Biological Molecules Flashcards
What is an electrolyte?
An ion in solution
What are 2 things calcium ions are necessary for?
Nerve impulse transmission
Muscle Contraction
What are the 2 things sodium ions are necessary for?
Nerve impulse transmission
Kidney Function
What are the 2 things potassium ions are necessary for?
Nerve impulse transmission
Stomatal opening
What are the 2 things hydrogen ions are necessary for?
Catalysis of reactions
pH determination
What is the key thing ammonium ions are necessary for?
Production of nitrate ions by bacteria
What is the key thing nitrate ions are needed for?
Nitrogen supply to plants for amino acid and protein formation
What is the key thing hydrogen carbonate ions are needed for?
Blood pH regulation
What is the key thing chloride ions are needed for?
Balance positive charge of sodium and potassium ions within cells
What are the 3 things phosphate ions are needed for?
Cell membrane formation
Nucleic acid and ATP formation
Bone formation
What 2 things are hydroxyl ions needed for?
Catalysis of reactions
pH determination
What elements are present in carbohydrates?
Carbon, Hydrogen, Oxygen
What elements are present in lipids?
Carbon, Hydrogen, Oxygen
What elements are present in proteins?
Carbon, Hydrogen, Oxygen, Nitrogen and Sulfur
What elements are present in nucleic acids?
Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorus
What are polymers?
Long repeating chains made up of monomers
What does polar mean?
Regions of positivity and regions of negativity
What are 3 unusual properties of water?
High boiling point
Cohesive
Solid less dense than liquid
What is capillary action?
The process of water rising up tubes against the force of gravity
What are the two different types of glucose?
Alpha and Beta
What bond is formed when two glucose molecules join together?
1,4 Glycosidic Bond
What type of reaction is it when two glucose molecules join together? Why?
Condensation reaction, water molecule released
How do you create maltose?
Alpha Glucose + Alpha Glucose
How do you create sucrose?
Glucose + Fructose
How do you create lactose?
Glucose + Galactose
What are pentose monosaccharides?
Sugars that contain 5 carbon atoms
What are hexomonosaccharides? Give 3 examples
Sugars with 6 carbons, glucose, galactose and fructose
What are hexomonosaccharides? Give 3 examples
Sugars with 6 carbons, glucose, galactose and fructose
What bonds are in amylose, what shape does the lead to?
1,4 glycosidic
Helix shape
What are the bonds in amylopectin, what shape does this lead to?
1,4 and 1,6 glycosidic
Branched monomer
What is the equivalent of starch in animals and fungi?
Glycogen
Does amylose or amylopectin release glucose faster, why?
Amylopectin, branching leads to more exposed bonds and so is broken down more easily and quickly
Describe solubility of amylopectin and glycogen
Insoluble
How is glucose released for respiration?
Hydrolysis reactions, breakdown using water into constituent monomers
How does cellulose form?
When alternate beta glucose molecules flip 180 so that 1-4 glycosidic bonds can form
What is the shape of cellulose?
Straight chain molecule
List process of building up from cellulose to cell walls
Cellulose, Hydrogen bonds form, Microfibrils Macrofibrils Cell walls
How is cellulose important to humans?
Provides roughage as part of diet as it is hard to break down
What is the Benedict’s test for and what is it?
Reducing sugars, copper sulfate
Explain in 3 steps the Benedict’s reagent test
1) Place sample in boiling tube, if not liquid grind and add water
2) Add equal volume of Benedict’s reagent
3) Heat mixture gently in boiling water Bath for 5 minutes
Explain the chemical reaction occurring in a Benedict’s test
Cu 2+ ions react with the reducing sugars, this adds electrons. Cu2+ is reduced to Cu+ forming a red precipitate
What is the positive test for the Benedict’s reagent?
Brick-Red precipitate
Why does the colour of the solution vary on volume of Benedict’s solution?
The more reducing sugar present, the more precipitate will be formed because less Cu2+ ions are left in solution, so creating a deeper red colour.
What are 3 main colours seen during the Benedict’s test? What do they indicate?
