Biological molecules Flashcards
(98 cards)
1
Q
What are carbohydrates?
A
- Carbohydrates are molecules which consist only of carbon, hydrogen and oxygen.
- They are long chains of sugar units called saccharides.
- There are three types of saccharides - monosaccharides, disaccharides and polysaccharides.
2
Q
Monosaccharide
A
Monosaccharide = simple sugar monomers in which the ratio of carbon: hydrogen: oxygen is 1:2:1
Monosaccharides are sometimes referred to as simple sugars. They have the general formula (CH2O)n where n can be any number but is usually low.
3
Q
Disaccharide
A
Disaccharide = are made up of two monosaccharides joined together by a glycosidic bond in a condensation reaction.
These are sometimes referred to as the double sugars and have the general formula (C6H10O5)n
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Q
Polysaccharide
A
Polysaccharide = are made of many monosaccharide units joined by condensation reactions that form glycosidic bonds
5
Q
Alpha and beta glucose
A
Glucose comes in two different forms known as alpha-glucose and beta-glucose.
On Beta glucose the hydrogen and hydroxide on carbon 1 are swapped
These two isomers are caused by the different arrangements of the atoms on the side chains of the molecule.
The change is only very subtle but gives the molecules very different properties.
6
Q
Name the reaction involved when a disaccharide is formed and name the type of bond formed
A
Disaccharides form in a condensation reaction which forms a glycosidic bond.
7
Q
What monosaccharides is the disaccharide MALTOSE formed with?
A
maltose = α-glucose + α-glucose
8
Q
What monosaccharides is the disaccharide SUCROSE formed with?
A
sucrose = glucose + fructose
9
Q
What monosaccharides is the disaccharide LACTOSE formed with?
A
lactose = glucose + galactose
10
Q
How are disaccharides formed?
A
Disaccharides are formed when two monosaccharides join together in a condensation reaction to form a glycosidic bond.
A condensation reaction involves the elimination of one molecule of H2O.
The use of numbers shows us which carbon atoms are involved in the glycosidic bond. eg: 1,4-glycosidic bond.
11
Q
How does the structure of polysaccharides give them properties which make them ideal as storage molecules within the cell?
A
They can form compact molecules which take up very little space.
They are physically and chemically inactive, so they do not interfere with other functions of the cell.
They have little solubility in water so have no effect on water potential and cause no osmotic movements.
12
Q
How can the glycosidic bond between two monosaccharides be split?
A
- The glycosidic bond between two monosaccharides is split by a process known as hydrolysis.
- The hydrolysis reaction is the opposite of the condensation reaction that formed the molecule, so water is added.
13
Q
What are polysaccharides broken down into?
A
-Polysaccharides are gradually broken down into shorter and shorter chains and eventually single sugars are left
14
Q
What are disaccharides broken down into?
A
Disaccharides break down to form two monosaccharides
15
Q
CARBOHYDRATES AS ENERGY STORES:
starch
A
Starch is an important energy store in plants.
The sugars produced by photosynthesis are rapidly converted into starch which is an insoluble and compact material that can be easily broken down.
All starch is made up of alpha-glucose but comes in two different forms.
These different forms are caused by different carbon atoms being used in each glycosidic bond.
16
Q
Amylose
A
Amylose is the first type of starch.
This is an unbranched polymer which forms a straight helix shape as the chain lengthens.
These chains are made up purely of 1,4-glycosidic bonds.
17
Q
Amylopectin
A
Amylopectin is the second type of starch.
This is a branched molecule made up of 1,4-glycosidic bonds and some 1,6-glycosidic bonds.
It is the 1,6 bonds that cause the branching in the molecule which results in chains being more easily removed which is especially useful when energy is required quickly.
18
Q
Why is starch a good source of energy for athletes?
A
This combination of straight and branched molecules means that starch is a good source of energy for athletes.
Amylose provides long release energy whilst amylopectin provides shorter release energy.
19
Q
CARBOHYDRATES AS ENERGY STORES:
Glycogen
A
Glycogen is another type of storage molecule.
