2.2* Flashcards
What is a hydrogen bond?
A weak interaction that can occur whenever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom.
What is a hydrolysis reaction?
A reaction that occurs when a molecule is split into two smaller molecules with the addition of water.
What is a monomer?
A small molecule which binds to many other identical molecules to form a polymer.
What is a polymer?
A large molecule made from many smaller molecules called monomers.
What do atoms consist of?
A nucleus ( protons and neutrons ) surrounded by shells of electrons.
When are its atoms stable?
When their outermost shell is full.
Describe covalent bonding.
Atoms of different elements have different amount of atoms in their outermost shells. For example, carbon has four electrons. By sharing electrons with other atoms, the atom’s outermost shell can be ‘filled’ and it becomes strongly bonded with the other atom.
What is a condensation reaction?
Reaction that occurs when two molecules are joined together with the removal of water.
How is a covalent bond drawn?
By a single line (the equivalent of sharing one electron)
Explain the covalent bonding of methane.
Because carbons outer shell is filled by four electrons, carbon forms four covalent bonds.
How many covalent bonds do oxygen, hydrogen and nitrogen form?
Hydrogen forms a single covalent bonds, oxygen two covalent bonds and nitrogen three covalent bonds.
Describe the carbon-hydrogen bond.
The carbon-hydrogen bond is one of the most important in organic molecules . Hydrogen has one electron. Carbon can therefore bind with four hydrogen atoms. The carbon-carbon bond is also very important in hydrocarbon chains. Sometimes a double bond can form (the equivalent of sharing two electrons).
Explain the condensation which happens on your windows on a cold day.
When condensation happens on your windows on a cold day, water vapour in the air has changed state and settled on a window as liquid. The water vapour has been removed from the air.
When does a condensation reaction occur? And what can this allow?
A condensation reaction occurs when two molecules are joined together with the removal of water. In the same way, two molecules can be split apart with the addition of water.
What is a hydrolysis reaction?
When water is split by a condensation reaction.
When do almost all condensation reactions happen?
Almost all condensation reactions happen in the same way, when two OH- groups react together. The reaction involves the breaking and formation of covalent bonds.
Describe what is added in hydrolysis and taken away in condensation reactions.
H2O is added in hydrolysis and a covalent bond is broken. H2O is removed in condensation. A new covalent bond is formed. In both hydrolysis and condensation reactions the OH groups of molecule 1 and molecule 2 are close to each other.
Name the type of molecule, monomer, and polymer that contain C, H and O.
Molecule; Carbohydrate Monomer; Monosaccharides - e.g. glucose Polymer; Polysaccharides e.g. Starch
What is responsible for linking and splitting apart biological molecules in living things.
Condensation and hydrolysis reactions.
The units which are linked together in condensation reactions are called what?
Monomers
What happens when two monomers join together?
They form a dimer.
What happens when lots of monomers join together?
They form a polymer.
Name the type of molecule, monomer, and polymer that contain C, H, O, N, S
Molecule; Protein Monomer; Amino acids Polymer; polypeptides and proteins.
Name the type of molecule, monomer, and polymer that contain C, H, O, N, P
Molecule; Nucleic acid Monomer; Nucleotides Polymer; DNA and RNA
How much of the human body do hydrogen and carbon make up?
Hydrogen atoms make up 60% of the atoms in the human body. Carbon atoms make up 11% of the atoms in the human body.
What does does water consist of?
Two hydrogen atoms, each covalently bonded to one oxygen atom.
Why is water polar?
Because the oxygen atom has a greater number of positive protons in its nucleus, this exerts a stronger attraction for the shared electrons. This means the oxygen atom becomes slightly negative, and the hydrogen atoms become slightly positive. When this happens, we say the molecule is polar.
On a water molecule are the hydrogen positive or negative?
Positive end (poles) of molecule.
On a water molecule are the oxygen positive or negative?
negative end (pole) of molecule.
What is a hydrogen bond?
A weak interaction which happens wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom.
What is the strength of a hydrogen bond compared to a covalent bond?
The bond is weaker than a covalent bond.
Where do thousands of hydrogen bonds stabilise a molecule?
In some polymers, thousands and thousands of hydrogen bonds form between chains of monomers. Having many bonds like this helps stabilise the structure of some biological molecules.
Water has a number of properties that are essential for life, many of which depends on what?
The polar nature of the water molecules and on hydrogen bonding between water molecules.
