M2C3 - Biological molecules Flashcards
Describe the structure and bonding of water:
-2 hydrogens share electrons with an oxygen
-Oxygen is more electronegative (attracts electrons). Means O has a slight negative charge, and H has a slight positive.
-Water is polar
What are some characteristics of water?
-Good solvent
-High cohesion
-High surface tension
-High SHC + latent heat
Why is water a good solvent?
Because water is polar which enables water molecules to bind to solute molecules.
Why is water a good transport medium?
Cohesion between water molecules means that when water is transported through the body it sticks together.
Describe and explain why water is a good coolant?
Helps to buffer temp changes during chemical reactions in prokaryotic and eukaryotic cells because of the large amount of energy needed to overcome the hydrogen bonding.
Maintaining constant temperatures is important due to the enzymes.
Why is water a good habitat?
-Water is stable - it doesn’t change temperature or become gas easily.
-Surface tension is strong enough to support small insects.
-Ice is less dense than water so floats - provides a habitat for species - ice insulates water below.
What are monomers?
Monomers are the smaller units from which larger molecules are made. e.g. Monosaccharides, amino acids and nucleotides
What are polymers?
Polymers are molecules made from a large number of monomers joined together.
What is a condensation reaction?
A condensation reaction joins two molecules together with the formation of a chemical bond and produces a molecule of water.
What is a hydrolysis reaction?
A hydrolysis reaction breaks a chemical bond between two molecules and involves the use of a water molecule.
How is maltose formed?
disaccharide formed by condensation of two glucose molecules
How is lactose formed?
a disaccharide formed by condensation of a glucose molecule and a galactose molecule.
How is sucrose formed?
a disaccharide formed by condensation of a glucose molecule and a fructose molecule
What type of bond is formed during a condensation reaction?
Glycosidic
Describe the structure of Amylose
Straight chain of a glucose molecules
1-4 glycosidic bonds forma helix shape
Stabilised by H bonds - makes it more compact and less soluble.
Describe the structure of Amylopectin
Branched chain of a glucose molecules
Joined by 1-4 and 1-6 glycosidic bonds
Describe the structure of Glycogen
Similar structure to amylopectin but contains even more 1-6 bonds so it has an even more branched structure.
How is the structure of amylose related to its function?
compact structure allows the amylose to be neatly compacted, thereby allowing cells to store larger amounts of amylose.
How is the structure of amylopectin related to its function?
The branches mean there are many glucose molecules accessible on the end of chains which can be easily broken off by hydrolysis for use in respiration.
So can provide a rapid supply of energy.
Branching also makes it compact, it takes up little space in the cell.
How is the structure of glycogen related to its function?
-Even more branched structure, making them even more compact which is ideal for storage. -branching also means there are many free ends where glucose molecules can be added or removed.
-These speeds up the processes of storing or releasing glucose molecules required by the cell.
How is cellulose formed?
-B glucose molecules can’t join in the same way that a glucose molecules can.
-The hydroxyl groups on c1 and c 4 of the two glucose molecules are too far apart to react.
-Only way that B glucose molecules can join and form a polymer is if alternate beta glucose molecules are turned upside down.
-When a polysaccharide is formed from glucose in this way it is unable to coil or form branches.
-So, the straight chain molecule cellulose is formed.
Describe the structure of cellulose
-Cellulose molecules make H+ bonds with each other forming microfibrils.
-These microfibrils join together forming macrofibrils which combine to form fibres.
How is the structure of cellulose related to its function?
Fibres of cellulose are strong and insoluble and used to make cell walls.
Which ion is required for the hydrolysis of starch by an enzyme?
Cl-
How are trigylcerides formed?
Hydroxyl groups interact leading to the formation of 3 water molecules and bonds between the fatty acid and glycerol molecule.
Explain how the structure of phospholipids is related to their function
-hydrophilic head and hydrophobic
tails
-hydrophobic tails repel water
-hydrophilic head, forms H
bonds with water
-So a bilayer forms
What is a saturated fatty acid?
Contains no double bonds between carbon atoms
What is an unsaturated fatty acid?
contains double bonds between carbon atoms
How are the structure of triglycerides related to their function?
