L3 Proteins 1 (+acid/bases continued) Flashcards
What is a buffer?
A buffer is a solution that can resist pH change upon the addition of acidic of basic components
What can act as a buffer?
Weak acids
What do you need for a buffer to buffer in both directions (resists both acid and base)
A weak acid and its conjugate base
What is a functional group?
Whenever something is attached to a carbon
What are some examples of macromolecules? (4)
- proteins
- nucleic acids
- carbohydrates
- lipids
What is an advantage of biochemical unity?
Organisms acquire their needed biochemicals and energy from eating/digesting other organisms, since all organisms are made up of the same macromolecules
What is a anabolic reaction?
An anabolic reaction is a reaction that requires an input of energy. It involves the building of larger more complex molecules from smaller simpler ones.
What is a catabolic reaction?
Catabolic reactions break chemical bonds in larger more complex molecules. They release energy
Polymer
A substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits
Condensation (polymerization)
Formation of a polymer linked by covalent bonds, releasing one water molecule with each monomer added
Is condensation / polymerization an anabolic or catabolic reaction?
Anabolic reaction
What are some examples of condensation / polymerization? (2)
- DNA replication
- protein synthesis
Hydrolysis (depolymerization)
The breaking of covalent bonds with the help of water to transform a polymer into its constituent monomers
Is hydrolysis / depolymerization an anabolic or catabolic reaction?
Catabolic reaction
What are an example of hydrolysis / depolymerization? (1)
Digestion of food molecules
What is ATP?
ATP is Adenosine triphosphate. It is the source of energy for use and storage at the cellular level.
What is ATP hydrolysis?
ATP hydrolysis is the catabolic reaction process by which chemical energy that has been stored in the high-energy phosphoanhydride bonds in adenosine triphosphate (ATP) is released after splitting these bonds, for example in muscles, by producing work in the form of mechanical energy.
What are proteins?
Proteins are macromolecules that comprise one or more long chains of amino acids
Examples of functions of proteins (5)
- build structures like hair
- replicate DNA
- catalyze metabolic reactions
- transport materials inside cells and across the membrane
- folding
What are amino acids?
An amino acid is an organic molecule that is made up of a basic amino group (-NH2), an acidic carboxyl group (-COOH), and an organic R group (or side chain) that is unique to each amino acidd
When are amino acids neutralized?
At a neutral pH
What composes the amino acid backbone? (3)
- amino group
- carboxyl group
- H
How are amino acids classified?
By the properties of their side chains
What are the 4 different classes of amino acids? (of their side chains)
- polar side chains
- non polar side chains
- hydrophobic side chains
- electrically charged side chains
What is the peptide bond formation? What groups are involved in the reaction? What is the resulting product?
Peptide bond formation is a condensation reaction that occurs between the carboxyl group of one amino acid and the amino group of the next amino acid which generates a peptide backbone.
What happens when you keep repeating peptide bond formation? (what is the product)
A polypeptide chain
What is special about the peptide bond between the C and N in a polypetide chain?
It is a covalent bond with a partial double bond character, which makes it unable to rotate.
What are peptides?
Peptides are short chains of amino acids linked between peptide bonds.
What is a polypeptide?
Polypeptide is another word for protein
What does an amino acid start with?
an amino group (N-terminus)
What does an amino acid end with?
a carboxyl group (C-terminus)
What is the primary structure?
The primary structure is the number of amino acids used and the sequence in which they are arranged (covalently bonded to each other)
What does the primary structure determine?
It determines all of the properties of the resulting protein
Does the formation of the primary structure require or release energy?
It requires energy
Why is the polypeptide backbone flexible?
Because it consists of a single covalent bond and rotation is possible in single bonds (but not in double bonds)
What does the flexibility of the polypeptide backbone allow for?
It allows for polypeptides to fold into proteins
What are the two steps of the folding of polypeptides into proteins?
1) Hydrogen bonds form within the polypeptide backbone between the O of a carboxyl group and the H of an amino group
2) This gives rise to 2 secondary structures that form very quickly after a polypeptide has been made
What are the two secondary structures?
- the alpha helix
- the beta pleated sheet
Does the formation of a secondary structure require or release energy?
It releases energy, ie it occurs automatically
Are the side chains involved in the Hydrogen bonds during the folding of a polypeptide?
No
What is the alpha helix? (2)
- Hydrogen bonds form in the direction of the helix, generating a rod like structure
- Side chains point outwards towards the helix
What is the beta- pleated sheet? (2)
- Hydrogen bonds form within the plane of the sheet, generating a stable sheet
- Side chains point away from the plane, up or down
Are there any rules of where you find alpha helices and beta sheets within a protein?
No
How can you determine the presence or absence of secondary structures within a protein?
Through protein structure determination
What is proline?
Proline is an amino acid
What makes proline special? (4)
- Its N-C bond cannot rotate, because its side chain is covalently bonded to the C and N of the peptide backbone
- The backbone Hydrogen bond can also not form
- So it is not possible for proline to form secondary structures
- Proline is often the last amino acid of an alpha helix
What determines the secondary structure (alpha or beta)?
H-bonding
What is the primary structure?
The sequence of amino acids with each amino acid linked to the next by peptide bonds
Does the polypeptide have to fold into the secondary structures (either alpha or beta) ?
No it can remain unfolded