Chemically it is very similar to amylopectin; it is made up alpha glucose only and is very compact.
However, glycogen molecules have more 1,6-glycosidic bonds giving the molecule more side branches.
As a result it is a molecule which can be broken down very quickly making it suitable for use in metabolically active organisms such as animals.
20
Q
Why are polysaccharides important for plants?
A
Polysaccharides are also very important for plants.
They provide the main energy source in plants and are also key structural materials.
21
Q
Carbohydrates in plants:
Cellulose
A
Cellulose is an important structural material in plants.
It is found in the cell wall and provides the cell with strength, protection and support.
22
Q
How does the structure of glucose relate to its function?
A
Glucose stores energy, can form compact molecules, is chemically inactive and is not soluble in water so causes no osmotic movements.
This makes it suitable as a storage molecule in cells.
23
Q
How does the structure of starch relate to its function?
A
Starch is made up of amylose and amylopectin meaning that it can provide both short release and long release energy.
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Q
How does the structure of glycogen relate to its function?
A
Glycogen is made up of mostly 1,6-glycosidic bonds meaning it has a highly branched structure.
This allows molecules to be easily removed for energy production making it a suitable storage molecule for metabolically active organisms such as animals.
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How does the structure of cellulose relate to its function?
Cellulose is made up of beta glucose and every alternate molecule is inverted.
This allows bonding to take place in straight lines and therefore allows hydrogen bonds to form resulting in a strong and rigid material suitable for use in the cell wall.
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Importance of inorganic ions:
Nitrate ions (NO^3-)
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Nitrate Ions are needed in plants for the formation of amino acids and therefore proteins from the products of photosynthesis, also for the formation of DNA
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Importance of inorganic ions:
| Calcium (Ca^2+)
Calcium Ions are needed for the formation of calcium pectate for the middle lamella between 2 cell walls in plants and muscle contraction in animals
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Importance of inorganic ions:
| Magnesium (Mg^2+)
needed for the production of chlorophyll in plants
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Importance of inorganic ions:
| Phosphate (PO4^3-)
needed in all living organisms including plants and animals in the formation of ATP and ADP as well as DNA and RNA
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Dipole nature of water
Water is a dipole and this underpins many of its properties.
In a molecule of H2O, the electrons in the covalent bonds are held closer to the large and positive charge of the oxygen atom.
This results in:
Oxygen having a partial negative charge
Hydrogen having a partial positive charge
Because of this water molecules can form weak forces of attraction between each other. These are known as hydrogen bonds and can be used to explain some of waters anomalous properties.
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Water is a polar solvent
Because water is a polar molecule many ionic substances will dissolve in it.
Many covalently bonded substances are also polar and they too will dissolve in water.
As a result most of the chemical reactions within cells occur in water (in aqueous solution)
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Water has a high specific heat capacity
Water is slow to absorb and release heat - it has a high specific heat capacity
The hydrogen bonds between the molecules means it takes a lot of energy to separate them
This means the temperature of large bodies of water such as lakes and seas does not change much throughout the year, making them good habitats for living organisms
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Incompressibility of water
Water is a liquid and so it cannot be compressed
This is an important factor in many hydraulic mechanisms in living organisms
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Water's maximum density is at 4 °C.
As water cools to 4°C, it reaches its maximum density
As it cools further the molecules bec more widely spaced. As a result, ice is less dense than water and flotas, forming an insulating layer and helping to prevent the water underneath it from freezing.
As a result organisms can live in water even in countries where it gets cold enough to freeze in winter
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Water has a very high surface tension
Water has a very high surface tension because the attraction between the water molecules (including hydrogen bonds) is greater thn the attraction between water molecules and air
As a result the water molecules hold together, forming a thin skin of suface tension. This allows some animals to "walk" on the water.
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What do all fatty acids have?
Fatty acids all have a long hydrocarbon chain with a carboxyl group attached.
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What is the difference between a saturated fatty acid and an unsaturated fatty acid?
