with HCl first so sucrose is hydrolysed into glucose and fructose
2) Then carry out normal Benedict’s test
What is the most common non-reducing sugar
Sucrose
What does an iodine test for
Starch
How do you carry out an iodine test?
Add few drops of iodine dissolved in potassium iodide solution
What is a positive test result for iodine?
Colour change from yellow/brown to blue/black
How else can reducing sugars be tested
Reagent strip with colour coded chart signifying concentration
What is a lipid?
Non polar macromolecule containing C H O known as fats and oils
Are lipids polar
No
What is a triglyceride
Lipid composed of one glycerol molecule and 3 fatty acids
Structure of a triglyceride
What functional group does glycerol belong to
Alcohol
-OH
What functional group do fatty acids belong to
Carboxylic acids
-COOH
What bonds form between glycerol and fatty acid
Ester bonds
C(=O)-O-
(Condensation reaction)
How many water molecules are required for reverse reaction
3
What is a saturated fatty acid
Fatty acids that have no double bonds between carbon atoms
What is an unsaturated fatty acids
Fatty acids with C=C double bonds
What is a monounsaturated fatty acid and a polyunsaturated fatty acid?
1 c=c
Or multiple c=c
What does the C=C bond do in a fatty acid
Causes chain to kink/bend
Not closely packed together
Liquid at room temperature
Oils not fats
What are healthier unsaturated or saturated triglycerides
Unsaturated
What is a phospholipid
Modified triglycerides where fatty acid has been replaced with a phosphate group
Inorganic phosphate ion formula
PO4 3-
How many of the fatty acids in triglyceride are replaced with a phosphate group
1
What is the structure of a phosphlipid
Non polar tail - fatty acid chains
-hydrophobic
Polar head - phosphate group
-hydrophilic
How do phospholipids interact with water
Form layer with hydrophilic phosphate heads in water and hydrophobic fatty acid tails facing inwards/away
Surfactants - surface active agents
Form bilayer
What is a sterol
Steroid alcohols - complex molecules based on a four carbon ring structure with polar hydrophilic OH group on the end
Name an example of a sterol
Cholesterol
Role of cholesterol in phospholipid bilayer
Positioned between phospholipids adding to stability of membrane and regulates fluidity
What are roles of lipids
-Membrane formation
-Hydrophobic barriers
-Hormone production
-Electrical insulation
-Waterproofing
-Thermal insulation
-Cushioning
-Buoyancy
How can you test for lipids
Emulsion test
1) sample mixed with ethanol
2) water added and then shaken
If white emulsion forms as a layer on top, lipid is present
What is an amino acid?
Monomer used to build polypeptides, therefore, proteins
What are proteins?
One or more polypeptides arranged as a complex macromolecule
What causes each amino acid to be different?
Different R-groups
What is a polypeptide?
Chains of three or more amino acids
What is the reaction between two amino acids?
Condensation reaction
Forming peptide bond
Removes water molecule
What enzyme catalyses the condensation reaction between amino acids?
Peptidyl transferase
What is the primary structure of proteins?
-Sequence which the amino acids join
-Peptide bonds
What is the secondary structure of proteins
O, H and N atoms interact
H bonds form
(can form alpha helix or beta pleated sheet)
What is the tertiary structure of proteins?
R-groups interact
Hydrophobic/hydrophilic interactions, hydrogen bonds, ionic bonds, disulfide bridges (strongest but only between R-groups containing sulfur)
(protein formed)
What is the quaternary structure of proteins?
Association of two or more proteins
Hydrophobic/hydrophilic interactions, hydrogen bonds, ionic bonds, disulfide bridges
What catalyses the hydrolysis reaction of polypeptides?
Protease
What are globular proteins?
Spherical, water-soluble, compact proteins
What makes globular proteins soluble in water?
Protein foods into tertiary structure so hydrophobic R groups are kept away from aqueous environment and hydrophilic R groups are on the outside of the protein
Give an example and the function of a globular protein
Insulin
Hormone involved in regulation of blood glucose conc
Transported in bloodstream so solubility necessary
What is a conjugated protein?
