Biological Molecules EFi Flashcards
What is the active site?
An indent/cleft on the surface of the molecule.
Why is a enzyme highly specific?
Only corresponding molecule will fit
How do enzymes work?
Lower activation energy of a reaction making it more efficient. Also controls reaction and ensures doesn’t occur spontaneously. Does not produce unwanted by-products.
Where can enzyme action occur?
Intracellular (in cells) or Extracellular
Give an example of where Extracellular Enzyme action may occur.
Blood
What are enzymes?
Biological catalysts that speed up metabolic reactions in living organisms
What is the equation for Adenosine Triphosphate being broken down into Adenosine Diphosphate?
ATP → ADP + Pi (Phosphate)
What type of reaction is ATP being converted into ADP?
Exergonic (release of energy), Hydrolysis
What enzyme is used to convert ATP into ADP?
ATP Hydrolase. Catabolic - Hydrolysis Reaction
What type of reaction is ADP being phosphorylated into ATP?
Endogonic (absorption of energy), Condensation
What enzyme is used to phosphorylate ADP into ATP?
ATP Synthase. Anabolic - Condensation Reaction
Why is ATP used for energy?
Small molecule so easily transported across membranes
Allows energy to be released in small usable, controlled amounts where required
What is ATP?
Adenosine Triphosphate is an energy containing molecule providing energy for ALL metabolic reactions in ALL organisms
What is ATP a product of? (AS Level)
Respiration
Where is Adenosine Triphosphate formed?
Mitochondrion/Mitochondria
What is the polypeptide primary structure?
The order of the amino acids
What is the polypeptide secondary structure?
β-pleats - folded
α-Helix - coiled
What is the polypeptide tertiary structure?
How the secondary structure is subsequently folded due to variable chemical properties of the R group
What is the quaternary structure of a polypeptide?
How multiple polypeptide chains fit together to form a complex protein. Might include a prosthetic group such as Iron (II) (Fe2+) in Haemoglobin
What are the 3 bond types in polypeptides?
Increasing bond strength as going down:
Hydrogen Bonds
Ionic Bonds
Disulphide Bridges
How many amino acids cannot be produced by our bodies and have to come from our diet?
9
How many amino acids are there?
20 (22 including the 2 STOP Amino Acids)
What are proteins made from?
Amino Acids
Why do phospholipids make up membranes?
Phosphate is polar and soluble in water (Hydrophilic) - Acts as heads in water
Fatty Acid Chains are non-polar and hydrophobic - tails out of the water
What do phospholipids make up?
Membranes, e.g. Phospholipid Bi-layer
What is the difference between a saturated and unsaturated fatty acid?
Saturated has no C=C double bond, so is carrying as much hydrogen as possible. Straight Chain
Unsaturated has C=C double bonds which can create a bend in the chain so pack less closely. More fluid @ room temp. Not carrying full hydrogen
What are the properties of a triglyceride molecule?
Insoluble in water
Non-polar
Large
What type of bond is formed b/w a Glycerol and a Fatty Acid?
Ester Bond
What is a Triglyceride?
A glycerol bonded w/ 3 Fatty Acids
What are the functions of lipids?
Insulation Long-term energy storage Protection Steroid Hormone Synthesis Waterproofing Source of Energy
How is cellulose suited to its function?
Made of β-glucose chains - long, straight, unbranched chains
Chains run parallel to one another and are cross-linked by hydrogen bonds which add collective strength
These are grouped to form microfibrils which are grouped to form fibres which provides even more strength
What happens between cellulose chains?
Hydrogen bonds are formed between adjacent cellulose chains. The sheer overall number makes it a lot stronger
Which is found in animal cells? Starch or Glycogen
Glycogen
It is found in animals and bacteria
What type of reaction occurs when starch is formed?
Condensation
Why is starch suited to be a store of energy? (Same for glycogen)
Insoluble - doesn’t affect water potential
Large and insoluble - doesn’t diffuse out of cells
Compact - can be stored in a small place
Branched form has many ends which can be acted on by enzymes to quickly release glucose monomers
What is starch made from?