In a saturated fatty acid, each carbon atom is joined to the one next to it by a single covalent bond
In an unsaturated fatty acid, the carbon chains have one or more double covalent bonds in them
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What is a monounsaturated fatty acid and a polyunsaturated fatty acid?
A monounsaturated fatty acid has one double bond
A polyunsaturated fatty acid has more than one double bond
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How is a triglyceride synthesised
A fat or oil results when one, two or three fatty acids combine with glycerol to produce either a monoglyceride, a diglyceride or a triglyceride.
These molecules are joined together by an ester bond which is formed during a condensation reaction between the carboxyl group (-COOH) of a fatty acid and one of the hydroxyl group (-OH) of the glycerol.
A molecule of water is removed.
40
How does the structure of lipids relate to their role in energy storage, waterproofing and insulation
Lipids are very compact meaning that they release twice as much energy as carbohydrates do gram for gram.
The fatty acid tail is hydrophobic meaning that lipids repel water. This makes them useful as waterproofers.
Lipids have a low density meaning that thick layer can be used to insulate animals well whilst still allowing them to move easily and float.
Finally, they are insoluble in water so do not interfere with reactions in the cell.
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phospholipids
Phospholipids have a similar structure to triglycerides, but with a phosphate group in place of one fatty acid chain.
Phospholipids have a polar hydrophilic head (the negatively-charged phosphate group)
Phospholipids have two hydrophobic tails (the fatty acid chains)
These properties are very important to biology.
42
How does the structure and properties of phospholipids relate to their function in cell membranes.
Phospholipids are used in cell membranes.
When mixed with water, phospholipids form droplet spheres with a double-layered phospholipid bilayer.
The hydrophilic dead faces the water with the tails facing one another.
This traps a compartment of water at the centre. This causes trapped spheres of water as the surrounds are hydrophobic.
This is called liposome, and is similar to a membrane surrounding a cell
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Structure of amino acids
All amino acids have the same basic structure.
They all contain an amino group (NH2) and a carboxyl group (-COOH) attached to a carbon atom.
They also have an "r-group" which determines the properties of each amino acid.
This is because it influences they way the amino acid folds and ultimately the resulting protein.
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How are proteins formed from amino acids
Amino acids are joined together by a reaction between the amine group of one amino acid and the carboxyl group of another.
This occurs through a condensation reaction in which a molecule of water is lost
A peptide bond forms when two amino acid join and the resulting molecule is known as a dipeptide
More and more amino acids can join together to form a polypeptide chain which will eventually make up the primary structure of a protein.
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Bonds in proteins
The peptide bonds in amino acids are strong but can be broken down through hydrolysis.
Other bonds also form between the "r-groups" of different amino acids to from the 3D structures of proteins.
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Which type of bond occurs and where is dependant on the different atoms present in the chain.
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What types of bonds are found in proteins?
The peptide bonds in amino acids are strong but can be broken down through hydrolysis.
Other bonds also form between the "r-groups" of different amino acids to from the 3D structures of proteins.
Hydrogen bonds, which are weak but numerous
Ionic bond between oppositely charged R-groups , these ionic bonds are stronger than hydrogen but not covalent
Covalent bonds of sulphur called sulphur bridges between cysteine which are very strong
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Primary structure of proteins
A sequence of amino acids in a polypeptide chain
Joined together by peptide bonds
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Secondary structure of proteins
The most basic level of protein folding, and consists of a few basic structures.
It is held together by hydrogen bonds between the carboxyl groups and the amino groups.
The α-helix. The polypeptide chain is wound round to form a helix. There are so many hydrogen bonds that is very stable
The β – pleated sheet. The polypeptide chain zig-zags back and forward forming a sheet of antiparallel strands. Held by hydrogen bonds.
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Tertiary structure of proteins.