Globular proteins containing a prosthetic group
3D
What is a prosthetic group
Non-protein component of a conjugated protein
Give an example of a conjugated protein and it’s function
Haemoglobin
Red, oxygen-carrying pigment found in rbc
Quaternary protein made from 4 polypeptides (2 alpha, 2 beta subunits)
Each subunit contains 1 harem group
Haem group contains iron II which combine reversibly with oxygen
Catalase
Enzyme that catalyses the breakdown of hydrogen peroxide
Quaternary protein containing 4 haem prosthetic groups
What is a fibrous protein?
Long, insoluble, structural protein
Not 3D
Why are fibrous proteins insoluble
High proportion of hydrophobic R-groups
Repetitive amino acid sequence in primary structure
Give 3 examples of fibrous proteins
Keratin
Elastin
Collagen
Describe the function of keratin
Group of fibrous proteins
Present in hair, skin, nails
Large proportion of sulfur containing amino acids, leads to many strong disulphide bridges
Results in strong, inflexible, soluble materials
Describe the function of elastin
Fibrous protein
Found in elastic fibres
Present in wall of blood vessels and alveoli of lungs
Provides structure and flexibility
Quaternary protein
Describe the function of collagen
Fibrous protein
Connective tissue
Found in skin, tendons, ligaments, nervous system
Consists of 3 polypeptides wound together
Strong, flexible
Diagram of haemoglobin
How can quantitative methods be used when carrying out Benedict’s test
Colour produced in Benedict’s test depends on concentration of reducing sugar in sample
1) Filter placed in colorimeter
2) Colorimeter calibrated using distilled water
3) Benedict’s test carried out on known concentrations of glucose
4) Solutions filtered to remove precipitate
5) % transmission of each solution measured
6) Calibration curve plotted
7) Carry out Benedict’s test on unknown solution, filter it and find its % transmission
8) Use calibration curve to find its concentration
How do you carry out TLC to separate amino acids?
1) Draw a pencil line 2cm from the bottom of the chromatography plate
2) Sample placed in centre of pencil line
4) Plate placed into dish with solvent no more than 1cm deep
5) Plate left in solvent until it’s reached 2cm from top
6) Plate sprayed with ninhydrin which reacts with amino acids to form a purple brown colour
Formula for Rf value
Distance travelled by component / distance travelled by solvent
What is a nucleic acid
Large polymer formed from nucleotides
Contain C H O N S
What is a nucleotide
Monomer used to form nucleic acid
Consists of pentose monosaccharide, phosphate group, nitrogenous base
What is a nucleotide made up of?
Pentose monosaccharide (sugar)
Inorganic phosphate group (acidic, negatively charged)
Nitrogenous base
How do nucleotides bond
Phosphodiester bond between phosphate group on carbon 5’ and OH group on carbon 3’
What is the sugar-phosphate backbone?
Structural component of DNA consisting of alternating deoxyribose sugars and phosphate groups involved in carrying the genetic code.
What is DNA
Deoxyribonucleic acid
Molecule responsible for the storage of genetic information
How are phosphodiester bonds broken down?
Hydrolysis
How do you differentiate between ribose and deoxyribose
Deoxyribose had one fewer oxygen atoms
How do DNA bases bond
Complimentary base pairing
Adenine to thymine
Cytosine to guanine
(pyramid to purine)
What is pyrimidine?
Smaller bases, contain single carbon ring
CT
What is a purine?
