Biological molecules:Proteins Flashcards
What are proteins made up of
What is the genreal structure of amino acids
Proteins are polymers, meaning they are made up of many repeating units. The monomers (single units) of proteins are called amino acids.
Amino acids.
Carboxyl group: ā O C -OH (-COOH)
Amino group: H N H (-Nh2)
R variable group: Side group consits of carbon chain and may include other functional groups e.g benzene ring or -OH
H R O
\ ! //
N-- C --C
/ ! \
H H OH
What are proteins?
Proteins are polymers made up of long chains of monomer amino acids. They are essential for the structure and function of cells.
e,g
enzymes: amylase, catalase - speed up chemical reactions
Structural proteins: collagen, keratin
Transport proteins: haemoglobin
Hormones: insulin
Antibodies
How are proteins formed?
(Dipeptides and polypeptides)
Proteins are formed when amino acids join together via condensation reactions, forming peptide bonds. eliminates water
When two amino acids join, they form a dipeptide.
When many amino acids join, they form a polypeptide (which folds into a functional protein).
peptide bonds form between OH of carboxyl and H of amine group
How many amino acids are there and how do they differ from one another?
20
Differ only by side group R
How many level of protein structure are there?
Proteins have four levels of structure, which affect their function.
Primary
Secondary
Teritary
Quaternary
Define primary structure of a protein
The order, Sequence, number and type of amino acids in the polypeptide chain.
* Determined by sequence of codons on mRNA
Define secondary structure of proteins
The sequence of amino acids cause parts of a protein molecule to bend into an alpha helix shapes or fold into beta pleated sheets.
Hydrogen bonds hold the secondary structure.
H bonds form between C=O groups of the carboxyl group of one amino acid and the H in the amine group of another amino acid. (O to H)
Alpha helix@ All N-H bonds on same side of protein chain, spiral shape. H bonds parralel to helic axis
B pleated sheet N-N and C=O alternate from one side to another
Define Tertiary structure of proteins
The protein gets further folded creating a unique 3d shape held in place by ionic, hydrogen and disulphide bonds.
Disulfide bridges:Strong covalent S-S bonds between molecules of amino acid cysteine
Ionic bonds: relatively strong bonds between charged R groups (Ph changes can break them)
Hydrogen bonds:numerous and easily broken
The ionic and disulfide bonds form between the R groups of different amino acids.
Disulphide bonds only sometimes occur as there must be a sulfur in the R groups for this bond to occur SāS
Define Quaternary structure of proteins
a protein made up of more than one polypeptide chain. e,g haemoglobin made up of four.
precise 3d structure held together by the same tpes of bonds as tertiary structure.
May involve addition of prosthetic groups e.g metal ions or phosphate groups
Describe the structure and function of globular proteins
Spherical and compact
Hydrophillic R groups face outwards and hydrophobic R groups face inwards- usually water soluble
Involved in metabolic processes e.g enzymes and haemoglobin
Describe the structure and function of fibrous proteins
Can form long chains or fibres
Insoluble in water
Useful for structure and support e.g collagen in skin
Enzymes are proteins, apply protein structure to the denaturing of enzymes
If a protein is denatured the bonds which hold the teritary and secondary structure in a shape break and therefore the uniqe 3d shape is lost (enzymes lose active site shape)
Conditions that denature a protein
a too high temperature (too much kinetic energy)
Too high/low a Ph (too many H+ or OH-)
What is the importance of the primary structure +apply to enzymes
If even one amino acid sequence is different then it will cause the ionic.hydrogen disulfide bonds to form in a different location resulting in a different 3D shape
Enzymes will have a different shaped active site and will be non functioning
Carrier proteins will have a different shaped binding site (molecules no longer complementary and cannot be transported across membrane)
What are enzymes
Enzymes are tertiary structure proteins which catalyse intra and extracellular reactions.
The specific tertiary structure determines shape of active site which is complementary to a specific substrate due to the specific bonding and folding in the tertiary structure of the protein.
Enzymes can only attatch to substrates that are complementary in shape.
Formation of enzyme substrate (ES) complexes lowers activation energy of metabolic reactions
What is the activation energy what do enzymes do to it?
minimum amount of energy equired for a reaction to occur
When enzymes attach to the substrate they can lower the activation energy needed for the reaction to occur and therefore spped up the reaction
Explain the induced fit model of enzyme action
Shape of active site is not directly complementary to substrate and is flexible
Active site is induced or slighty changes shape to mould around the substrate, when the substrate complex is formed it puts strain on the bonds and lowers the activation energy, products are then removed and the enzyme active site returns to its orginal shape.
Expla
Explain the lock and key model for enzyme action
This model suggests that the enzyme is like a lock and key the substrate being the key that fits into the enzyme due to the complimentary shape.
It also suggests that the enzyme active site is a fixed shape and taht due to random collisions the substrate can collide and attach to the enzyme forming the enzyme substrate complex.
Once the enzyme substrated complex has formed, the charged groups within the active site are thought to distort the substance and therefore lower the activation energy, the products are then released and the enzyme can be reused
How have models of enzyme action changed
- Initially lock and key model: rigid shape of active site complementary to only 1 substrate
- Currently induced fit model also explains why binding at allosteric sites can change shape of active site
Name five factors that affect the rate of enzyme controlled reactions
- temperature
- PH
- Enzyme concentration
- substrate concentration
- concentration of inhibitors
How does temperature affect the rate of enzyme controlled reactions
If the temperature is too low there is not enough kinetic energy for successful collisions between the enzyme and substrate.
If the temperature is too high enzymes denature, the active site changes shape and enzyme substrate complexes cannot form.
Rate uncreases as kinetic energy increases and peaks at optimum temperature. above optimum ionic and H bonds in 3D structure break and active site is no longer complimentary to substrate.
How does PH affect enzyme controlled reactions?
Too high or too low pH will interfere with the charges in the amino acids in the active site this can break the bonds holding the teritary structure in place and therefore the active site changes shape.
The enzyme denatures and fewer es complexes form.
How does substrate and enzyme concentration affect enzyme controlled reactions>
If there is insufficient substrate then the reaction will be slower as there will be fewer collisions between the enzyme and the substrate (Gradient levels off)
If there is in sufficient enzymes then the enzyme active sites will become saturated with substrate and unable to work any faster. rate levels off when maximum of ES complexes for at any given time
What are competitive inhibitors
Competitive inhibitors are the same shape as the substrate and can bind to the active site. this prevnts the substrate from binding and the reaction occuring if you add more substrate this will flood/out-compete the inhbitor knowcking them out of the active site.
What are non competitive inhibitors
Non competitive inhbitors bind to the enzyme away from the active site (the allosteric site) this causes the active site to change shape and therefore the substrate can no longer bind regardless of how much substrate is added.
Compare competitive and non competitive inhibitors
Competitive inhibitors: similar shape to substrate=bind to active site, do not stop reaction ES complex forms when inhbitor is released. INcreasing substrate conc reduces affect
Non competitive inhibitors: Bind at allosteric binding site. may permanently stop reaction triggers active site to change shape. Increasing substrate conc has no affect
