Unit 1.2c(i) Flashcards
What are some examples of what proteins function as?
- enzymes
- hormones
- antibodies
- regulators
- transporters
- structural proteins (form skin, hair etc)
What do polymers of amino acids make?
Monomoers
How many amino acids are there?
20
What does amino acid structure determine?
Proteins structure
What are R-groups?
Amino acid side groups
Do all R groups have the same functional groups?
No they all have different functional groups
What are the 4 groups that amino acids R groups fall into?
- Basic (+ charge)
- Acidic (- charge)
- Polar
- Hydrophobic
What are R group’s important for?
The protein function
What gives amino acids their unique chemical properties and their specific shapes?
R groups
What determines how proteins fold and interact?
R groups
What do basic r-groups have?
NH2
If the r-group is basic what can it accept and why?
It accepts H+/protons because of its NH2 becoming NH3+
Why would basic r groups become hydrophilic?
If they accept a proton
What group do acidic R groups have?
They have carboxylic acidic groups, COOH
Do acidic R groups gain or donate proteins/H+ ions?
They donate to other atoms
What is formed when acidic r groups donate a proton?
The become COO-
What halogens to acidic r groups when they donate a proton?
They become negatively charged and strongly hydrophilic
Are polar r groups hydrophilic or hydrophobic?
Hydrophilic
Why are polar r groups hydrophilic?
They form weak hydrogen bonds with water molecules
Why do polar R groups look for water contact?
They have a more positive and negative side
What do polar groups have on the side of their r side chains?
Oxygen, nitrogen and sulfur
What is the simplest of amino acid r groups?
Hydrophobic
What do hydrophobic R groups not contain?
OH, COOH, NH2, SH
Is hydrophobic polar or non polar?
Non polar
Do hydrophobic R groups ever develop a charge?
They don’t become charged
Is hydrophobic water loving or water hating?
Water hating
What are the 4 levels of proteins?
Primary, Secondary, Tertiary, Quaternary
What is the primary amino acid structure?
The order in which amino acids are synthesised during translation into the polypeptide
What do peptide bonds do?
They join the amino acids together that make the protein
How are peptide bonds formed?
Condensation reactions between carboxylic groups and amine groups on neighbouring amino acids
What does the carboxylic acid loose when it makes a condensation reaction?
OH
What does the amine group lose in a condensation reaction?
H
How is the amino acid group extended?
By the continuous addition onto the end of the chain
What is the amine end and the carboxylic acid end called?
The N and C terminus
What are amino acid names represented by?
Their 3 letter abbreviations
What forms the secondary structures?
Hydrogen backbones
What are the secondary structures called?
- a-helices
- parallel, antiparallel B-sheets, or turns
How do secondary structure 3-d shaped form?
The backbone folds
What does an a-helix secondary structure look like?
Spirals
What sticks out the the a-helix?
R-groups stick out
Why do a-helix’s form their specific shape?
Because hydrogen bonds form between the 4th peptides (between oxygen of carboxy and hydrogen of the amine)
How are the peptide bonds formed in the a-helix?
The weak positive hydrogen is attracted to the weak negative oxygen
How many amino acids are in each turn of the a-helix turn?
3.6
How many amino acids are in a typical section of an a-helix?
11 amino acids
Why are the R-groups free to interact?
Because they face outwards
How are beta pleated sheets formed?
Hydrogen bonds form between parts of the polypeptide stands running next to each other
Are the hydrogen-oxygen bonds the same as they are in the a-sheet?
Yes
Where do the R-groups sit on the beta pleated sheet?
Above and below
What direction do beta pleated sheets usually run in?
Antiparallel (opposite directions)
What determines how antiparallel structures run?
Where the N and C terminal are
What do turns do?
Reverse the polypeptide direction
What do turns allow?
Interactions between secondary structure elements
What is the tertiary structure?
The complex 3D conformation that the final polypeptide structure takes
What interactions establish the tertiary structures?
Interactions between amino acid R groups
How do prosthetic groups improve tertiary structures?
By giving an added function
What are the 6 interactions tertiary structures undergo?
Hydrogen Bonds
Disuphilde Bridges
Ionic Bonds
Hydrophobic Interactions
London Dispersion Forces
Van de Waals Interactions
How is a hydrogen bond formed?
Formed by hydrogen and oxygen atoms from the main chain and R groups
How are disulphide bridges formed?
They’re formed if the R-groups in two amino acids contain a sulphur atom and are near each other
How are ionic bonds formed?
They’re formed in solutions of carboxylic acid and amino groups that form charged groups in a solution. If the charges are opposite an ionic bind will form
How are hydrophobic interactions formed?
They are formed when hydrophobic R groups cluster towards the interior of the protein molecule
What are LDFs?
They are temporary attractive forces that individually weak but collectively contribute to maintaining protein structure
What are van de Waals interactions?
they are electrical interactions between 2+ atoms/molecules that are very close to each other
Are van de Waals weak or strong interactions?
They are both;
Weak by themselves
Strong when working together
Wha quaternary structures?
They are several connected polypeptide sub-units that exist in proteins and are held together by tertiary interactions
What happens if a protein only contains 1 polypeptide subunit?
No quaternary structure it formed, it stops at the tertiary structure.
Haemoglobin in a quaternary structure, how many polypeptide subunits is it made of?
4
Are prosthetic groups added to quaternary structures?
Yes they are
Wha are prosthetic groups?
They are additional non-protein structures with no necessary functions
What’s an example of a non-prosthetic group and where can it be found?
Haem found in Haemoglobin
What does Haem contain?
An iron atom for oxygen binding
How is iron bound to Haemoglobin?
It is covalently bound due to histidine amino acids
What are the two main factors that impact protein structure?
Temperature and pH
What happens to a protein when it denatures?
It looses its shape and function
What influences R-group interactions?
Temperature and pH
What is impacted when temperature increases?
First weak then strong covalent bonds are disrupted
What does the alteration of pH from optimum result in?
The ionic intercations between R-groups becoming lost