α-Glucose
What is cellulose made from?
β-Glucose
What is formed when Glucose is bonded with Galactose?
Lactose
What is formed when glucose is bonded with Fructose?
Sucrose
What is formed when two glucose are bonded together?
Maltose
What enzyme is used to hydrolyse Lactose?
Lactase
What enzyme is used to hydrolyse Sucrose?
Sucrase
What enzyme is used to hydrolyse Maltose?
Maltase
What happens when you heat Sucrose with dilute acid?
It is broken down into α-Glucose and Fructose
What is Benedict’s Solution?
Alkaline solution of Copper (II) Sulphate
What happens when Benedict’s Solution is mixed and heated with a reducing sugar?
Cu2+ ions in the solution are reduced to Cu+ ions
What happens when a Reducing Sugar is mixed and heated with Benedict’s Solution? (colour/ppt)
Orange Precipitate (ppt) is formed
What are reducing sugars?
ALL Monosaccharides
&
SOME Disaccharides
What is a reducing sugar?
Any sugar that is capable of acting as a reducing agent because it has a free aldehyde or ketone group
Give an example of a polysaccharide
Cellulose
Starch
Glycogen
What is the name of the bond formed between monosaccharides?
Glycosidic Bond
What is the term for two monosaccharides bonded together?
Disaccharide (Di=2)
What is the general formula for ALL Monosaccharides?
(CH2O)n (n= number of carbons)
What is the term for a single monomer?
Monosaccharide
What is catabolism?
Breaking larger molecules into smaller units by Hydrolysis Reaction
Polymer → Monomer
What is Anabolism?
Synthesis of complex molecules in living organisms from simpler ones together with strong energy
Monomer → Polymer
What is the collective term for all chemical processes that occur in living organisms?
Metabolism
Give an example of a Hydrolysis Reaction
Nucleic Acids → Nucleotides
Carbohydrates → Monosaccharides
Lipids → Fatty Acids
→ Glycerol
Proteins → Amino AcidsGive an example of a Condensation Reaction
Nucleotides → Polynucleotides (Nucleic Acids)
Monosaccharide → Polysaccharide (Carbohydrate)
Fatty Acids → Lipids
Glycerol → Lipids
Amino Acids → Polypeptides (Proteins)
What is the name for a type of reaction that USES water to break bonds?
Hydrolysis
Hydro = Water
Lysis = Splitting
What is the name for a type of reaction that PRODUCES water?
Condensation Reaction
What is the name of the process in which a monomer becomes a polymer?
Polymerisation
Name a Carbohydrate Monomer (Monosaccharide)
Glucose
Galactose
Fructose
What are the properties of Ionic Bonding?
Stronger than Hydrogen and Covalent. (Chemistry) Donation of electron Weaker than Covalent bonds (Biology) e.g. Na+ + Cl- → NaCl
What do Ionic Bonds form between?
A metal and a non-metal
What are the properties of Covalent Bonding?
Strong. The main bonds holding atoms together in organic molecules.
Can only be broken with a lot of energy and presence/action of enzyme
Atoms share a pair of electrons in their outer shells
What do Covalent Bonds form between?
Non-metals only
Summarise Hydrogen Bonding
Weak electrostatic bond formed between two polar molecules at the negatively charged and positively charged area on the other molecule
What are the properties of Hydrogen Bonding?
Very Weak
Gives Water Surface Tension
Formed Between Atom with a slight positive and slight negative charge
Form spontaneously at temperatures found in living cells so don’t require enzymes
Name a Non-Organic (Biological) Compound
Iron - Haemoglobin (Hb)
Water
Minerals
Name an Organic (Biological) Compound
Carbohydrates Proteins Nucleic Acids - Adenosine Triphosphate (ATP), Deoxyribonucleic Acid (DNA) Lipids - Fats Vitamins All Have Carbon-Carbon Bonds
Why is water important for metabolism?
