Transcript of Amino Acids and Proteins Protein Structure and Function: An Overview.
- Slide 1
- Amino Acids and Proteins Protein Structure and Function: An
Overview
- Slide 2
- What We Will be Learning 1.Amino acid and Protein Structure and
Function: 2.Types of Amino Acids and properties 3.Acid Base
Properties of Amino Acids, zwitterions & isoelectric points
4.Molecular Handedness and Amino Acids, identifying enatiomers
5.Peptide bonding 6.Mechanism and properties for higher levels of
protein organization
- Slide 3
- Amino Acid Structure Amino acid refers to the presence of two
specific functional groups: A carboxylic acid An amine group
http://www.johnkyrk.com/aminoacid.html
- Slide 4
- DiPeptide bond When the carbonyl carbon atom loses an oxygen
atom, and the second amino acid contributes two hydrogen atoms, a
dipeptide bond forms joining the two amino acids.
- Slide 5
- Polypeptide Chains A chain of amino acids that contains more
than about 5 amino acids is called a polypeptide.
Ser-Leu-Thr-Ser-Val.
- Slide 6
- Variations of Amino Acids This central carbon is bound to 4
distinct groups While each amino acid has an amine group and a
carboxylic acid, there is variation in the side chain Glycine
variation in the side chain
- Slide 7
- The R Group There are four different classes of amino acids
determined by different side chains (R group): 1. non-polar and
neutral, 2. polar and neutral, 3. acidic and polar, 4. basic and
polar.
- Slide 8
- Non Polar Amino Acids Aliphatic side chains of hydrocarbon give
non polar amino acids Even though the Sulfur is electronegative,
the length of the chain makes methionine non polar and
hydrophobic
- Slide 9
- Identifying Side Chains
http://www.johnkyrk.com/aminoacid.html
- Slide 10
- Non polar Amino Acids with Aromatic Rings Phenylalanine
Tyrosine Tryptophane
- Slide 11
- Polar Amino Acid R groups that give polar amino acids: Amides
Hydroxyl Sulfur in a short chain
- Slide 12
- Amino Acids with Charged Side chains Basic R groups contain an
amino functional group (not amide- these are not polar enough to
ionize). Acidic R groups contain a carboxylic acid functional
group
- Slide 13
- Acid Base Properties of Amino Acids The carboxyl group of an
amino acid can lose a hydrogen ion R-COOH R-COO + H + The amine
group can accept a hydrogen ion R-NH 3 + R-NH 2 + H +
- Slide 14
- Neutral dipolar ions are known as zwitterions. can form
crystals have high melting points are soluble in water not soluble
in hydrocarbon solvents Amino acids share many of the properties we
expect from salts:
- Slide 15
- Ionization state of the Zwitterions depends on pH At neutral
pH, amino acids in solution exist as dipolar ions The amino group
is protonated -NH 3 + carboxyl group is deprotonated (-COO - )
- Slide 16
- In acidic solution (low pH), amino acid zwitterions accept
protons on their basic COO - groups to leave only the positively
charged NH 3 + groups. As the pH increases, the carboxyl group will
lose the proton, and both groups will be charged At high pH basic
conditions, both groups become deprotonate
- Slide 17
- Isoelectric point The pH at which the net positive and negative
charges are evenly balanced Each amino acid has at least two pKa
values (the pH at which the weak acid and its conjugate base are
present in equal amounts), one for the alpha carboxyl group and one
for the alpha amino group
- Slide 18
- PKa 9.7 Pka = 2.4
- Slide 19
- Handedness Chiral: Having right- or left- handedness non
superimposable mirror images Achiral: superimposable mirror images
and thus no right- or left handedness
- Slide 20
- Handiness in Molecules Like the mirror image of the hand these
molecules can not be superimposed they have handiness If a molecule
has an atom bonded to four different groups, it is chiral
- Slide 21
- Alanine is Chiral The mirror-image forms of a chiral molecule
like alanine are called enantiomers or optical isomers.
- Slide 22
- R & S Nomenclature Identify the group with the lowest
priority (low atomic number as #4 highest priority as #1 Draw an
arrow from low number to high number If the arrow traces a
clockwise movement, the enantiomer is the R enantiomer. If it is
counterclockwise, it is the S enantiomer.
- Slide 23
- Archiral lacking in handiness Propane is an achiral molecule.