Green- low concentration of reducing sugar
Yellow- medium concentration of reducing sugar
Red- high concentration of reducing sugar
Is the Benedict’s test qualitative or quantitative?
Qualitative
What is the extra step required in the Benedict’s test for non-reducing sugars?
The non-reducing sugar is boiled in hydrochloride acid to hydrolyse into two constituent monomers which are reducing sugars
What is the colour change(from and to) in the iodine test?
Yellow/Brown to purple/black
What does the iodine test test for?
Starch
Explain the method for the iodine test for starch
Iodine solution(potassium iodide) added to sample Wait for colour change
What are reagent strips used to test for? Why is it beneficial?
Reducing sugars, use of a colour coded chart the concentration of sugar can be determined
What is a colorimeter?
A piece of equipment used to quantitatively measure absorbance, transmission or light by a coloured solution
Discuss the polarity of lipids, explain why it is this way
Non-polar molecules
Elections in outer orbitals distributed more evenly
No positive or negative areas so non- polar
What type of molecule is a lipid? Explain what this term means
Macromolecules
Large complex molecule built from monomers
What is a triglyceride made of?
One glycerol molecule, 3 fatty acids
What group of molecules do fatty acids belong to? Why?
Carboxylic acids. Have a -COOH group with a hydrocarbon chain
What is an esterification reaction?
Hydroxyl groups on glycerol and fatty acids interact.
3 water molecules are produced
Ester bonds for between glycerol and fatty acid
How do you break a triglyceride down?
Hydrolysis reaction using 3 water molecules
What is a saturated fatty acid?
Fatty acid chains which contain no double bonds present between carbon atoms, all carbons are taken up with max number of hydrogens
What is an unsaturated fatty acid?
A fatty acid with double bonds between some of the carbon atoms
What is the result of an unsaturated fatty acid?
Causes kinks in the molecule
Cannot pack so closely
Liquid at room temp rather than solid
What lipid do plants contain?
Unsaturated triglycerides
What is a phospholipid made from?
2 fatty acids, glycerol and a phosphate group
Explain the hydrophilic/hydrophobic nature of a phospholipid bilayer
Due to its length the phospholipid bilayer has a hydrophobic tail and a hydrophilic head
Why is a phospholipid called a surfactant?
Forms a layer on the surface of the water with phosphate heads in the water and fatty acid tails sticking out of the water
What is the structure of a sterol?
4 ring carbons structure with a hydroxyl group on the end
How do sterols have a dual hydrophobic/ hydrophilic nature?
Hydroxyl group is polar so hydrophilic, rest of molecule is hydrophobic
What type of molecule is cholesterol? What is its function?
Sterol. Adds stability to membranes and regulates their fluidity
What are the 4 biological roles of lipids?
Membrane formation and creation of hydrophobic barriers
Hormone production
Electrical insulation necessary for impulse transmission
Waterproofing
Where are lipids stored within the body?
Under the skin and around vital organs
What function do lipids provide in the skin and vital organs?
Thermal insulation
Cushioning to protect organs
Buoyancy
Explain the method for the emulsion test
Sample mixed with ethanol
Water added and shaken
White emulsion forms a layer on top- lipid present
What is a peptide?
A polymer made up from amino acid molecules
How many amino acids are found in cells?
20 different amino acids
How do two proteins synthesise to form a dipeptide?
Amine and carboxylic acid groups connected to the central carbon atoms react. The hydroxyl in the carboxylic acid group reacts with hydrogen in amine group to form a peptide bond
What catalyses the reaction of a polypeptide being formed?
Peptidyl transferase
What is the primary structure of the protein?
Sequence in which the amino acids are joined. Only involves peptide bonds.
What is secondary structure of the amino acid?
Hydrogen bonds forming within the amino acid chain, pulling into a specific shape.
What are the two shapes that can form during secondary proteins? What does this mean?
Alpha helix- hydrogen bonds pull into a coil shape
Beta pleated sheet- polypeptide chains lying parallel to each other with hydrogen bonds between them
What is the tertiary structure of a protein?
