proteins Flashcards
Draw the structure of an amino acid
what are proteins made of?
what’s it called when two amino acids join together ?
heats it called when multiple amino acids join together?
Monomers called amino acids
dipeptide
polypeptide-proteins are made up one or more polypeptides
what do all amino acids contain
carbon, oxygen,hydrogen and nitrogen and some have sulphur
what two groups are the same for every amino acid
amine and carboxyl
what chemical bond forms dipeptide and polypeptides
peptide bonds
what’s released during this reaction an what’s it called
water-condensation
where does the reaction take place
ribosomes-site of protein synthesis
what enzyme carries out the hydrolysis of this reaction
protease- adds water back to reaction breaking peptide bond
difference between polypeptide and protein?
to be a protein a polypeptide has to fold into a complex 3d shape correctly.
it carries out its functions as an enzyme or hormone and at this point we call it a protein molecule.
many proteins contain diff polypeptides what does this then form?
Large complex molecule.
what’s the primary structure for a protein
this is the sequence of amino acids in the polypeptide.diff proteins have a diff sequence of AA in their primary structure. A change in one amino acid may change the whole structure of protein.The amino acids are held together by peptide bonds.
If one amino acid affects the sequence and change the shape of the protein what would happen
it would prevent the protein from carrying out its function effectively
What happens in the secondary structures
Hydrogen bonds form between -NH and -CO groups of amino acids in chain. This makes it coil into a alpha helix or beta pleated sheet.
why do hydrogen bonds form
the oxygen atoms in the CO groups have a small negative charge and the Hydrogen atoms in the NH group have a small positive charge.These charges attract and hydrogen bonds form along polypeptide chains
what happens in the tertiary structure?
the coiled or folded chain of amino acids folded further and more bonds form along chain.
describe the bonds that form along the chain in the tertiary structure
ionic-attraction between negatively charged R groups and positively charged R groups.
disulphide- when two molecules of AA cystein come close tg the sulfur atom in one cysteine bonds to the other sulfur in other cysteine forming a disulphide bond.
hydrophilic and hydrophobic-when hydrophobic R groups are close together in protein they clump tg. So hydrophilic R groups pushed to outside which affects how protein folds to its final structure.
Hydrogen bonds-formed between slightly + charged r groups and slightly -charged r groups
what proteins have the tertiary structure a their last structure
ones made form a single polypeptide chain
what happens in quaternary
this is for proteins made from several diff polypeptide chains and the QS is how these chains are assembled. The QS Is determined by tertiary structure of the individual polypeptide chains being bonded tg. SO its influenced by all the bonds
Describe globular proteins
Round and compact.They are soluble and so easily transported in fluids
How are globular proteins soluble
The hydrophilic R groups on the amino acids are pushed to the outside of molecule and this is caused by hydrophobic and hydrophilic interactions in tertiary structure.
Name examples of three globular proteins
Hämoglobin
Insulin
Amylase
Describe Hämoglobin
Carries 02 around body in rbc.
It’s a conjugated protein so it has a protein with a prosthetic group.
Each of the 4 polypeptide( 2 alpha and 2 beta) chains in Hämoglobin has a prosthetic group called haem.
Haem group contains iron which oxygen binds to and bindings easier due to tertiary structure changing.
Water soluble so dissolved in plasma
Describe insulin
Hormone secreted by pancreas. Helps to regulate blood glucose level. It’s soluble so it can be transported in blood to tissues where it acts. An insulin molecule consists of 2 polypeptide chains which are held together by disulphide bonds. Where they’re in pancreas 6 of these molecules bind to form a large globular structure.
Describe amylase
Enzyme which catalyses breakdown of starch in digestive system. It’s made of a single chain of amino acids. Secondary structure contains alpha helix and beta pleated sheet sections.
What’s a prosthetic group
Non protein part
Describe fibrous proteins
Tough and rope shaped so can form long chains. They are also insoluble and strong. They’re structural and fairly unreactive
Give three fibrous proteins
Collagen
Keratin
Elastin
Describe collagen
Found in animal connective tissues like bone skin and muscle.
It’s very strong
Minerals can bind to protein to inc rigidity
Describe keratin
Found in many external structures of animas like skin hair nails feathers and horns. Either flexible or tough
Describe elastin
Found in elastic connective tissues such as skin, large blood vessels and some ligaments. It’s elastic so it allows tissues to return to Og shape after they’ve been stretched.