Water is used to break down many complex molecules by hydrolysis, e.g. proteins to amino acids. Water is also produced in condensation reaction
Chemical reactions take place in an aqueous medium
Water is a major raw material in photosynthesis
Why is water important as a solvent?
Water readily dissolves other substances:
Gases such as Oxygen and Carbon Dioxide
Waste such as Ammonia and Urea
Inorganic ions and small hydrophilic molecules such as amino acids, monosaccharides and ATP
Enzymes, whose reactions take place in solution
What are other important features of water?
Its evaporation cools organisms and allows them to control their temperature
It is not easily compressed and therefore provides support, for example the hydrostatic skeleton of animals such as the earthworm and turgor pressure in herbaceous plants
It is transparent and therefore aquatic plants can photosynthesise and also light rays can penetrate the jelly-like fluid that fills the eye and so reaches the retina
What percentage of a mammal is typically water?
65%
What percentage of a jellyfish is water?
98%
What is the term for when water is pulled back to the body of water rather than escaping from it?
Surface Tension
This means that the water surface acts like a skin and is strong enough to support small organisms such as Pond Skaters
Why does water have a large cohesive force?
Due to its Hydrogen Bonding. These allow water to be pulled up through a tube such as a Xylem Vessel
What is the term for the tendency of molecules to stick together?
Cohesion
What is the Latent Heat of Vaporisation of Water?
The energy required for to evaporate 1g of water.
Evaporation of water such as sweat in mammals is therefore a very effective means of cooling because body heat is used to evaporate the water
Why does water have a high specific heat capacity? (Biological Explanation)
Water molecules stick together due to hydrogen bonding
Without Hydrogen bonding, water would be a gas at common temperatures on Earth
Therefore it takes more energy to heat a given mass of water
Water therefore acts as a buffer against sudden temperature variations, making the aquatic environment a temperature-stable one
Why is water described as ‘Dipolar’?
Oxygen atom is slightly negative
Hydrogen atoms are slightly positive
Water has both positive and negative poles and is therefore described as Dipolar
Name some of the energy-requiring uses of Adenosine Triphosphate in Cells?
Metabolic Processes Movement Active Transport Secretion Activation of Molecules
What are the 3 ways in which ATP is synthesised from ADP? Simplified Terms
1) Phosphorylation
2) Oxidative Phosphorylation
3) Substrate-level Phosphorylation
What are the 3 ways in which the Synthesis of ATP from ADP occurs?
1) In Chlorophyll-containing plant cells during Photosynthesis (Photophosphorylation)
2) In plant and animal cells during respiration (Oxidative Phosphorylation)
3) In plant and animal cells when phosphate groups are transferred from donor molecules to ADP (Substrate-level Phosphorylation)
What are the 5 stages of Semi-conservative Replication?
1) DNA Helicase breaks the hydrogen bonds linking base pairs
2) Double helix separates as a result into 2 strands and unwinds
3) Each exposed polynucleotide chain acts as a template to which complementary free nucleotides bind by specific base pairing
4) Nucleotides are joined together in a condensation reaction by the enzyme DNA polymerase to form the ‘missing’ polynucleotide strand on each of the two strands of DNA
5) Each of the new DNA molecules contains one of the original DNA strands, that is, half the original DNA has been saved and built into each of the new DNA molecules
What are the 4 main requirements for Semi-Conservative Replication to Occur?
1) The 4 types of nucleotides, each with their bases of A, C, G or T must be present
2) Both strands of the DNA molecule act as a template for the attachment of these nucleotides
3) The enzyme DNA Polymerase
4) Source of Chemical Energy is required to drive the process
What are the 2 main stages of cell division?
1) Nuclear Division - Process by which the nucleus divides. Two main types: Mitosis and Meiosis
2) Cytokinesis - Follows Nuclear Division and is the process by which the whole cell divides
How is the DNA molecule adapted to carry out its functions?
