3 - Biological molecules Flashcards
what kind of bonding occurs between water molecules, and what feature does this give?
- hydrogen bonds
- cohesion and adhesion
What are the features of water and give an example of how it is useful.
- high specific heat capacity: provides a stable environment for aquatic organisms.
- high latent heat of evaporation: sweating cools down organisms.
- cohesion/adhesion: useful property in the transpiration stream in plants.
- good solvent: internal transport medium, medium for reactions.
- transparent: allows underwater photosynthesis.
- ice is less dense than water: provides a habitat for polar bears, it is an insulating layer for water underneath so aquatic organisms do not freeze.
- surface tension: habitat for pond skaters.
What elements make up carbohydrates?
C, H, O
What elements make up lipids?
C, H, O
What elements make up proteins?
C, H, O, N, S
what elements make up nucleic acids (DNA, RNA)?
C, H, O, N, P
α - glucose
OH groups: down down up down
β - glucose
OH groups: up down up down
What is a hexose monosaccharide?
A monosaccharide with six carbon atoms.
What is a pentose monosaccharide?
A monosaccharide with five carbon atoms.
function of glucose?
- good energy source in animals and plants.
- soluble: easy to transport.
what type of monosaccharide is glucose?
hexose
What is an example of a pentose sugar?
ribose
What bond is formed between monosaccharides, what type of reaction is this, and how does it form?
- glycosidic bonds
- condensation reaction
- H atom from one monosaccharide and OH group from another bond to form a water molecule.
How are bonds between monosaccharides?
- hydrolysis reaction
- addition of a water molecule to break the glycosidic bond.
Reactions of α-glucose with other monosaccharides to produce disaccharides?
glucose + glucose -> maltose
glucose + fructose -> sucrose
glucose + galactose -> lactose
What two polysaccharides make up starch?
- amylose
- amylopectin
amylose
- α-glucose
- 1,4 glycosidic bonds only
- helix structure
- hydrogen bonding further stabilises the molecule
- coiled structure: compact, good for storage
- insoluble
amylopectin
- α-glucose
- 1,4 and 1,6 glycosidic bonds.
- branched structure
- compact, good for storage
- branched structure allows enzymes to easily access the glycosidic bonds: glucose can be released quickly.
- insoluble
glycogen
- α-glucose
- energy store in animals.
- 1,4 and 1,6 glycosidic bonds.
- branched structure, more branching than amylopectin
- compact, good for storage (more compact than amylopectin)
- branched structure allows enzymes to easily access the glycosidic bonds: glucose can be released quickly. (faster than amylopectin).
- insoluble: (does not affect water potential of cell)
- can be broken down quickly
cellulose
- β - glucose
- 1, 4 glycosidic bonds only
- forms straight chains
- adjacent glucose units in alternate orientation.
- cellulose chains make hydrogen bonds with each other, forming macrofibrils.
- macrofibrils combine to form fibres.
- cellulose provides structural support in plant cells.
- insoluble.
test for reducing sugars
- bendict’s solution
- sample in test tube
- add equal vol of benedict’s solution
- water bath 5 mins
- blue to brick red if reducing sugar is present.
test for non-reducing sugars
- remains blue after benedict’s solution added.
- add dilute HCl
- add benedict’s solution
- blue to red.
Example of reducing sugars?
monosaccharides
- glucose
- fructose
- galactose
Example of non-reducing sugars
disaccharides
- sucrose
- maltose
- lactose
Why is dilute HCl added to non-reducing sugars before benedicts?
- hydrolyses the disaccharide into monosaccharides which are reducing sugars (positive result with benedict’s).
Test for starch?
- iodine test
- iodine dissolved in potassium iodide solution mixed with sample
- brown to purple/black (positive result)
what else can be used for the test for reducing sugars?
- reagent strips.
do lipids have polarity? what does this mean?
- they are non-polar molecules
- insoluble in water
What kind of molecules are lipids?
- macromolecules
- built from repeating units/monomers.
- complex molecules with a relatively large molecular mass.
What is triglyceride composed of? What bonds are between these?
- one glycerol
- 3 fatty acids
- ester bonds between them.
- insoluble, non polar
What group are fatty acids in?
- carboxylic acids
How do triglycerides form?
- 3 ester bonds form between the 1 glycerol molecule and 3 fatty acids.
- when they combine, 3 water molecules are produced (condensation reaction) since 3 ester bonds are formed
- the reaction that leads to the formation of the ester bonds is called esterification (condensation reaction).
saturated and unsaturated fatty acids?
saturated: only contain single C-C bonds
unsaturated: contain C=C double bonds.
How do unsaturated fatty acids affect tryglycerides?
- kink/bend in fatty acid
- fatty acids cannot pack as closely together.
- liquid at room temp.
How are triglycerides broken down into glycerol and fatty acids?
- 3 water molecules are supplied to break the 3 ester bonds between the glycerol and fatty acids.
- hydrolysis reaction.
phospholipid structure?
- modified triglycerides.
- 1 glycerol molecule
- 2 fatty acids
- 1 phosphate group.