Larger bases, contain double ring structures
AG
How many H bonds form between adenine and thymine
2
How many H bonds form between cytosine and guanine
3
What is the structure of DNA
-Two strands of polynucleotides coiled into the DNA double helix
-Two strands held together by hydrogen bonds between bases
-Each strand has a phosphate group (5’) and OH group (3’)
-Strands are antiparallel
Why is DNA said to be antiparallel
Two parallel polynucleotide strands run in opposite directions
What is RNA
Ribonucleic acid
Polynucleotide molecule involved in the copying and transfer of genetic information from DNA
Why is RNA necessary
DNA is too large to leave the nucleus
RNA is smaller so can leave the nucleus
Difference between DNA and RNA nucleotides
Thymine is replaced with uracil
Ribose sugar instead of deoxyribose sugar
What is DNA replication
Semi-conservative process of the production of identical copies of DNA molecules
How does semi-conservative DNA replication work
-DNA helix causes the double helix structure to unwind and separates the two stands
-Hydrogen bonds between complementary bases are broken
-Separates two strands
-Free DNA nucleotides pair with exposed complimentary base pairs
-Hydrogen bonds form between them
-New nucleotides bond to adjacent with phosphodiester bond
Why is it called semi conservative replication
Each new DNA molecule consists of one old strand and one new strand
What is the sense strand
Strand of DNA that runs 5’ to 3’ and contains genetic code for a protein
What is the anti-sense strand
Strand of DNA that runs 3’ to 5’ and is complementary to sense strand
Acts as a template strand during transcription
What enzymes are present in DNA replication
-DNA helicase: Enzyme that catalyses the unwinding and separating of strands
-DNA polymerase: Enzyme that catalyses the formation of phosphodiester bonds between adjacent nucleotide
What is a mutation
Change in genetic material that may affect the phenotype of an organism
What is a genetic code
Sequences of bases in DNA are the instructions for the sequences in amino acids in the production of proteins
What is DNA described as
-Triplet code: each codon (series of 3 bases) codes for an amino acid
-Degenerate: different codons can code for the same amino acid
-Universal
What are the two key stages of protein synthesis?
Transcription: Process of copying sections of DNA base sequence to produce mRNA
Translation: Process by which mRNA is decoded by tRNA into sequence of amino acids
Describe transcription
Sense strand (5’ to 3’) codes for protein
Antisense strand (3’ to 5’) acts as template
Section of DNA coding for gene unzipped by DNA helicase
Complimentary RNA lines up against DNA
Phosphodiester bond form by RNA polymerase forming mRNA
mRNA leaves through nuclear pore
DNA double helix reforms
Describe translation
mRNA binds to specific site on small subunit of ribosome at its start codon
tRNA with complimentary anticodon binds to mRNA start codon
tRNA carries complimentary amino acid
Repeats
Maximum of 2 tRNA can be bound at a time
First amino is transferred to second tRNA by formation of peptide bond catalysed by peptidyl transferase (rRNA)
Ribosome moves along mRNA releasing first tRNA, second becomes first
Repeated until stop codon reached, polypeptide released
Amino acid sequence forms primary structure
What enzyme catalyst is important in translation
Peptidyl transferase
What is ATP
Adenosine triphosphate is a nucleotide composed of a nitrogenous base (adenine), a pentose sugar and three phosphate groups
Universal energy currency for cells
What activities do cells require energy for?
Synthesis
Transport
Movement
Structure of ATP
How does ATP release energy
Small amount of energy needed to break bond between last phosphate group
Large amount if energy released when liberated phosphate undergoes other reactions
Net energy release
What type of reaction occurs when phosphate group is removed
Hydrolysis
Hydrolysis of ATP
Why is ATP not a good long term energy store?
Instability of phosphate bonds in ATP
Rapidly broken down and reformed
Hydrolysis of ATP diagram
What is ADP
Adenosine diphosphate is a nucleotide composed of a nitrogenous base (adenine), a pentose sugar and two phosphate groups
Properties of ATP
Small: moves into and out of cells easily
Water-soluble: energy-req process happen in aqueous environments
Contains bonds between phosphate with immediate energy: large enough for cellular reactions, not too large creating waste
Releases energy in small quantities: suitable to cellular needs, reduces waste
Easily regenerated: can be recharged with energy
What is the reverse reaction of hydrolysis of ATP
Phosphorylation, condensation reaction
What ion is required for hydrolysis of starch by enzyme
Cl
Most to least soluble out of ribose, amylopectin, amylose, glucose
Glucose
Ribose
Amylose
Amylopectin
