U1-KA2 - PROTEINS- 2)protein Structure Flashcards
What are amino acids
Amino acids are the building blocks of proteins ; amino acid sequence determines protein structure
What is a monomer
- a monomer is a molecule that may bind chemically to other molecules to form a polymer
Proteins are ________ of amino acid ________
Proteins are polymers of amino acid monomers
How are the amino acids in a protein linked
- the amino acids in a Protein are linked by peptide bonds to form polypeptides
- peptide bonds are covalent and very strong , they are difficult to beak
Peptide bonds are ________ and very strong. They are _________ to break
Peptide bonds are covalent and very strong , they are difficult to break .
Amino acids have the same basic structure , what does it consist of
All amino acids have a central carbon with four groups attached( an amine (NH2), a carboxylic acid group (COOH) , a hydrogen and a variable R group
How are amino acids classed
Amino acids are classed according to their properties
When are amino acid monomers linked together
Amino acid monomers are linked together during translation at ribosome
How are amino acids linked together
- Amino acids linked together at ribosome during translation
- an enzyme causes a condensation reaction between two adjacent amino acids
- a water molecule is removed by joining the OH a of the COOH of one amino acid to a hydrogen from the NH2 from the other amino acid
- the bond that links amino acids is peptide bond
What is N terminus and C terminus
- the chain has an NH2 group at the N terminus and a COOH group at the C terminus
- the order in which the amino acids are synthesised into a polypeptide chain from N terminus to C terminus is called the primary structure
Classification :
- how are amino acids actually classified
- how many groups are there of amino acids
- what are these groups
- amino acids are classified according to there R groups
- there are 4 classes
- the classes are : acidic (negatively charged) , basic( positively charged)
, polar and hydrophobic (non polar)
How do R groups vary
The R groups of amino acid vary in size , shape , charge , hydrogen bonding capacity and chemical reactivity
- how is there such a wide range of functions carried out by proteins
The wide range of functions carried out by proteins results from the diversity of R groups.
Why are interactions between R groups so important
- interactions between R groups are very important in determining the overall shape of proteins , and the R can influence the position of protein molecules in a cell.
Basic (positively charged)
- what other group defines the Molecule
- charge
- hydrogen bonds? Hydrophobic or hydrophilic
- ionic bonds ?
- side chain contains a second NH2 (amine)
- additional amino group gives net positive charge : The NH2 group gains a proton to become positively charged
- the R groups form hydrogen bonds if they are on the surface of the protein or with other amino acids if they are within the molecule
- therefore are hydrophilic : :attracted to water
- can form ionic bonds
Acidic (negatively charged)
- contains second COOH group (carboxyl group )
- the COOH group donates a proton to become negatively charged
- R groups form hydrogen bonds with water if they are on the surface of the protein or with other amino acids if they are within the molecule
- hydrophilic
- can form ionic bonds
Polar (neutral )
- what is electronegativity
- how do polar bonds occur
- hydrogen bonds ?
- Hydrophilic or hydrophobic
- common groups in polar molecules
- electronegativity is the measure of the attraction of an atom for the electrons in a bond
- polar bonds occur due when an atom has high electronegativity and one has low - the one with higher electronegativity has a greater share of electrons
- this results In the atom having a slight negative charge compared to the other atom which has a slight positive charge
- these side chains are also hydrophilic as they form weak hydrogen bonds with water molecules
- Polar r groups usually at surface of soluble protein
- polar amino acids generally have nitrogen /sulphur / oxygen groups
Etc (OH) group (-SH) group or (NH2)
Hydrophobic / non polar
- hydrophobic side chains only have hydrogen and carbon atoms ie hydrocarbon
- these R groups carry no charge / cluster together away from the surface of the protein molecule in a hydrophobic pocket so they do not interact readily with water molecules (do no form hydrogen bonds)
How is the structure of a protein determined
The structure of a protein is determined by the sequence of amino acids
How is the sequence of amino acids determined
The sequence of amino acids is determined by the order of bases on the DNA and subsequently the mature mRNA molecule
Explain what “levels” of of protein structure means
- so, as we already know a protein is a linear sequence of amino acids linked together by peptide bonds
- under appropriate conditions proteins spontaneously fold into a specific three dimensional shape
- this unique shape will form a functional protein
- ALL proteins will have 3 levels of structure : primary, secondary ,tertiary.
- how many levels of protein structure are there
- how many do ALL a proteins have
- There are 4 possible levels : primary , secondary , tertiary and quaternary
- all proteins have 3 : primary,secondary , tertiary
What is the primary structure
-how does this contribute to function of protein
- the primary structure is the sequence in which the amino acids are synthesised into the polypeptide
- the amino acid sequence determines the proteins structure and hence the function of the proteins
- the amino acids along the length of the polypeptide chain interact with one another
What is the secondary structure
- how is it stabilised
- some amino acids form hydrogen bonds which results in the secondary protein structure
- the secondary structure of a protein is stabilised by hydrogen bonds between atoms of the same chain
How / between what do the hydrogen bonds in the secondary structure form
The hydrogen of the N-H has a weak positive charge , so it is electrically attracted to the weak negative charge on the oxygen of the C - - O of another peptide bond
What are the 3 types of secondary structure
- a helix
- b pleated sheet (beta sheet)
- turns
The a helix
- a spiral with the R group sticking outwards
Beta sheet
- the B pleated sheet has parts of the polypeptide chain running alongside each other to form a corrugated sheet , with the R groups sitting above and below
B pleated sheet
Antiparallel and parallel?