A level of 3D organisation
Chains are folded into further complicated shapes
Hydrogen, ionic and disulfide bonds hold these 3D structures in place
Globular proteins are an example of tertiary structures
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Quaternary structure of proteins
A level of organisation that is not found in all proteins
Only seen in proteins containing several polypeptide chains
This structure describes how separate polypetide chains join together
The bonds between these chains can easily be removed causing the protein to become denatured
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FIBROUS PROTEINS
These are made up of long parallel polypeptide chains with little or no tertiary structure.
They have few cross links and form fibres with important roles in the body such as connective tissue.
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Example of a fibrous protein
Collagen is an example of a fibrous protein that gives strength to tendons, ligaments, bone and skin.
Collagen is extremely strong, the fibres have a high tensile strength due to the unusual structure it has.
It is made up of three polypeptide chains which are arranged into a triple helix held together by a large number of hydrogen bonds.
This results in collagen being a material of considerable strength making it suitable for its purpose as a connective tissue.
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Globular proteins
These are proteins that have a complex tertiary and sometimes quaternary structure.
They fold into large and spherical shapes which affect their behaviour in water.
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Structure of globular proteins
Globular proteins fold so that the hydrophobic parts are on the inside and the hydrophilic parts are on the outside.
This makes them soluble in water.
They also play an important role in holding molecules in position in the cytoplasm as well as making up antibodies.
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Example of a globular protein
Haemoglobin is the most well known globular protein.
It is a very large molecule made up of 574 amino acids arranged into 4 polypeptide chains held together by disulfide bonds.
Each chain is arranged around an iron containing haem group. It is the iron that enables the molecule to bind to and release oxygen.
This makes haemoglobin suitable to transport oxygen around the body efficiently.
56
What is an enzyme?
An enzyme is a biological catalyst - something that changes the rate of reaction without being used up and is reformed at the end of the reaction.
Enzymes are globular proteins produced during protein synthesis as the mRNA transcribed from DNA molecules is translated
57
Explain enzyme specificity
Enzymes have a very specific shape as a result of their primary, secondary, tertiary and quaternary structures and this means each enzyme will only catalyse a specific reaction or group of reactions.
We say enzymes show great specificity.
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Intracellular enzymes
Intracellular enzymes act within the boundaries of the cell membrane such as DNA polymerase.
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Extracellular enzymes
Extracellular enzymes act outside the confines of the cell membrane. For example, amylase.
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How do enzymes reduce activation energy?
Enzymes do this by destabilising bonds in a substrate molecule, lowering the activation energy and therefore allowing the reaction to occur more quickly.
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The Lock and Key Model
The lock and key hypothesis is the model that explains enzyme action by an active site in the protein structure that has a very specific shape.
The enzyme and substrate slot together to form a complex as a key fits in a lock
However, this model fails to account for the flexibility found within enzymes.
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The induced-fit hypothesis
A substrate molecule is drawn into the active site with a very similar shape.
The substrate induces a change upon the enzyme so that there is a perfect fit and an enzyme-substrate complex is formed.
The bonds in the substrate are strained and become weaker resulting in an enzyme-product complex.
The products are released and the enzymes returns to its original shape.
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Why is the induced fit model the currently accepted model?
This model accounts for the flexibility found in enzymes and explains why some enzymes are effective on more than one substrate.
Because this the induced fit model is the currently accepted model.
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Describe the effect of temperature on enzyme activity
As temperature increases so does kinetic energy
Reactants now move faster increasing the frequency of collisions between substrates and enzymes and this increases the rate of reaction
However, if the temperature is increased too much, bonds in the enzymes active site will break, causing the enzymes to denature.
The enzyme will no longer work effectively meaning an increase in temperature will only increase the rate of reaction to a certain point.
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Describe the effect of PH on enzyme activity
Ph has a major effect on enzyme activity by affecting the shape of protein molecules
Different enzymes work in different ranges of PH, because changes in PH affect the interactions between R groups, for example hydrogen bonds and ionic bonds that hold the 3d structure of the protein together
The optimum PH for an enzyme is not always the same as the PH of its normal surroundings
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Describe the effect of substrate concentration on enzyme activity
As the substrate concentration increases, so does the rate of reaction
This is because there are more successful collisions
This relationship is directly proportional until all of the active sites are in use and therefore no more substrate can be catalysed
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Describe the effect of enzyme concentration on enzyme activity
As long as the substrate is in excess, an increase in enzyme concentration will increase the rate of reaction
However, if the substrate is limited the rate of reaction will only increase up to a certain point as there will eventually be more active sites than substrate molecules
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How can the initial rate of enzyme activity can be measured and why this is important?