Folding of a protein into its final shape, secondary structure pulls R groups close enough that they can interact.
What are hydrophobic hydrophilic interactions?
Weak interactions between polar and non-polar R groups
What are ionic bonds?
Bonds formed between oppositely charged R groups
What are disulfide bridges?
Covalent bonds that form between R groups that contain sulfur atoms
How many amino acids are common in the human body?
20
How do two peptides join together?
Amine and carboxylic acid group connected to central atoms react. Hydroxyl groups of one amino acid reacts with a hydrogen in the amine group.
Why type of reaction is it when two peptides react?
Condensation
What enzyme catalyses reaction of formation of polypeptide chains?
Peptidyl transferase
What is primary protein structure?
The sequence in which the amino acids are joined
What bonds are present in the protein structure?
Peptide bonds
What is the secondary protein structure?
The basing repeating structure of amino acids interact and hydrogen bonds are formed within the amino acid chain
What two shapes are formed from secondary protein structure? Explain the shapes.
Alpha Helix- coil shape of amino acids with hydrogen bonds between the helix
Beta Pleated Sheet- Polypeptide chains lying parallel to each other with hydrogen bonds between
What is the tertiary structure?
The folding of protein into its final shape. Coiling and folding in secondary brings R groups close enough to interact, holding sections together.
What are hydrophobic and hydrophilic interactions?
Weak interactions between polar and non-polar R groups
What are ionic bonds?
Bonds between oppositely charged R groups
What are disulfide bridges?
Covalent bonds between R groups that contain sulfur atoms
What is the quaternary structure?
Interaction between 1 or more polypeptide chains
How are peptides broken down?
Protease enzyme breaks down the peptide into its constituent amino acids
Give 3 features of a globular protein
Compact
Water Soluble
Spherical
When do globular proteins form?
Hydrophobic R groups are moved into the middle to be kept around the aqueous environment. So hydrophilic R groups on the outside
Why does insulin have to be globular?
Hormone involved with the regulation of blood glucose concentration.
Hormones transported in blood stream so needs to be soluble
Hormones have to fit specific receptors on cell surface membranes so need to have precise shape
What are conjugated proteins?
Globular proteins with a prosthetic group
What is a prosthetic group?
A non-protein part of a protein
Give 4 examples of molecules that make up prosthetic groups
Lipids
Carbohydrates
Metal ions
Vitamins
Explain the structure of haemoglobin
Quaternary protein made up of 4 polypeptide chains, two alpha and two beta subunits, 4 haem groups
What does haem contain, and what is its role?
Fe II, allows it to combine reversibly with an oxygen molecule
What prosthetic group does catalase contain? What does this allow for?
Fe II ions, allow catalase to interact with hydrogen peroxide and speed up its breakdown.
What are fibrous proteins made from?
Long insoluble molecules
Give 3 examples of fibrous proteins
Keratin, Elastin and Collagen
Why do fibrous proteins form?
High proportion of amino acids with hydrophobic R groups, and a limited range of amino acids with small R groups
What is the structure of a fibrous protein?
Strong, long molecules which do not fold into 3D molcules
Where is keratin found?
Hair, skin and nails
What characteristics does keratin have? Why?
Strong, Inflexible and Insoluble
Due to high proportion of disulfide bridges which decrease flexibility
What is elastin made from?
A quaternary protein made of tropoelastin
Where are elastic fibres found? Why?
Walls of blood vessels and alveoli
Give structures flexibility
What is collagen and where is it found?
Fibrous protein that is a connective tissue found in skin, tendons, ligaments and the nervous system.
Describe the structure of collagen
3 polypeptide chains wound in a long strong rope-like structure
What are the 2 roles of nucleic acids?
Storage and transfer of genetic material
Synthesis of polypeptides
What 3 components make up a nucleotide?
A pentose monosaccharide
A phosphate group
A nitrogenous base
Explain how two nucleotides join together
Condensation reaction
Phosphate group on 5th carbon forms a covalent bond (phosphodiester) with hydroxyl group on 3rd carbon of the pentose sugar on adjacent nucleotide
What type of bond is formed when two nucleotides join together?