-The presence of long hydrocarbon chains in the fatty acids allows for a lot of chemical energy to be stored in them.
-Slow conductor of heat = thermal insulation.
Describe the structure of cholesterol
Has a hydroxyl group and 4 carbon rings
how does the structure of cholesterol relate to its function?
Positioned between phospholipids in membranes and regulates fluidity by keeping fluidity at low temps and preventing them from becoming too fluid at high temperatures.
Give some functions of triglycerides
-energy source for respiration
-thermal insulation
-buoyancy
How is a peptide bond formed?
Condensation reaction between two amino acids
Describe the primary structure of proteins
The sequence of amino acids
Describe the Secondary structure of proteins
Coiling or folding of the amino acid chain due to the hydrogen bonds between them.
What are the two forms of the secondary structure?
alpha helix
beta pleated sheet
Describe the tertiary structure of proteins
Formed by the folding of coils and pleats to form a complex 3D shape.
Outline and describe the 4 types of bonds involved in the tertiary structure?
-Disulphide - If 2 cysteine are found close together a strong covalent bond can form between 2 sulfur atoms.
-Ionic - + and - parts of R groups can form ionic bonds.
-Hydrogen - H+ bonds can form between polar parts of the R groups.
-Hydrophobic and Hydrophilic interactions - Some parts of the R group are hydrophilic and some are hydrophobic, in a water environment the hydrophobic areas cluster together.
Describe the Quarternary structure of proteins
results from the association between 2 or more individual proteins.
Describe the structure of globular proteins
-Usually have a spherical shape caused by tightly folded polypeptide chains.
-The chains are usually folded so hydrophobic groups are on the inside, and hydrophilic groups are on the outside.
-This makes many globular proteins soluble in water.
Describe insulin as an example of a globular protein
Hormone secreted by the pancreas.
Quaternary structure consists of two polypeptide chains
Important its soluble as its transported in the blood.
What is a prosthetic group?
Parts of proteins that are not made up of amino acids
What is a conjugated protein?
Proteins that have a prosthetic group
Describe haemoglobin as an example of a conjugated protein
-A haemoglobin molecule is made of four polypeptide chains.
-Each chain is wrapped around a group of atoms, called a haem group, which holds an iron Fe2+ ion in the centre.
-Each iron ion is able to bond with two oxygen atoms (one oxygen molecule).
Describe catalase as an example of a globular/conjugated protein
Catalaseis a commonenzymefound in nearly all living organisms.
It catalysesthe decomposition ofhydrogen peroxidetowaterandoxygen
What is a fibrous protein?
Formed from parallel polypeptide chains held together by cross-links.
These form long, rope-like fibres.
What are some properties of fibrous proteins?
high tensile strength and are generally insoluble in water.
What is collagen and where is it found?
Collagen is a fibrous protein found in connective tissues (e.g. skin, muscles, tendons)
What is keratin and where is it found?
Group of fibrous proteins found in hair skin and nails.
The degree of sulphide bonds determines flexibility
What is elastin and where is it found?
Found in elastic fibres such as skin, blood vessels and the alveoli of the lung
Allows structures to return to their original shape and size after stretching
What is a colorimeter (quantitative)
Able to measure light absorbance (how much light is absorbed) or light transmission (how much light passes through) a substance.
Describe the method of using a colourometer
-Colorimeter calibration: a weak iodine solution can be used to calibrate the colorimeter as the end point (or 100% transmission)
-Preparation of a starch solution of known concentration, from which a range of concentrations are made using serial dilutions.
-Following calibration and switching on the red filter, the colorimeter is used to measure the percentage absorbance or percentage transmission values
-A calibration graph is then plotted of starch concentration (X-axis) vs percentage absorbance or percentage transmission (Y-axis)
How do you calculate the Rf value?
Distance moved by solvent
What are the components of a nucleic acid?
-Pentose sugar
-Phosphate group
-Nitrogenous base
What bonds join nucleotides and how are they formed and broken?
Phosphodiester bonds formed by a condensation reaction between the phosphate group at the 5th carbon of the pentose sugar of one nucleotide forms a covalent bond with the hydroxyl group at the third carbon of the pentose sugar of an adjacent nucleotide. These bonds are broken by hydrolysis.