To work out the level of enzyme activity present, scientists measure the initial rate of reaction.
This is done by drawing a tangent that passes through 0 on a rate graph and then calculating the gradient of this tangent to work out the initial rate.
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What is an enzyme inhibitor?
Enzyme inhibitors are substances that slow down enzymes or stop them from working
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Reversible inhibition
When an inhibitor affects an enzyme in a way that does not permanently damage it, this is reversible inhibition.
It is often used to control reaction rates within a cell
There are 2 major forms of reversible inhibition - competitive inhibition and non competitive inhibition
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Competitive inhibition
In competitive inhibition, the inhibitor molecule is similar in shape to the substrate molecule and competes with the substrate molecule for binding at the active sites of the enzyme, forming the enzyme/inhibitor complex
If the amount of inhibitor is fixed, the percentage of inhibition can be reduced by increasing substrate concentration
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Non - competitive inhibition
In non competitive inhibition, the inhibitor does not compete for the active site but forms a complex with the enzyme or enzyme/substrate complex.
It changes the shape of the active site so it can no longer catalyse the reaction.
It is only affected by concentration of inhibitor
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End product inhibition
End product inhibition is an important part in the regulation of metabolic pathways.
In end product inhibition, the regulatory enzyme is found near the beginning of the pathway and it is inhibited by one of the end products of the chain
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Differences between fibrous and globular proteins
Fibrous:
- Insoluble / large
- Hydrophobic on outside
- Mainly secondary structure
- Repeated amino acid sequences
GLOBULAR:
- Soluble / small
- Hydrophilic on outside ;
- Mainly tertiary structure
- Little repetition
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Structure of nucleotides
Each nucleotide is made up of 3 parts - a pentose sugar, a nitrogen-containing base and a phosphate group
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Difference in sugar between DNA and RNA
In DNA the sugar is deoxyribose whereas in RNA the sugar is ribose.
Deoxyribose contains one fewer oxygen atom than ribose
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Purine base
Has 2 nitrogen-containing rings
Adenine and guanine
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Pyrimidine base
Has only 1 nitrogen-containing ring
Thymine, Cytosine and uracil
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Base pairing rules
Each pair must have three rings and they are joined together by hydrogen bonds.
Therefore each bond must involve hydrogen.
Because of these rules a purine base always pairs with a pyrimidine base.
The following bases are complementary:
A - T
G - C
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Nucleotide Polymerisation
Nucleotides polymerise by forming a phosphodiester bond between carbon 3 of the sugar and an oxygen atom of the phosphate.
This is a condensation reaction (water is produced). The bases are obsolete in this reaction.
Polymerisation ensures the sugar-phosphate backbone continues the structure.
A polynucleotide has a free phosphate group at one end, called the 5 end as it is attached to the carbon 5 of the sugar and a free OH group on the other side coming out of the carbon 3 of the sugar
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What are the two strands of the DNA double helix held together by?
The two strands of the DNA double helix are held together by hydrogen bonds between the complimentary base pairs
These hydrogen bonds form between the amino and the carbonyl groups of the purine and pyrimidine bases on the opposite strands
There are three hydrogen bonds between C and G but only two between A and T
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Difference in strands between DNA and RNA
RNA molecules form single strands and can fold into complex shapes.
DNA molecules form two stands which twist around each other to form a double helix.
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Explain how DNA is replicated semi conservatively
A double helix of DNA is taken.
The chains of nucleotides fit perfectly together as long as the base pairs are matched correctly.
When the DNA replicates, the two strands if the DNA molecule "unzip" as DNA Helicase breaks the hydrogen bonds between each of the base pairs.