Very stable structure which normally passes from generation to generation without change. Only rarely does it mutate
Two separate strands joined only with Hydrogen Bonds which allow them to separate in DNA replication
Extremely large molecule and therefore carries immense amount of genetic information
By having base pairs within the helical cylinder of the deoxyribose-phosphate backbone, the genetic information is to some extent protected from being corrupted by outside chemical and physical factors
Base pairing leads to DNA being able to replicate and to transfer information as mRNA
Why is DNA a stable molecule?
Phosphodiester backbone protects the more chemically reactive organic bases inside double helix
Hydrogen bonds link the organic base pairs forming bridges (rungs) between the phosphodiester uprights.
As there are more Hydrogen bonds between Cytosine and Guanine (C and G), the higher the proportion of C-G pairings, the more stable the DNA molecule
How many hydrogen bonds between Cytosine and Guanine?
3
How many Hydrogen bonds between Adenine and Thymine?
2
What different types of RNA is there?
mRNA (messenger) regulatory RNA μRNA (micro) rRNA (ribosomal) tRNA (transfer) mtRNA (mitochondrial)
What are Nucleotides held together by?
Phosphodiester Linkage/Bond
What nucleotides are present in RNA?
Adenine and Uracil
Cytosine and Guanine
Which nucleotides are present in DNA?
Adenine and Thymine
Cytosine and Guanine
Which carbon is the Phosphate group attached to?
Carbon No. 5
Which Carbon is the Nitrogenous base attached to?
Carbon No. 1
What is the sugar present in RNA?
Ribose (RiboNucleic Acid)
What is the sugar present in DNA?
Deoxyribose (DeoxyriboNucleic Acid)
What are Nucleic Acids?
Long chains created by the joining of monomers, which are the nucleotides
Nucleotides are building blocks of nucleic acids
Small molecules composed of 3 sub-units:
A Nitrogenous Base
5 Carbon Sugar and
A Phosphate Group
What is Non-Competitive Inhibition?
Where inhibitor binds to Allosteric Site
In binding, they alter the shape of the enzyme tertiary site
This disrupts the shape of the active site so that the substrate can no longer bind to the enzyme
IRREVERSIBLE
What does level of inhibition depend on?
Concentration of Substrates
What is an Irreversible Inhibitor called?
An Inactivator
What is Competitive Inhibition?
Inhibition by competitive inhibitors, mostly reversible
Could be overcome by increasing the amount/concentration of substrate
By increasing the substrate, it would reduce the effect of REVERSIBLE competitive inhibition
Are Enzyme Inhibitors Permanent or Temporary?
Either
How do Enzyme Inhibitors work?
They bind with enzyme molecule in a way that influences how the substrate binds to the enzyme so affects its turnover rate
Can either:
Block Active Site
Alter turnover rate of the enzyme
What are enzyme inhibitors?
Inhibitors are substances that reduce the activity of an enzyme
What is the effect of pH on Enzyme Action?
Change in pH alters charge on the amino acids that make up the active site. As a result, substrate can no longer bind
Depending on level of pH change, it can break the bonds responsible for maintaining the tertiary structure of the enzyme
The enzyme therefore changes shape
Summarise the effect of temperature on Enzymes
Heat causes vibration Vibrations break bonds Broken bonds disrupt Tertiary Structure This changes the shape Temp too high = irreversible
What is the effect of temperature on enzymes?
Heat causes molecules to vibrate
This may break some of the weak hydrogen bonds and weak ionic bonds holding tertiary structure in place
Changing the shape means that substrate can no longer bind to the active site
With too high a temperature the active site is irreversibly changed
The enzyme is DENATURED and the enzyme no longer works
What is Induced Fit?
Substrates induces a change in the enzyme that makes it fit
Enzyme when it contacts, will mould around substrate
Confirmation change so that the enzyme moulds to fit the substrate
This forms an enzyme-substrate complex