The molecule and its mirror image are identical and it has no left-
and right-handed isomers
- Slide 24
- Amino Acids are Chiral The naturally occurring amino acids are
classified as left-handed or L-amino acids In nature, only one
enantiomer of most chiral biological compounds, such as amino acids
is present. As a result, different enantiomers of a compound may
have substantially different biological effects. Only glycine is
achiral
- Slide 25
- Enantiomers Enantiomers of a compounds have the same formula
and atomic connections but different spatial arrangements. The same
physical properties except they always differ in their effect on
polarized light They differ in how they react with other chiral
molecules. Pairs of enantiomers often differ in their biological
activity, odors, tastes, or activity as drugs.
- Slide 26
- Amino Acids are Chiral Spearmint leaves and caraway seeds have
very different flavors - imparted by a pair of enantiomers Pairs of
Enantiomers often differ in their biological activity, odors,
tastes, or activity as drugs.
- Slide 27
- Levels of Protein Structure Primary protein structure: The
sequence in which amino acids are linked by peptide bonds in a
protein.
- Slide 28
- Convention in Writing Peptide Chains 1.peptides are always
written with the N-terminal on the left, and the carboxyl terminal
on the right 2.Individual amino acids joined in the chain are
referred to as residues
- Slide 29
- Proteins have four levels of structure 1.Primary structure is
the sequence of amino acids in a protein chain 2.Secondary
structure is the regular and repeating spatial organization of
neighboring segments of single protein chains 3.Tertiary structure
is the overall shape of a protein molecule produced by regions of
secondary structure combined with the overall bending and folding
of the protein chain. 4.Quaternary structure refers to the overall
structure of proteins composed of more than one polypeptide
chain
- Slide 30
- Intermolecular forces determine the shapes and functions of
proteins The non-polar hydrophobic side chains are pushed and
pulled into clusters within a large protein molecule Hydrophilic
groups on the surface of folded proteins impart water solubility to
the proteins. Myoglobin has hydrophobic amino acid R groups packed
into the interior, while those on the surface are hydrophilic
making the molecule water soluble Link
- Slide 31
- Intermolecular Forces In Proteins
- Slide 32
- Secondary Protein Structure The secondary structure includes
two kinds of repeating patterns known as the -helix and the -sheet.
In both, hydrogen bonding between backbone atoms holds the
polypeptide chain in place.
- Slide 33
- Alpha-helix Secondary Structure The stabilizing hydrogen bonds
of the alpha helix point to the C-terminus and are nearly parallel
to the long axis of the spiral of the helix.
- Slide 34
- Beta-sheet secondary structure. The protein chains usually lie
side by side. the R groups point above and below the sheets
- Slide 35
- Tertiary Protein Structure The three-dimensional shape that
results from the folding of a protein chain is the proteins
tertiary structure. Depends on interactions of amino acid side
chains that are far apart along the same backbone.
- Slide 36
- Quaternary Protein Structure The way in which two or more
polypeptide subunits associate to form a single three- dimensional
protein unit.
- Slide 37
- Protein Structure in Review
- Slide 38
- Quaternary structure This is found in proteins that have
multiple polypeptide subunits. 1.Noncovalent interactions:
hydrophobic interactions : interactions between nonpolar R groups
on different subunits hydrophilic interactions (electrostatic)
interactions between polar R groups on different subunits 2. salt
bridges (electrostatic) Interactions between acidic R group and
basic R group on different subunits generally buried in the
interior of a protein 3.Covalent interactions: disulfide bridges
between two cysteine residues that have been oxidized (form after
protein has folded to further stabilize structure)
- Slide 39
- What is it all For?
- Slide 40
- Goals Recaped 1.Recognize an amino acid and describe the basic
structure 2.illustrate how amino acids link together to form
peptide chains and proteins. 3.Use the structure and size of side
chains to predict polarity and charge in acid and basic conditions
4.Understand amino acids as zwiterions and the concept of
isoelectric point.
- Slide 41
- 5.Be able to identify chiral molecules and chiral carbon atoms
6.Be able to identify enatiomers 7.Draw and name a simple protein
structure from the amino acid sequence 8.The importance and meaning
of disulfide bonds, hydrogen bonds, and non covalent interactions
in determining secondary, tertiary and higher levels of protein
structure 9.Be able to describe protein hydrolysis and
denaturation, and give some examples of agents that cause
denaturation.