Phosphodiester
What structure is a polynucleotide said to have?
A long strong sugar phosphate backbone with a base attached to each sugar
What are pyrimidines? Give 2 examples
Small bases which contain one single carbon ring
Thymine and Cytosine
What are purines? Give 2 examples
Large bases which contain a double carbon ring structure
Adenine and Guanine
What does it mean for DNA to be ‘anti parallel’?
Each strand has a phosphate group at one end and hydroxyl group at the other. The two strands run in opposite direction.
In complementary base pairing, describe which pairs join and how many hydrogen bonds they form
Adenine and Thymine- 2 hydrogen bonds
Cytosine and Guanine 3 hydrogen bonds
How do the two strands of DNA remain parallel?
As a purine always binds to a pyrimidine, so there is a constant distance
What are 2 structural differences of RNA to DNA?
Ribose rather than deoxyribose
Uracil rather than thymine
Explain the 4 steps in semi conservative replication
1) DNA helicase causes two strands of DNA to separate
2) Free nucleotides activated are attracted to complementary bases
3) Hydrogen bonds formed between nucleotides and complementary bases
4) DNA polymerase catalyses formation of phosphodiester bonds between adjacent nucleotides.
What is semi conservative replication?
Two new molecules of DNA produced from one strand. Each one consists of one old strand of DNA and one new strand.
What is the role of DNA helicase?
Enzyme that travels along DNA backbone, breaking hydrogen bonds between complementary base pairs. ‘Unzipping’ them
What is the role of DNA polymerase?
Catalyses the formation of phosphodiester bonds between nucleotides
What is the genetic code?
The sequences of bases in DNA are the ‘instructions’ for the sequences of amino acids in the production of proteins.
What is a codon?
A sequence of 3 bases coding for 1 amino acid
What is a gene?
A section of DNA that contains the complete sequence of bases to code or an entire protein
What is the most common start protein?
Methionine
Why is genetic code said to be ‘degenerate’?
Many amino acids can be coded for by more than one codon
Where does protein synthesis occur?
Ribosomes in the cytoplasm
What is the process of ‘transcription’?
The base sequence of genes being copied and transported on to smaller molecules of RNA so they can move out of the nucelus.
What is the sense strand?
Strand of DNA that contains the code for the protein to be synthesised
Runs from 5’ to 3’
What is the anti-sense strand?
Complementary copy to the sense strand
Acts as a template strand so complementary RNA strand formed has the same sequence as the sense strand
Explain the process of transcription
1) Section of DNA unzips via DNA helicase
2) Free RNA nucleotides pair with complementary bases on anti-sense strand
3) Phosphodiester bonds are formed by RNA polymerase
4) Stops at the end of the gene and mRNA is formed
5) mRNA detaches from DNA template and leaves via nuclear pore
What are the two roles of rRNA?
Maintaining structural stability
Biochemical role in catalysing reaction
What is the process of translation?
mRNA binding to a specific site on a small subunit of ribosome
Ribosome holds mRNA in position whilst it is decoded into sequence of amino acids
What is an anti codon?
A sequences of 3 bases on the tRNA that is complementary to specific codon on mRNA
Where is energy supplied from for translation?
Hydrolysis of ATP
Describe 5 step process of translation
1) mRNA binds to ribosome
2) tRNA with specific anticodon and amino acid binds to mRNA
3) another tRNA molecule binds to next complementary codon
4) 1st amino acid binds to 2nd amino acid via peptide bond and peptidyl transferase
5) tRNA leaves mRNA moves along
What are the 3 main types of cell activity that require energy?
Synthesis
Transport
Movement
What is ATP made up of?
Adenine, Ribose, 3 phosphate groups
What is the process of phosphorylation?
Reattaching a phosphate group to a molecule of ADP
Explain 5 key properties of ATP
Small Water Soluble Contains bonds with phosphates with intermediate energy Releases energy in small quantities Easily regenerated
How is energy released by cells?
ATP converted to ADP, the phosphate ion releases energy