What is the difference between RNA nucleotides and DNA nucleotides?
DNA:
-Deoxyribose sugar
-Double stranded
-Thymine pairs with adenine
-DNA is longer
RNA:
-Ribose sugar
-Single stranded
-Uracil pairs with adenine
-RNA is shorter
What are pyrimidines?
The smaller bases, which contain single carbon ring structures - Thymine + Cytosine
What are Purines?
The larger bases, which contain double carbon ring structures - Adenine + Guanine.
Describe the structure of the double helix:
The 2 strands are held together by hydrogen bonds between the bases.
Each strand has a phosphate group (5’) at one end and a hydroxyl group (3’) at the other – the 2 strands run in opposite directions so are said to be antiparallel.
The 2 strands coil up to form the double helix structure.
Describe complementary base pairing:
Adenine and Thymine form 2 hydrogen bonds so pair with each other, Cytosine and guanine form 3 hydrogen bonds so pair with each other.
Explain the process of semi-conservative DNA replication
1) The double helix unwinds and the DNA is ‘unzipped’ by DNA helicase as hydrogen bonds are broken between the polynucleotide chains.
2) Complementary base pairing occurs between free nucleotides and the exposed bases.
3)As the free nucleotides are added strong phosphodiester bonds are formed by DNA polymerase between the phosphate and the sugar groups to form the sugar phosphate backbone.
This way, two new strands of DNA are produced and wind into the double helix, consisting of an old and new strand of DNA. That’s why this is called semi-conservative.
How can mutations occur during DNA replication?
Sequences of bases are not always matched exactly and an incorrect sequence may occur in the copied strand. These errors occur randomly and spontaneously and lead to a change in the sequence of bases, known as a mutation.
Why is genetic code described as a triplet code?
Involves three nucleotide bases that make up a codon, which code for a particular amino acid.
What is genetic code?
The sequences of bases in DNA are instructions for the sequence of amino acids in the production of proteins.
Why is genetic code described as a non-overlapping?
The codons do not overlap. Once the ribosome has ‘read’ one codon and the appropriate amino acid has been recruited, the ribosome moves onto a new codon.
Why is genetic code described as a degenerative?
Different codons can code for the same amino acid. E.g. the codons CUU and CUC both code for the amino acid leucine. This means that some mutations will have no effect on the organism since the same protein will still be produced
Why is genetic code described as a universal?
all organisms use the same genetic code
Describe the process of transcription:
-RNA polymerase enzyme attaches to the double helix at the beginning of a gene – the hydrogen bonds between the 2 DNA strands break.
-Only one side of the DNA molecule is copied – this is the sense strand (Template strand). The other, uncopied side is the antisense strand (Coding strand).
-The RNA polymerase moves along the DNA adding complimentary mRNA nucleotides and connecting them through phosphodiester bonds to the DNA bases to form one complimentary strand of mRNA.
-The mRNA molecule then leaves the nucleus via a pore in the nuclear envelope.
Describe the process of translation:
-mRNA moves out of the nucleus into the cytoplasm through a nuclear pore.
-The ribosome attaches itself to the mRNA and slides along it (translocation). The ribosome ‘reads’ the mRNA in a series of 3 bases (AUG, CGA, AAG) called codons. Each codon corresponds to a particular amino acid.
-As the ribosome reaches the codons, a tRNA molecule (present in the cytoplasm) which has a complementary anticodon on one end and region where a specific amino acid can attach at the other carries an amino acid to the ribosome, this ensures amino acids are joined in the correct sequence. Once the ribosome has read through the length of the mRNA, a series of different amino acids will have been dropped off by several tRNA molecules.
-The rRNA catalyses peptide bond formation (condensation reaction) between the amino acids to form a polypeptide.
-This process continues until a ‘stop’ codon on the mRNA molecule is reached – this acts as a signal for translation to stop and at this point the amino acid chain coded for by the mRNA molecule is complete.
Describe the structure of ATP
-Nitrogenous base
-Pentose sugar
-3 phosphate groups
Describe the structure of ADP
-Nitrogenous base
-Pentose sugar
-2 phosphate groups
What type of glucose makes up sucrose?
Alpha glucose
What monosaccharides make up sucrose?
Glucose and fructose