What do water molecules do unlike other liquids.
As in any liquid, water molecules constantly move around. Unlike other liquids, as they move they continually make and break hydrogen bonds.
Why is water a liquid at room temperature?
The hydrogen bonds between water molecules make it more difficult for them to escape as a gas. By contrast, other less polar, but similarly sized molecules (e.g. H2S) are gasses at room temperature. Even with hydrogen bonds, water has quite a low viscosity, which means it can flow easily.
What can water do because it is a liquid at room temperature? (4 things)
Provide habitats for living things in rivers, lakes and seas. Form a major component of the tissues in living organisms. Provide a reaction medium for chemical reactions. Provide an effective transport medium, e.g. in blood and vascular tissue.
What does the density of water provide?
The density of water provides an ideal habitat for living things. If water was less dense, aquatic organisms would find it very difficult to float.
What happens when most liquids get colder and what would happen if this was the case with water?
When most liquids get colder, they become more dense. if this was the case with water at the top of the pond would freeze and sink. The water replacing it at the top of a pond would freeze and sink. The water replacing it at the top would do the same, until the pond was full of ice
How does water behave when it freezes?
But ice behaves differently. It becomes more dense as it gets colder until about 4 degrees. As it goes from 4 degrees to freezing point, because of its polar nature, the water molecules align themselves in a structure which is less dense than liquid water.
What happens because ice is less dense than water?
Aquatic organisms have a stable environment in which to live through the winter. Ponds and other bodies of water are insulated against extreme cold. The layer of ice reduces the rate of heat loss from the rest of the pond.
What is water a good solvent for?
Water is a good solvent for many substances found in living things. This includes ionic solutes such as sodium chloride and covalent solutes such as glucose.
Why is water a good solvent?
Because water is polar, the positive and negative parts of the water molecules are attracted to the negative and positive parts of the solute.The water molecules cluster around these charged parts of the solute molecules or ions, and will help to separate them and keep them apart. At this point they dissolve and a solution is formed.
What can take place because water is a good solvent?
Molecules and ions can move around and react together in water. Many such reactions happen in the cytoplasm of cells which is over 70% water. Molecules and ions can be transported around living things whilst dissolve in water.
How does a drop of water demonstrate cohesion?
A drop of water on a flat surface does not spread out, but can look almost spherical. This is because hydrogen bonding between the molecules pulls them together. The water molecules demonstrate cohesion.
How does cohesion happen at the surface of water as well?
The water molecules at the surface are all hydrogen-bonded to the molecules beneath them, and hence more attracted to the water molecules beneath than to the air molecules above. This means the water contracts (because the molecules are being pulled inwards), and it gives the surface of the water an ability to resist force applied to it. This is known as surface tension.
What can happen because of cohesion and surface tension.
Columns of water in the plant vascular tissue are pulled up the xylem tissue together from the roots. Insects like pond skaters can walk on water.
What is water temperature a measure of?
The kinetic energy of the water molecules.
How are water molecules held together, and what does this mean for heating it up?
Water molecules are held together quite tightly by hydrogen bonds. Therefore, you have to put in a lot of heat energy to increase their kinetic energy and temperature.
What is the amount of heat energy required to raise the temperature of water known as?
The amount of heat energy required is known as specific heat capacity (4.2 KJ of energy to raise the temperature of 1 kg of water by 1 degree)
What does the specific heat capacity of water mean for living things?
Because the main component of many living things is water, and many organisms live in water, its high specific heat capacity is important; Living things, including prokaryotes and eukaryotes, need a stable temperature for enzyme controlled reactions to happen properly. Aquatic organisms need a stable environment in which to live.
What is the latent heat of vapourisation?
When water evaporates, heat energy known as the latent heat of vapourisation, helps the molecules to break away from each other to become a gas.
Why has water got a high latent heat of vapourisation?
Because the small molecules are held together by hydrogen bonds, a relatively large amount of energy is needed for water molecules to evaporate.
What does the high latent heat capacity of vapourisation of water mean for living things?
Water can help to cool living things and keep their temperature stable. For example, mammals are cooled when sweat evaporates, and plants are cooled when water evaporates from mesophyll cells.
What is water a reactant in?
Water is also a reactant in reactions such as photosynthesis, and in hydrolysis reactions such as digestion of starch, proteins and lipids.
Describe waters properties as a reactant.