- phosphate (group) head is hydrophilic (polar)
- fatty acid tails are hydrophobic (non-polar)
- this occurs due to length of molecule.
functions of triglycerides?
good long term energy storage because:
- long hydrocarbon fatty acid tails means that they contain a lot of chemical energy. A lot of energy is released when they are broken down.
- insoluble, doesn’t affect cell water potential.
function of phospholipids?
- found in cell membranes of all organisms (eukaryotes and prokaryotes).
- form a phospholipid bilayer due to hydrophilic phosphate heads, and hydrophobic fatty acids.
- centre of phospholipid bilayer is hydrophobic therefore water soluble substances cannot easily pass through (acts as a barrier to these type of substances).
function of cholesterol?
- They are positioned in between the phospholipids by binding to the hydrophobic tails.
- they add stability to cell surface membranes.
- they regulate the fluidity of cell surface membranes.
- more fluid at low temps, more rigid at high temps.
roles of lipids as a whole?
- membrane formation, hydrophobic barriers.
- hormone production
- waterproofing (e.g bird feathers).
- thermal insulation
- protects vital organs (cushioning)
- provides buoyancy for aquatic animals.
test for lipids?
- emulsion test
- mix sample with ethanol
- mix with water and shake
- white emulsion layer forms on top of solution (insoluble in water).
- indicates that a lipid is present.
- remains clear if test is negative.
Structure of an amino acid?
- attached to a carbon atom,
- amine group
- carboxyl group
- R group
What type of bonds form between amino acids, how are they formed, and what is formed when amino acids join together?
- peptide bond
- by a condensation reaction. A water molecule is formed for every peptide bond formed.
- OH from carboxyl group of one amino acid and H from amine group of another amino acid combine to form a water molecule. The C and N atom join together to form a peptide bond.
- polypeptides are formed (multiple amino acids).
- dipeptide formed (2 amino acids).
How are peptide bonds broken?
- water molecule is added to break the peptide bond.
- hydrolysis reaction
- amine and carboxyl groups are reformed.
What is the primary structure?
- The sequence of the amino acids in a polypeptide chain.
- different proteins have different amino acid sequences.
What is secondary structure? What bonds are present?
- oxygen, nitrogen, hydrogen of the amino acids in the chain interact.
- hydrogen bonds form within the amino acid chain.
- coil into alpha helix
- fold into beta pleated sheet.
What is tertiary structure? What bonds are present?
- the 3D folding of a protein into its final shape.
- R groups of amino acids get closer together.
- the 3D folding gives specialised characteristics and functions.
- hydrophobic and hydrophilic interaction
- hydrogen bonds
- ionic bonds
- disulfide bridges
What is quaternary structure? What bonds are present?
- found in proteins containing more than one polypeptide chain (subunits) (can be identical or different).
- same interactions occur as in tertiary structure, but the interactions are between the subunits.
- hydrophobic and hydrophilic interactions
- hydrogen bonds
- ionic bonds
- disulfide bridges.
Example of a protein with a quaternary structure?
- haemoglobin
- 4 subunits: 2 sets of 2 identical subunits.
- 2 alpha chains, 2 beta chains
- has haem groups containing iron.
test for proteins?
biuret test
- add 3cm^3 liquid sample into test tube.
- add equal volume of KOH solution and stir
- and few drops of copper sulfate solution and stir until blue
- turns blue to purple if protein is present.
- remains blue for negative test.
What are globular proteins?
- compact
- soluble in water
- they are proteins which are compact and soluble in water, due to the hydrophobic and hydrophilic interactions formed in the tertiary structure.
- roughly spherical in shape
How are globular proteins formed?
- when proteins fold in their tertiary structure.
- hydrophobic R groups kept away from aqueous environment.
- hydrophilic R group on outside of protein.
- hydrophobic and hydrophilic interactions make the proteins soluble in water.
What are conjugated proteins?
- they are globular proteins that contain a non-protein component (prosthetic group).
- opposite is called simple proteins.
Example of a conjugated protein?
haemoglobin
- quaternary protein (4 subunits, 2 alpha, 2 beta)
- each subunit contains a prosthetic haem group.
- haem groups contain iron II ions, which oxygen binds to and are released from.
Example of an enzyme conjugated protein?
- catalase
- quaternary protein
- contains 4 prosthetic haem groups.
- iron II ions in the haem groups allows catalase to interact with hydrogen peroxide and speed up its breakdown.
- catalase prevents the accumulation of hydrogen peroxide (damaging to cells if accumulate).
Example of a globular protein?
- insulin
- hormone involved in regulation of blood glucose concentration.
- solubility is important as hormones are transported in the bloodstream.
- precise shape (to match specific receptors on cell surface membranes).
- 2 polypeptide chains held by disulfide bridges.
What are fibrous proteins?
- long, insoluble proteins.
- insoluble due to high proportion of amino acids with hydrophobic R-groups in the primary structure.
- fibrous proteins tend to make long, strong molecules which are not folded into 3D shapes like globular proteins.
Keratin
- fibrous protein
- found in hair, skin, nails.
- can be flexible like in skin. or hard and tough like in nails.
