Amino Acids, protein structures Flashcards
What are all proteins formed from
All proteins are formed from amino acids
How many different amino acids are there
There are 20 different amino acids
Draw the general structure of an amino acid
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What are the three main parts to an amino acid
Amine group (NH2)
Carboxyl group (COOH)
R group (the R group is different for each of the twenty amino acids)
Which part of the amino acid is different for each of the twenty amino acids
The R group is different for each of the twenty amino acids
e.g. in glycine the R group is a carbon atom
in another one
carbon atom bonded to three hydrogen atoms
Which parts/groups of an amino acid are the same for every amino acid
The amine group and carboxyl group are the same for every amino acid
Describe the general structure of amino acids
Three main parts to an amino acid:
Amine group (NH2)
Carboxyl group (COOH)
R group (the R group is different for each of the twenty amino acids)
What elements are present in proteins
They contain
carbon hydrogen nitrogen oxygen
Some amino acids also contain the element sulfur
How amino acid molecules can bond together
Bond together by a peptide bond
Describe how a peptide bond can be formed
Formed when two amino acids react together and form a chemical bond
h from amine group
and oh from carboxyl group is lost - to form water
The bond formed is called a peptide bond
A molecule of water is also formed. Therefore this is an example of a condensation reaction
formed when two amino acids are joined together
When two amino acids are joined together, what is it called
The molecule formed when two amino acids join together/bonded together is called a dipeptide
Formed in a condensation reaction
how are dipeptides formed
Dipeptides are formed by the condensation of two amino
acids.
how are polypeptides formed
Polypeptides are formed by the condensation of many amino
acids.
A condensation reaction between _______ amino acids forms _____
A condensation reaction between two amino acids forms a peptide
bond
Draw the reaction between two amino acid molecules
label the bond formed
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how many polypeptide chains may a functional protein contain
A functional protein may contain one or more polypeptides.
Where does the reaction of the formation of a dipeptide occur
This reaction takes place in the ribosomes (which is where proteins are synthesised in cells)
The reaction is catalysed by a specific enzyme
What is formed when three or more amino acids are joined together
A polypeptide - formed when three or more amino acids are chemically bonded/joined together -
1 molecule of water for every peptide bond formed
often consist of hundreds of amino acids joined together
Describe how a peptide bond can be broken
Add water to the peptide bond
Breaks the peptide bond
Converts the dipeptide/polypeptide into original amino acids
Called a hydrolysis reaction
Where do hydrolysis reactions for dipeptides/polypeptides occur in the body
This reaction is carried out by protease enzymes in the digestive system
Difference between a polypeptide and protein
To be classed as a protein, a polypeptide has to fold into a complex, three dimensional shape
Once the polypeptide has folded into the correct shape - it can then carry out its function e.g. as an enzyme or a hormone
At this point, it would be referred as a protein molecule
Many proteins made from many different polypeptides forming a large and complex molecule
also contains other molecules to help carry out their function
What are the different levels of protein structure
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Describe what is meant by the primary
First level of protein structure is called the primary structure
The primary structure is the specific order of amino acids in a polypeptide
e.g. two polypeptides with different primary structures
a - b - c - d - a
a - a - b - d - c
How is the primary structure really important for a protein
The primary structure is really important for a protein
This is because it helps to determine the final 3 dimensional shape of the protein molecule
And the shape of a protein is critical for its function
Even changing a single amino acid in the primary structure can change the final shape of the protein
this can prevent a protein from carrying out its function effectively
What is the primary structure of a polypeptide determined by
The primary structure of a polypeptide is determined by the DNA sequence of the gene which encodes that polypeptide
what is the secondary structure of proteins
how the secondary structure forms
In a/along the polypeptide chain, there are C=O groups and N-H groups
The oxygen atoms in the C=O groups have a small negative charge and
The hydrogen atoms in the N-H groups have a small positive charge
These positive and negative charges can attract each other
When this happens, hydrogen bonds form between amino acids all along the polypeptide chain
These hydrogen bonds cause the polypeptide chain to twist and fold into shapes.
These twists and folds are called the secondary structure
What is secondary structure
When hydrogen bonds form between amino acids in the chain, it causes the chain to begins to coil into alpha helix or fold into a beta pleated sheet - secondary structure
where specific regions of the chain then fold
examples of secondary structure
alpha -helix - polypeptide chain has twisted into a helical shape held in place by hydrogen bonds
beta-pleated sheet - the polypeptide chain folds into a flatter, sheet-like structure. Hydrogen bonds between amino acids hold the shape in place
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Can proteins have both alpha and beta pleated sheets
Many proteins have regions with alpha helices and beta-pleated sheets
what does the type of secondary structure formed depend on
The type of secondary structure formed depends on the primary structure in that region
Certain amino acids tend to be found in alpha helices and others tend to be found in beta-pleated sheets
depends on amino acids present
how is secondary structure stabalised
Secondary structure is stabilised by hydrogen bonding between different parts of the polypeptide chain
what is meant by tertiary structure of proteins
The tertiary structure is the overall complex 3-dimensional shape of a polypeptide chain
- when you have an unfolded polypeptide chain - has not started folding
- first the chain folds into regions of secondary structure - alpha helix - beta-pleated sheet
- once regions of secondary structure form, the chain now continues folding forming the final tertiary structure
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tertiary structure contains 5 alpha helices wrapped in a very specific pattern around a beta pleated sheet
explain why tertiary structure is important
The tertiary structure is important for how a protein functions.
E.g. the active site of an enzyme depends on the protein forming a very specific tertiary structure.
If we change the tertiary structure of an enzyme e.g by heating it, the the shape of the active site changes and the enzyme can no longer function effectively
enzyme has denatured
what is meant by quaternary structure of proteins
some proteins consist of one polypeptide chain
however a large number of proteins consist of several different polypeptide chains working together as a large molecule
e.g. haemoglobin - formed from four polypeptide chains - these polypeptide chains are called subunits
_______
The quaternary structure shows how the individual subunits are arranged (fit together) AND also the position of any prosthetic groups to form a larger three dimensional complex protein molecule structure
quaternary structure only applies to proteins with at least two sub units
made from several different polypeptide chains held together by bonds
what do some proteins also contain/what other molecules
prosthetic groups meaning
Some proteins contain other non-protein molecules forming part of the structure
These are called prosthetic groups and they help the protein to carry out its role
e.g. haemoglobin, contains the prosthetic group haem which bind to oxygen
what are conjugated proteins
Proteins with a prosthetic group