Its properties do not directly draw on its polarity, but its role as a reactant is extremely important for digestion and synthesis of large biological molecules.
What is an amino acid?
Monomers of all proteins, and all amino acids have the same basic structure.
What is a peptide bond?
A bond formed when two amino acids are joined by a condensation reaction.
What do proteins comprise of?
Proteins are large polymers comprised of long chains of amino acids.
The properties of proteins give them a variety of functions. Describe three functions of proteins.
They form structural components of animals in particular. For example, muscles are made of protein. Their tendency to adopt specific shapes make proteins important as enzymes, antibodies and some hormones. Membranes have protein constituents that act as carriers and pores for active transport across the membrane and facilitated diffusion.
What do both plants and animals need to make proteins?
Both plants and animals need amino acids to make proteins. Animals can make some amino acids, but must ingest the others (called essential amino acids). Plants can make all the amino acids they need, but only if they can access fixed nitrogen (such as nitrate).
What elements are in each amino acid?
Each amino acid contains the elements carbon, hydrogen, oxygen and nitrogen. Some amino acids contain sulphur.
How does the amount of amino acids compare to the amount found in proteins?
There are over 500 different amino acids, but only 20 of them are proteinogenic, which means they are found in proteins.
What does each protein chain of amino acids have at each end?
An amino group (-NH2) at one end, and a carboxyl (-COOH) group at the other end. Molecular structure of an amino acid is on pg. 65
On a molecular structure of an amino acid what does the R group stand for?
It does not stand for a particular element, but is different in each amino acid. In glycine, it is simply an H atom.
Give an example of where the R group can be a lot more complicated.
In alanine it is CH3 whereas in cysteine it is CH3S.
What does the name of almost all amino acids end in? And what are the exceptions.
-ine. The only exceptions are those which have an acidic R group, such as aspartic acid and glutamic acid.
What do the R groups in amino acids vary in?
By size, by charge and by polarity, with some being hydrophobic and some being hydrophilic.
What’s the simplest amino acid?
Glycine
When cab amino acid can act as buffers?
When in dissolved water.
Amino acids can act as buffers; What happens when amino acids are dissolved in water?
When dissolved in water, the amino group and carboxyl group can ionise. This means that the amino group can accept an H+ ion to change from NH2 to NH3+. The carboxyl group can give up an H+ ion to change from COOH to COO-.
Amino acids can act as buffers; What are the symbol equations for the carboxyl and amino groups accepting or giving up H+ ions to change form.
-COOH ~ –COO- + H+ The carboxyl group acts as an acid, in producing H+ ions. -NH2 + H+ ~ -NH3+ The amino group acts as a base, in accepting H+ ions:
Amino acids can act as buffers; How will this change with the pH.
At a low pH (where there are lots of H+ ions in a solution), the amino acids will accept H+ ions. At high pH (where there are fewer H+ ions in solution), the amino acid will release H+ ions.
Amino acids can act as buffers; What does the amino acids reaction to acids and alkalis tell you about its properties.
This means an amino acid has acidic and basic properties, and so is known as amphoteric. In a long chain of amino acids, you will find amino acids, you will find amino and carboxyl groups on each end, but there are also may on the R-groups of different amino acids.
Explain what buffering is?
Protein chains can be affected by this amphoteric nature. By accepting and releasing H+ ions, amino acids can help regulate changes in PH. This is known as buffering. A buffer is a substance which helps to resist large changes in PH.
How are amino acids joined together?
Amino acids are joined together by by covalent bonds called peptide bonds.
What does making a peptide bond involve?
Just like the glycosidic bond and the ester bond, making a peptide bond involves a condensation reaction, and breaking a peptide bond involves hydrolysis.
What breaks down peptide bonds in the body.
Enzymes catalyse these reactions. Protease enzymes in the intestines break down peptide bonds during digestion. They also break down hormones so that their effect is not permanent.
As more amino acids join together, how do their names change?
All amino acids are joined together in a similar way, whatever R groups they may have. Two amino acids joined together are known as a dipeptide. Joining a longer chain of amino acids together forms a polypeptide. A protien may consist of a single polypeptide chain, or more than one chain bonded together.
How do two amino acids join to form a dipeptide molecule?
amino acid + amino acid = dipeptide molecule + water. It is a condensation reaction, a peptide bond (covalent) is formed and water is used up. The of part of the carboxyl group is released along with a hydrogen from the amino group to form water. The carbon from the carboxyl group then joins to the nitrogen form the amino group.