- the B pleated sheet are usually antiparallel (chains in opposite directs with respect to the N-C polarity) but they can also be parallel B pleated sheets (chains that run same direction with respect to N-C polarity. )
- the sheets are parallel or antiparallel depending on their N and C termini ( look In scholar book)
Turns
- what are they
- what do they do
- what stabilises the interaction
- where do they lie, and what does it mean they can do
- turns are parts of polypeptide : parts of a polypeptide may also revere the direction of the chain making a turn
- turns usually join different secondary structures together or allow changes in the direction of the polypeptide causing folding or creat compact molecule
- hydrogen bonds again stabilise this interaction
- turns often lie on the surface of the proteins and so participate in interactions between proteins and other molecules
What is tertiary structure
- what does it consist of
- the tertiary structure is the final overall folded shape of the whole polypeptide
- consists of : this three dimensional conformation contains regions of secondary structure , which are stabilised in position by the interactions between R groups of amino acids
How are the R groups in different secondary structures close enough to react to form tertiary structure
- the R groups may have been far apart in the primary structure but the folding at the secondary level brings some R groups close enough to react
What are possible interactions between R groups
- hydrophobic interactions
- ionic bonds
- London dispersion forces
- hydrogen bonds
- disulphide bridges
Hydrophobic interactions
- occur between which molecules
- why do they fold
- occur between non polar R groups along the length of the polypeptide
- folding or these regions occurs, so that they form a central hydrophobic core forming hydrophobic pockets : this separates non polar hydrophobic R groups from water while the polar hydrophilic R groups are expressed on the outside of the structure free to interact with water
Ionic bonds
- occur between what molecules
- pH effect on ionic bonds
- give examples of ionised groups
- charge depends attraction occluding between oppositely charged polar R groups
- these groups are strongly charged and strongly attract to each other
- pH effects ionic bonding and can result in the denaturation of the protein at extremes of pH as the H+ and OH- ions in solution interact with the charge across the ionic bond
- COOH and NH2 groups ionise to become COO- and NH3+. These groups are strongly attracted to each other as they are strongly charged
London dispersion forces
- what are they
- occur between which molecules
- weak temporary attractions between atoms caused by localised movements of their electrons
- between non polar R groups
Hydrogen bonds
- what are they
- occur between which molecules
- hydrogen bonding is a weak polar interaction based in differences in electrical charge
- usually occurs between polar side chains
- often between hydrogen and electronegative elements such as Nitrogen , oxygen
Disulphide bridge
- what is it
- occurs between what molecules
- how does it occur
- where can they occur
- covalent bond - between R groups containing sulphur
- hydrogen is removed from each -SH R group to join with a free oxygen and the e atoms join with a very strong bond
- these can occur within a single polypeptide (tertiary structure) or between adjacent polypeptides (subunits , quaternary structure)
How are interactions in tertiary structure affected by
- temperature
- pH (which groups are affected by pH)
- increasing temperature disrupts the interactions that hold the protein in shape : the protein begins to unfold eventually becoming denatured
- changes on acidic and basic R groups are affected by pH : as pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost , which gradually changes the confrontation of the protein until it becomes denatured
What is quaternary structure
- how does it exist
- what brings about the structure
Quaternary structure exists in proteins with tow or more connect polypeptide subunits.
- the subunits are linked to each other by bonds or interactions between certain R groups of the different subunits.
- quaternary structure describes the spatial arrangement of these subunits
Example of protein with quaternary structure
Eg - collagen is made of three polypeptide subunits. Some proteins such as lysosome or myoglobin have only one polypeptide chain so tertiary structure is the final level of there structure.
What is a prosthetic group
- give an example
- in addition to the four levels of protein structure , some proteins can also have a prosthetic group
- this is a non protein group which is tightly bound to the polypeptide unit and is essential for the proteins function
- for example , myoglobin in muscles has a complex haem group which helps to draw oxygen into the muscle cells from the blood.
Talk about the role of amino acid R groups - in determining the location of proteins within cells
- the membrane consist of a phospholipid bi layer and the phospholipids have hydrophilic heads and hydrophobic tails, and the bi layer has some embedded proteins , and other proteins on the surface
- polar R groups are found on the surface of soluble proteins - soluble proteins are in the cytoplasm
- hydrophobic / non polar r groups cluster away from the surface , at the centre of the protein in a hydrophobic pocket
- membrane proteins are integral / peripheral
- integral proteins are embedded , as they have hydrophobic R groups which interact with hydrophobic region (tails) of the membrane
- peripheral proteins are loosely associated with the membrane , they have hydrophilic R groups reacting with hydrophilic heads of phospholipids