This results in two separate strands which can now act as templates for new DNA molecules.
The new template stands have exposed bases which now attract free DNA nucleotides and new hydrogen bonds are formed between the matching base pairs. DNA Polymerase lines up the nucleotides and catalyses the formation of phosphodiester bonds.
DNA Ligase then joins sections of DNA together to form a new strand.
The result is two new molecules of DNA, each containing one original and one new strand. This is called semi-conservative replication.
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Define gene
A gene is a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypetide chain
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Nature of the genetic code
The Triplet Code - each set of three bases codes for one amino acid resulting in 64 possible combinations (4x4x4).
Degenerate - this means that each amino acid is coded for by more than one triplet (the word codon can also be used to describe a triplet).
Non-overlapping - this means that each triplet is separate and one base can only be part of one triplet.
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Why is having a degenerate genetic code a big advantage to life?
Having a degenerate genetic code is a big advantage to life.
This is because point mutations will not always change the amino acid that is coded for meaning the protein will still be produced as intended.
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Protein denaturing
Secondary, tertiary and quaternary structures are largely held together by hydrogen bonds.
The structure is dependent on the integrity of these bonds.
If the bonds do break the chain will fold into random coils and the protein loses its function.
This process is called denaturing and happens generally at >50 degrees or at low or high pH.
Covalent bonds and the primary structure remain intact.
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mRNA
mRNA is formed in the nucleus and is the product of DNA being transcribed.
The strand of mRNA formed from DNA being transcribed generally equates to one polypeptide.
mRNA is a sense strand that codes for a protein.
The DNA being transcribed is caused by RNA polymerase.
mRNA can pass out of the nucleus through the nuclear pores due to its small size.
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tRNA
tRNA is found in the nucleus and is comprised of three bases that are the anti codon of the mRNA.
This creates a cloved leaf like structure.
This is imperative to the overall function as it allows the tRNA is correspond to the specific amino acid that the bases code for.
The tRNA transports the amino acids, then the anti codon lines up with the codon on the mRNA then the correct sequence to form a polypeptide is made
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rRNA
rRNA makes up 50% of the structure of a ribosome and is the most common form of RNA.
It is made in the nucleus and then moves into the cytoplasm to bind with proteins to form ribosomes.
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Transcription
RNA polymerase attaches to the start of the gene and the DNA "unwinds".
Free bases are attracted to the antisense strand of the DNA.
RNA polymerase moves along the strand forming phosphodiester bonds between nucleotides.
This form a strand of mRNA which then exits the nucleus through a nuclear pore.
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Translation
mRNA enters the cytoplasm and attaches itself to a ribosome.
tRNA molecules line up to the codon complementary to its anticodon.
The tRNA anticodon is specific to the amino acid that it is carrying.
Enzymes link the amino acids together to form a polypeptide chain.
Hydrogen bonds hold the tRNA and mRNA in place while this occurs.
The ribosome will then continue to move down strand of mRNA adding more amino acids to the polypeptide chain until it reaches a STOP codon.
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What is a gene mutation?
A gene mutation is a permeant change in the sequence of bases in an organism.
There are three different types of mutations.
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Substitution
Substitution - when one base is added and another is removed.
This usually has a small impact since it only affects one triplet.
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Insertion
Insertion - occurs when one base is added, again causing all of the bases to shift by one position.
This is also known as a frame shift.
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Deletion
Deletion - when one base is removed, causing all of the following bases to move by one position.
This is known as a frame shift and can have serious consequences.
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What is sickle cell anaemia?
This is a genetic condition caused by a point mutation, resulting in a potentially fatal condition.
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How does sickle cell anaemia occur
Point mutation substitutes a T to A
This results in the wrong amino acid being coded for,
resulting in a faulty polypeptide chain
This reduces the solubility of haemoglobin when deprived of oxygen, causing it to precipitate out of the blood
The red blood cells become deformed into a sickle shape
This new shape restrict their movement through capillaries, so the body removes these cells resulting in anaemia