How does a dipeptide molecule form amino acids?
Dipeptide molecule + water = amino acid + amino acid. This is a hydrolysis reaction, a peptide bond (covalent) is broken and water is used up. The carbon from the carboxyl group and the nitrogen form the amino group split, and a hydrogen bonds with the nitrogen and a hydroxide bonds with the carbon.
What makes a polypeptide chain relatively stiff and rigid?
The peptide bond is depicted as a single bond, but due to the electron arrangement around the bond, it has some of the properties of a double bond. This means that the bond is shorter than a conventional C-N bond. It also inhibits rotation around the peptide bond. This makes the polypeptide chain relatively stiff.
What is a primary structure?
The sequence of amino acids found in a molecule.
What is a secondary structure?
The coiling or folding of an amino acid chain, which arises often as a result of hydrogen bond formation between different parts of the the chain. The main forms of secondary structure are the helix and the pleated sheet.
What is a quaternary structure?
Protein structure where a protien consists of more than one polypeptide chain.
What is a tertiary structure?
The overall three-dimensional shape of a protien molecule. Its shape arises due to interactions including hydrogen bonding, disulphide bridges, ionic bonds and hydrophobic interactions.
Why is the number and order of amino acids in a protien chain important?
Changing just one amino acid can alter the function of the protien.
How many possible ways are there of ordering amino acids are there and why?
Because there are 20 amino acids, at every point in the chain there are 20 alternatives. Given that most proteins are at least 100 amino acids long, this gives an enormous number of different proteins that could be formed. There are 20 x 100 possible ways of ordering 100 amino acids.
What determines a proteins, function and shape.
The function of a protien is determined by its structure. The order of amino acids in the primary structure will determine the shape of the protien molecule, through its secondary, tertiary and quaternary structure.
Protein structure and bonding; How is a helix created?
The chain of amino acids is not straight, but twists into a shape called the secondary structure. Some chains coil into a alpha helix, with 36 amino acids per 10 turns of the helix.
Protein structure and bonding; How is a helix held together?
The helix is held together by hydrogen bonds between the -NH group of one amino acids and the -CO group of another four places ahead of it in the chain.
Protein structure and bonding; How is a zig-zag structure created?
Other chains fold very lightly in a zig-zag structure. When one such chain folds over on itself, this produces a Beta-pleated sheet.
Protein structure and bonding; How is a zig-zag structure held together?
Hydrogen bonds between the -NH group of one amino acid and the -CO group of another further down the strand hold the sheet together.
What makes the beta-pleated sheet stable structures at optimal temperature and PH.
Although hydrogen bonds are relatively weak, many are formed, which makes both the alpha-helix and the beta-pleated sheet stable structures at optimal temperature and PH.
How do secondary structures vary, do they all have a regular patten?
Some chains do not adopt any regular structure, and some chains may have more than one secondary structure at different ends of the chain.
When is a tertiary structure formed?
When these coils and pleats themselves start to fold, along with areas of straight chains of amino acids, this forms the tertiary structure.
How is the tertiary structure held together?
The tertiary structure is a very precise shape which is held firmly in place by bonds between amino acids which lie close to each other.
What shape may the tertiary structure form?
The tertiary structure may adopt a super-coiled shape (e.g. in fibrous proteins) or a more spherical shape (in globular proteins).
What does a quaternary structure describe?
Many proteins are made up of more than one polypeptide chain. The quaternary structure describes how multiple polypeptide chains are arranged to make the complete protien molecule.
How may a quaternary structure be held together?
This may also be held together with the same types of bond that hold the tertiary structure together.
How is the primary structure of proteins bonded together?
The primary structure of proteins, the chains of amino acids, is held together by peptide bonds which are covalent bonds, hence very strong.
How is the secondary, tertiary and quaternary structure of proteins bonded together?
Other types of bond form between amino acids in different parts of the polypeptide chain. The secondary structure is primarily held together by hydrogen bonds, but the tertiary structure and quaternary structure are held together by hydrogen bonds and many others.
What do the terms primary, secondary and tertiary structure refer to?
A single polypeptide chain.
What does the quaternary structure describe?
The association between two or more polypeptide chains.
Hydrogen bonds: How are hydroxyl, carboxyl and amino groups formed?