Elastin
- fibrous protein
- found in elastic fibres (in walls of blood vessels and alveoli of lungs).
- gives flexibility to expand, and return to normal size.
Collagen
- fibrous protein
- connective tissue found in skin, bone, muscle.
- very strong molecule
- minerals can bind to the protein to increase rigidity.
Examples of inorganic CATIONS involved in biological processes
Ca2+ Na+ K+ H+ NH4+
Examples of inorganic ANIONS involved in biological processes
NO3- HCO3- Cl- PO43- OH-
formula for retention value?
Rf = distance moved by solute / distance moved by solvent.
What does a nucleotide consist of?
- pentose sugar
- phosphate group
- nitrogenous base
What bonds are between nucleotides and how are they formed? What is a bunch of nucleotides joined together called?
How are these bonds broken?
- phosphodiester bonds
- condensation reaction
- polynucleotide
- bonds are broken by hydrolysis (water molecule is used to break the bonds) and release individual nucleotides.
What are the 4 bases and which ones pair up? Also, which ones are purines and which ones are pyrimidines?
A - T, G - C
A and G are purines (bigger bases)
T and C are pyrimidines (smaller bases)
between A and T, 2 hydrogen bonds form
between G and C, 3 hydrogen bonds form.
what is the pentose sugar in DNA nucleotides?
deoxyribose
what is the pentose sugar in RNA nucleotides?
ribose
What bonds are formed between the bases?
hydrogen bonds.
Differences in DNA nucleotides and RNA nucleotides?
in RNA nucleotides:
- ribose (pentose sugar) instead of deoxyribose
- Uracil (U) instead of thymine (T). U replaces T base.
Characteristics of DNA strands?
- antiparallel strands
- two strands are coiled into a DNA double helix
- Hydrogen bonds occur between complementary bases on two antiparallel polynucleotides, leading to the formation of a DNA molecule.
- complementary base pairing.
What are DNA backbones composed of?
deoxyribose-phosphate molecules.
DNA extraction steps?
- grind sample (break down cell walls)
- mix with detergent (breaks down cell membrane)
- add salt (breaks hydrogen bonds between DNA and water molecules)
- add protease enzyme
- add layer of alcohol (causes DNA to precipitate out of solution)
- DNA can be seen as white strands between sample and alcohol layer.
steps of semi-conservative replication?
- DNA helicase unzips the DNA double strand by breaking the H bonds between complementary bases.
- Free nucleotides are attracted to exposed complementary bases and form H bonds.
- DNA polymerase joins the new lines of nucleotides together.
- Nucleotides are joined together by phosphodiester bonds.
- Two identical DNA molecules are formed.
- Each molecule is semi-conservative: composed of one old and one new strand.
Which direction does DNA polymerase travel?
3’ to 5’
mutation?
- sequences of bases are not always matched correctly.
- incorrect sequence in the newly copied strand
- these errors happen randomly and spontaneously and are known as mutations.
Nature of genetic code?
- triplet code
- degenerate
- non-overlapping
- universal
triplet nature of genetic code?
- the code in the base sequences is a triplet code
- sequence of three bases, codon.
- each codon codes for an amino acid.
degenerate nature of genetic code?
- there are several different codons that can code for the same amino acid.
- 64 different codons possible.
- reduces effects of mutations to base sequence.
non-overlapping nature of genetic code?
each base can only be part of one codon.
universal nature of genetic code?
the same sequences of 3 bases (codons) code for the same amino acid in all organisms.
how does a gene determine protein primary structure?
- the gene determines the sequence of amino acids produced to form a polypeptide chain, which is the primary structure of a protein.
What are the stages of protein synthesis?
- transcription
- translation
stages of transcription:
- DNA helicase unzips the DNA double strand and exposes the nucleotide bases.
- one strand acts as a template strand.
- free RNA nucleotides pair up with complementary bases on the template strand.
- RNA polymerase join the RNA nucleotides together to form mRNA.
- the mRNA formed is almost identical to the sense strand of the DNA.
stages of translation:
- mRNA leaves the nucleus via nuclear pores and travels to the ribosomes.
- the ribosome attaches to the start codon of mRNA.
- bases are read in triplets (codons).
- a specific tRNA with complementary anticodons to the mRNA codons pair pair with the mRNA.
- The tRNA molecule has a specific amino acid attached.
- The ribosome moves along the mRNA and the process is repeated.
- Amino acids are joined together by an enzyme, forming peptide bonds. A chain of amino acids is produced.
Structure of ATP?
- 3 phosphate groups
- pentose sugar (ribose)
- nitrogenous base (adenine)
- phosphorylated nucleotide
How does ATP release energy?
ATP + H2O -> ADP + Pi + energy
Pi is inorganic phosphate
- Adenosine triphosphate
- Adenosine diphosphate
- hydrolysis reaction
Structure of ADP?
- 2 phosphate groups
- pentose sugar (ribose)
- nitrogenous base (adenine)
- phosphorylated nucleotide
Why is ATP such a good source of energy?
- single step reaction.
- measurable quantities of energy released.
- not stored in large quantities therefore ADP is easily reformed.
