Molecules and Amino Acids Flashcards
What are small molecules?
- sugars, amino acids, nucleotides, carboxylic acid derivatives
- act as building blocks for macromolecules
- may be used to store or release energy, which is the basis of metabolism
What are macromolecules?
- Proteins – chains of amino acids
- Polysaccharides – chains of simple sugars
- Nucleic acids – chains of nucleotides
- Can comprehend macromolecules due to their modular construction from much simpler smaller molecular units
- Basis of macromolecule assembly is the reversible formation of certain kinds of bonds
- Ex. Ester or amide bonds to link up smaller units into long chains
What are unique about each of the amino acids?
- Each amino acid has a unique side chain
- The combination of different side chains R1, R2, R3, etc gives each protein its unique properties
- Since the ⍺-amino/⍺-carboxylate core is constant, the side chain R determines the specific properties of a particular amino acid and the role it plays as a protein
What is myoglobin?
a protein that stores O2 in muscle tissue
a macromolecule
How large is a protein molecule?
- Most proteins: 10,000 to 100,000 g/mol
- Protein size is expressed in kiloDaltons (kDa)
- 1 Dalton (Da) = 1 g/mol (mass of H atom)
- 1 kDa = 1000 g/mol
- Myoglobin is 16.5 kDa – small protein
- P-glycoprotein is 170 kDa – large protein
- Largest known single protein molecule is titin at 10,000 kDa
Proteins form complex structures capable of many functions such as…
structural components of cells, catalysis of reactions, and communication processes
What is the building block principle of macromolecular structure?
What are proteins? What does each protein have?
- linear chains of amino acids
- linked by peptide bonds (type of amide bond)
- Each protein has:
- a unique sequence of different amino acids
- a well-defined size and structure
- Proteins have diverse functions including:
- catalyzing reactions (enzymes)
- forming complex subcellular structures
What is the basic amino acid structure?
- Each amino acid has an amino group and a carboxylate group
- Each amino acid has a different side chain R
- 20 different amino acids are found in proteins
- Side chain R: These give the protein molecule as a whole its unique properties
What are two peptide bonds?
(Condensation, Hydrolysis)
What are the bonds formed by condensation and broken by hydrolysis?
Condensation involves the removal of H2O from the units being linked
Hydrolysis regenerates the original carboxylic acid and an amino group
The C=O group of the amide is the point of weakness allowing H2O attack
Bonds formed by condensation and broken by hydrolysis:
Carboxylic acid + amino group ⇔ amide
Carboxylic acid + alcohol ⇔ ester
Large numbers of amino acids can be linked together to form a ___________ chain
What is a chain with many amino acids called? few?
Large numbers of amino acids can be linked together to form a peptide chain
Polypeptide – a chain with many amino acids, usually a complete protein Greek poly = many
Oligopeptide – a chain with a few amino acids, usually a fragment Greek oligo = a few
What are at each end of a polypeptide chain?
How many amino acids are in myoglobin?
One end of the chain has an amino acid with an uncombined amino group, usually protonated; this is called the N-terminal amino acid. The other end has an amino acid with an uncombined carboxylate group, called the C-terminal amino acid
there are 153 amino acids in myoglobin (16.5 kDa)
What are the carbons of the amino acid core identified by?
What do these carbons represent?
Carbon atoms of the amino acid core are identified by Greek letters
The ⍺-carbon is the central backbone atom
The β-carbon is the first atom of the side chain, the 𝜸-carbon is the second, etc
Functional groups may be linked to different core atoms:
- ⍺-amino
- ε-amino
Amino acid chains linked in this way are called peptide chains; the amide bonds linking them are called peptide bonds
What do amino acids have in common? What differs?
How can amino acids be grouped? What do you need to know for tests?
Amino acids share a common backbone, but differ in the side chain
Amino acids can be grouped according to structures or by similar properties
You need to be able to associate particular properties with each amino acid
- polarity
- charge
- hydrogen bonding ability
What are the amino acids with very non-polar side chains
- Alanine
- Valine
- Leucine
- Isoleucine
- Phenylalanine
- Methionine
What are the amino acids with moderately non-polar side chains?
- Glycine
- Cysteine
- Proline
- Tryptophan
- Tyrosine
What amino acids are polar but uncharged side chains
- Serine
- Threonine
- Asparagine
- Glutamine
What are amino acids with very polar positively charged side chains?
- Histidine
- Lysine
- Arginine
Atoms with similar electronegativity share what? What about different electronegativity?
- Atoms with similar electronegativity share bonding electrons equally, e.g. C-C, C-H, and are non-polar
- Pairs of atoms with different electronegativity distribute bonding electrons unequally – more electronegative atoms such as O or N get greater than 50% share, and this leads to unbalanced charges and polar bonds
What are hydrogen bonds?
- Hydrogen bonds are electrostatic interactions between a donor consisting of the dipole of a polar O-H or N-H bond and an acceptor, consisting of an available lone pair of electrons on a nearby N or O atom (which may be on different molecule)
- Highly polar –OH or –NH groups are good H-bond donors
- An acceptor is an electronegative atom with an available lone pair of electrons such as O or N
- Are not permanent bonds like covalent bonds, instead they result in temporary attractive forces that help hold molecules together
- H-bonding attracts H2O molecules to each other, and this makes water a liquid rather than a gas like methane CH4 whose molecules don’t form H-bonds
- Water molecules are excellent H-bond donors and acceptors; so polar amino acids interact well with H2O
- The hydrogen bond ( - - ) is about 5-10% as strong as a covalent bond, enough to make molecule R1 stick loosely to R2 but not to form a permanent link
What is the correct structure to represent an individual amino acid at neutral pH
How is it different when the amino acid is part of the peptide chain?
But when the amino acid is part of a peptide chain, the a-amino groups and a-carboxylate groups are linked as uncharged amide bonds
x-NH-CHR-CO-x
When combined as an amide, the ⍺ -amino groups and ⍺-carboxylate groups are not free to protonate or deprotonate, so in the peptide bonded state, the amino acid backbone is uncharged
Which aa contains a carboxylate group in their side chain? What are their charges?
Aspartate and glutamate contain carboxylate groups in their side chains (negatively charged at pH 7)
Side chain neutral (COOH) when protonated and -1 (COO-) when deprotonated
Which aa ionizes on their side chain N atoms?
What are their charges?
Arginine, Lysine and Histidine ionize on their side chain N atoms (positively charged at pH 7)
Side chains are +1 (= NH2+, -NH3+, -NH+) when protonated and neutral (= NH, -NH2, -N) when deprotonated
Which aa also have ionizable side chains?
What are their charges?
Cysteine and Tyrosine also have ionizable side chains (Neutral at pH 7)
Side chain neutral (SH, OH) when protonated and -1 (S-, O-) when deprotonated
The ionization state of each group depends on its pKa value and the pH of the solution chart
How do you calculate the exact state of ionization (and therefore charge) of a group at a given pH
(we need to do this when the pH is less than 1 unit away from pKa)
▪ Histidine side chain has pKa = 6.5
▪ At pH = 7, the major form will be deprotonated His, but some protonated His [HisH+] is present
pH = pKa + log [His]/[HisH+]
7.0 = 6.5 + log [His]/[HisH+]
[His]/[HisH+] = 100.5 = 3.2
If ratio [His] / [HisH+] = 3.2, what percentage (or fraction) of the total histidine is deprotonated?