Like in water, hydrogen bonds from between hydrogen atoms with a slight positive charge and other atoms with a slight negative charge. In amino acids, these form in hydroxyl, carboxyl and amino groups.
Give some examples, hydrogen bonds forming in hydroxyl, carboxyl and amino groups.
For example, hydrogen bonds may form between the amino group of one amino acid and the carboxyl group of another. They may also form between polar areas of the R groups on different amino acids.
What may hydrogen bonds forming between polar areas of the R groups on different amino acids be particularly involved in?
These in particular are involved in keeping the tertiary and quaternary structure of the protien in the correct shape.
What can the presence of multiple hydrogen bonds give?
A lot of strength.
What is importance of ionic bonds in a polypeptide chain?
Ionic bonds can form between those carboxyl and amino groups that are part of R groups. These ionise into NH3+ and COO- groups. Positive and negative groups like this are strongly attracted to each other to each other to form an ionic bond.
What is the importance of disulphide links in a polypeptide chain?
The R group of the amino acid cysteine contains sulphur. Disulphide bridges are formed between the R groups of two cysteines. These are strong covalent bonds.
Where do Hydrophobic and hydrophilic parts of R groups tend to associate in a polypeptide?
Hydrophobic parts of the R groups tend to associate together in the centre of the polypeptide to avoid water. In the same way, hydrophilic parts are found at the edge of the polypeptide to be close to water.
What does hydrophobic, hydrophilic interactions cause?
Hydrophobic and hydrophilic interactions cause twisting of the amino acid chain, which changes the shape of the protien. These interactions can be a very important influence, given that most proteins are to be found surrounded by water inside a living organism.
What is carbohydrate?
A group of molecules containing C, H and O.
What is a glycosidic bond?
A bond formed between two monosaccharides by a hydrolysis reaction.
What do carbohydrates contain?
Carbon, hydrogen and oxygen.
How are the atoms bonded in carbohydrates?
Carbohydrates are hydrated carbon which means that for every carbon there are two hydrogen atoms and one oxygen atom.
What are functions of carbohydrate?
The functions of carbohydrates are three-fold. They act as a source of energy (e.g. glucose), as a store of energy (e.g. starch and glycogen) and as structural units. (e.g. cellulose in plants and chitin in insects). Some carbohydrates are also part of other molecules, such as nucleic acids and glycolipids.
What are the three main groups of carbohydrates?
There are three main groups of carbohydrates: monosaccharides, disaccharides ad polysaccharides. The common monosaccharides and disaccharides all have names ending in -ose.
Why are monosaccharides important?
Monosaccharides are the simplest carbohydrates. They are particularly important in living things as a source of energy.
What are monosaccharides?
They are sugars, which taste sweet, are soluble in water and are insoluble in non-polar solvents.
Why are monosaccharides suited to their role?
They are well suited to this role because of the large number of carbon-hydrogen bonds.
What is arrangement of atoms in a monosaccharide?
Monosaccharides can exist as straight chains or in a ring or cyclic forms. They have a backbone of single bonded carbon atoms, with one double-bonded to an oxygen atom to form a carbonyl group
How do different structures of monosaccharides vary in the amount of carbon atoms?
Hexose sugars have six carbon atoms, pentose sugars have five carbon atoms and triose sugars have three carbon atoms.
Why can monosaccharides be monomers?
Monosaccharide hexose sugars, like glucose, are the monomers of more complex carbohydrates, and they bond together to form disaccharides or polysaccharides.
Give an example of which monosaccarides exists as straight chains and which can be found in a ring.
In solution, triose and tetrose sugars exists as straight chains. However, pentose and hexoses are more likely to be found in a ring or cyclic form.
In both a straight chain and cyclic forms glucose can exists as a number of isomers, how does it form these isomers?
In the straight-chain form, the -H and -OH can be reversed. In a ring shape, isomers can also form. The ring is formed when the oxygen attached to the carbon 5 bonds to carbon 1. Because the -OH and -H on carbon 1 can be above or below the plane of the ring when the ring forms, there are two isomers alpha and beta - glucose. This small difference appears insignificant, but it becomes very important when glucose molecules polymerise into starch or cellulose.
Where has the word saccharide been derived from?
The Greek word sakkharon, which means sugar.
Give some examples of a disaccharide.
Like monosaccarides, disaccharides are sweet and soluble. The most common disaccharides are maltose (malt sugar), sucrose and lactose (milk sugar).