How does Hämoglobin structure make it easier for oxygen to attach
When oxygen attaches the quaternary structure of proteins slightly chabges
Making it easier for oxygen to attach
Amylase is an enzyme explaij how criticism the specificity of its shape is
Amylase is made of a single polypeptide chain and this chain folds to form a groove along surface which is active site.
Shape of active site means it fits perfectly to the substrate molecule
As the active site is perfectly shaped to fit substrate it makes amylase extremely soecific
Describe and explain shape of collagen
Polypeptide chains wrap together to form a TRIPLE HELIX.
In the polypeptides every third AA is glycine and R group is H so glycine has smallest R group
So this allows collagen polypeptides to wrap tightly around each lther
As they wrap tightly around each other hydrogen bonds form between polypeptide chains
What do the hydrogen bonds in collagen do
Help stabilise quaternary Structure of the protein
How else is collagen so strong aside from its triple helix shape
Polypeptide chains held together by string crosslinks and there’s cross linking between diff helical molecules.
Collagen molecules are staggered to prevent weak spots
How is keratin strong
Has a high number of AA cysteine which is shed to form disulfide bonds(string covalent bonds).
How does it allow tissues to return to Og shape after stretcg
The hydrophobic regions would usually allow elastin strands to associate but when they’re stretched the strands move apart but remain attached at crosslinks.
After stretching the elastin molecules spring back tg
What are lipids and name three types
Macromolecules containing carbon hydrogen and oxygen.
Triglycerides,phospholipids and cholesterol.
Describe a tryglecride
They have one molecule of glycerol with three fatty acids attached to it. It’s synthesised by the formation of an ester bond between each fatty acid and glycerol molecule.
Describe synthesis and breakdown of triglycerides
One triglyceride had three ester bonds. Each ester bond is formed by a condensation reaction (in which a water molecule is released). The process in which triglycerides are synthesised is esterification. Triglycerides break down when ester bonds are broken. Each ester bonds broken in a hydrolysis reaction ( in which a. Water molecule is used up)splitting the faty acids to wheter theyre rleased
what makes lipids insoluble in water
Fatty acids have long tails made of hydrocarbons. The tails are hydrophobic. These tails make lipids insoluble in water. All fatty acids have the same basic structures but hydrocarbon tail varies
Describe the enzyme that facilates breakage of ester bonds between fatty acids
lipase
What are the two diff types of fatty acids and contrast
Saturated- don’t have double bonds between carbon atoms in hydrocarbon tails.it’s saturated with hydrogen. Straught chain molecules have many contact points.Higher mp solid at rtp.found in animals fats
Unsaturated- one double bond between carbon atoms which causes the chain the kink. Kinked molecules have fewer contact points.lower mp-liquid at room temp.Found in plant oils
What are phospholipids
It has one phosphate group with glycerol and two fatty acids. The phosphate group is hydrophilic and fatty acids tails are hydrophobic
What is cholesterol
Another type of lipid with a hydrocarbon ring structure attached to a hydrocarbon tail.The ring structure has a polar hydroxyl group attached to it.
What’s the function of triglycerides
Energy storage molecule in animals and plants. Some bacteria used triglycerides to store both energy and carbon. Triglycerides are good for storage because long hydrocarbon tails of fatty acids contain lots of chemical energy which releases lots of energy when broken down.
Cuz of these tails lipids contain twice as much energy per gram as carbs.
Triglycerides are also insoluble so they don’t cause water to enter the cell by osmosis which makes it swell.
Triglycerides bundle tg as insoluble droplets in cells cuz fatty acid tails are hydrophobic - tails face inwards facing the selves from water w their glycerol heads.
What’s the function of phospholipids
Forms phospholipid bilayer- component of membranes
Tails are hydrophobic so they splay outwards so it’s waterproofing eg skin
As the centre(tails) are HydroP water soluble substances can’t easily pass through it and membranes acts a barrier to those substances
Are phospholipids and tryglycerides polymers
No they’re made from a small repeating unit so they’re macromolecules
Function of cholesterol
Helps strengthen the cell membrane by interacting with phospholipid bilayer.
Cuz of its small and flattened shape it allows cholesterol to fit between phospholipid molecules in membrane making them more packed tg. This helps it more rigid and less fluid.
Relate structure of tryglecrides to its function
High energy:mass ratio=high calorific value from energy storage
Insoluble hydrocarbon chain=no effect on osmotic water potential and used for waterproofing
Slow conductor of heat-thermal insulation
Less dense than water- buoyancy of aquatic animals
How to test for proteins
Biuret test
Add equal volume of sodium hydroxide to make solution alkaline
Add drops of dilute copper(||) Sulfate and swirl to mix
Positive-blue to purple
Negative-purple to purple
How to test for starch
Iodine text
Add iodine dissolved in potassium iodide to sample
Positive-brown orange to blue black
Negative-stays brown orange
How to test for lipids
Emulsion test
Dissolve samples with ethanol
Add an equal volume of water and shake
Positive- cloudy white emulsion
Negative - colourless
Test for sugars
Benedict’s
Reducing sugars-
Add benefits reagent and heat in a water bath that’s been brought to boil
Positive -it will form a coloured precipitate
negative -stays blue
Non reducing sugars-get new sample of solution
Add dilute hcl Then neutralise it with sodium hydrogencarbonate. and carefully heat in a water bath that’s been brought to boil.
Then do bennets test again
Positive-coloured precipitate
Negative-starts blue
Whats a gene
Sequence of DNA nucleotides that codes for a polypeptide. The sequence of amino acids in a polypeptide that forms the primary structure of a protein.
What determines order of amino acids
Order of nucleotide bases
What is each amino acid coded by and role of dna in protein synthesis
-triplet base and different triplets code for a diff amino acid.
Too large to move out of the nucleus so a section of the dna is copied into mrna, the mrna leaves nucleus to join ribosome in cytoplasm synthesising a protein.
What does mrna do
Carries the genetic code from dna in nucleus to cytoplasm where it makes protein during translation. In mrna the three bases are codons
What does TRNA AND RRNA do
TRNA is folded into a clover shape and hydrogen bonds between specific base pits hold modules in shape. Every TRNA molecule has a specific sequence of three bases at one which is an anticodon. And another amino acid binding site and other end. TRNA found in cytoplasm where it’s involved in cytoplasm. Carries amino acids that are used to make proteins to ribosomes
Rrna- ribosomes moves along mrna strand during protein synthesis, helps catalyse formation of peptide bonds between amino acids
Why do base triplets not share their codes
It’s non overlapping as each nucleotide is only part of 1 triplet codon
so fewer mistakes - no mutations
Codons are redgenerate what does this mean
There will be a neutral effect on protein outcome as point mutations will give rise to same amino acids
What is a colorimeter
a device that measures the strength of a coloured solution by seeing how much light passes through it — A colorimeter measures absorbance the amount of light absorbed by the solution).
The more concentrated the colour of the solution, the higher the absorbance is.
How to find glucose concentration of an unknown solution
Make up solutions of known glucose concentrations, then measure the absorbance of these solutions and plot these absorbances and plot absorbance to make calibration curve to estimate conc of glucose in unknown conc
How to make known concentrations of glucose
1.Line up five test tubes in a rack.
2. Add 10 cm’ of the initial 40 mM sucrose solution to the first test tube and 5 cm of distilled water to the other four test tubes
3. Then, using a pipette, draw 5cm3 of the solution from the first test tube, add it to the distilled water in the second test tube and mix the solution thoroughly.
You now have 10 cm of solution that’s half as concentrated as the solution in
10 cm of 40 mM
the first test tube (it’s 20 mM).
4. Repeat this process three more times to create solutions of 10mm,5mm and 2.5mm
How to measure absorbance of known solution
Do a Benedict’s test on each solution (plus a negative control of pure
Water.Use the same amount of Benedict’s solution in each case.
• Remove any precipitate — either leave for 24 hours (so that the precipitate settles out) or centrifuge them.
Use colorimeter to measure absorbance of the benedicts solution remaining in eacg tube
What’s a biosensor
a device that uses a biological molecule eg an enzyme to detect a chemical. biological molecule produces a signal (e.g. a chemical signal),then converted to an electrical signal by a transducer (another part of the biosensor). The electrical signal is then processed and can be used to work out other information.
Example of a biosensor
glucose biosensor is used to determine the concentration of glucose in a solution.
It does this using the enzyme glucose
oxidase and electrodes. The enzyme catalyses the oxidation of glucose at the electrodes — this creates a charge, which is converted into an electrical signal by the electrodes (the transducer). The electrical signal is then processed to work out the initial glucose concentration.
