Protein Review Flashcards
What are proteins composed of?
A long sequence of amino acids
Describe an amino acid structure at cellular pH (~7)
A central carbon
bonded to an H
bonded to an R group
bonded to an amino group (NH3+)
bonded to a carboxyl group (COO-)
H
|
H3N (+) -- C -- C = O
| |
R O (-)
What is cellular pH?
~7 (neutral)
How is the amino acid structure different at cellular pH than outside of cellular pH?
It is charged
There is a positive charge on the N of the amino group and a negative charge on the single bonded O of the carboxyl group
What is the only difference between individual amino acids?
The R groups attached
How many amino acids are there that form proteins?
20
How are amino acids categorized and what are the categories?
Categorized based on their R groups/side chains at pH 7
acidic (- charged)
basic (+ charged)
polar but uncharged
non polar
How are each of the 20 amino acids named?
With 3 letter names and with 1 letter names
ex. Alanine = Ala = A
Give an example of a positively charged amino acid
Lysine (Lys/K)
Give an example of a negatively charged/acidic amino acid
Aspartic acid (Asp/D)
Give an example of a polar but uncharged amino acid
Serine (Ser/S)
Give an example of a non-polar amino acid
Glycine (Gly/G)
What atoms will a polar side chain of an amino acid involve?
Oxygen or Nitrogen (no full charge at pH 7)
ex. amide group or hydroxyl group
What are non polar side chains of amino acids usually composed of?
hydrocarbons
What do SOME non polar side chains of amino acids have? which ones?
Sulphur groups
Methionine and Cysteine
Describe peptide bonds
Bonds between two amino acids formed by a dehydration reaction
OH lost from carboxyl group
H lost from amino group to form a peptide bond between carbonyl carbon and amine nitrogen
Why is a string of amino acids flexible?
the N-C and C-C bond in the backbone can rotate
Where are peptide bonds formed/located?
between the carbonyl carbon (carbon in the carboxyl group) and amine nitrogen (nitrogen in the next amine group)
What is generated when many peptide bonds link many amino acids?
polypeptide
What orientation (in regards to N and C) are polypeptides?
Head to tail or
Amino group to carboxyl group
There is always a N terminus and a C terminus
What is included in the backbone of a polypeptide?
everything except the R groups
What contributes to the polarity of a polypeptide backbone?
the chain ends are charged amino (head) and carboxyl (tail) groups
every other amino and carboxyl group in the backbone are involved in peptide bonds so they are not charged
What are the 4 structures of proteins?
primary
secondary
tertiary
quaternary
Why is protein structure so important?
Structure dictates function
Proteins require a specific shape to do any job
Describe primary protein structure
A specific linear sequence of amino acids connected by peptide bonds
T or F: because there’s only 20 amino acids, for a peptide 127 amino acids long, there’s not many possible structures
FALSE
there is 20^127 possible primary structures
T or F: 1 change in 1 amino acid at 1 position can dramatically change the protein structure and its function
TRUE
What direction is primary structure always read/notated?
from the amino end (N terminus or head) to the carboxyl end (C terminus or tail)
What dictates all other structure levels?
the primary structure because all other structure levels are dependent on the specific order of amino acids set out in the primary structure
Describe secondary protein structure? What are the 2 structure shapes?
Formed by small sections of a primary protein folding into patterns
- alpha helices
- beta sheets
Describe alpha helices in secondary protein structures. How are they formed?
Create coils by forming hydrogen bonds between amino acids that are four amino acids apart
formed by hydrogen bonds between a hydrogen on an amino group and an oxygen in a carboxyl group (ON THE BACKBONE)
How are the side chains organized in an alpha helix secondary protein structure?
the R groups project outwards, away from the helix and all 360 degrees around the helix
(R groups are not localized to one side)
T or F: alpha helices are ordered and consistent structures
TRUE
When are alpha helices amphipathic?
ONLY when all the hydrophobic R groups project off one half of the helix and all the hydrophilic R groups project off the other half
Describe the structure of beta sheets in secondary protein structures. How are they formed?
Composed of flat, pleated strands stacked on top of each other (sheets)
formed when a hydrogen bond occurs between backbone atoms (carbonyl of 1 amino will H bond with the amine of another amino) in adjacent strands
How do beta sheets form antiparallel beta strands?
If there are a few amino acids between each layer that form a curve/u-turn, the beta strands will go in opposite directions (antiparallel)
How are side chains organized in beta sheet secondary structures?
they alternate projecting above and below the plane of the sheet
Are parallel or antiparallel beta sheets more stable? why?
Parallel sheets are less stable because they have angled/distorted hydrogen bonds
Antiparallel sheets are more stable because they have straight hydrogen bonds
Describe non-repetitive structures
Portions of a polypeptide that are not organized into alpha helices or beta sheets
very flexible, form loops, hinges, or turns
usually drawn by a thick line
Describe tertiary protein structure
the OVERALL shape of the protein that results from the interactions between SIDE CHAINS
How are tertiary protein structures formed?
hydrophobic interactions aggregate parts of the protein with hydrophobic R groups
clusters the hydrophobic parts on the inside of the protein to protect from the aqueous environment
How do R groups interact within a tertiary protein?
ionic bonds between charged R groups
hydrogen bonds between polar R groups
Disulfide bridges between cysteines
What is the difference between the folding that occurs in secondary structures vs tertiary structures?
Secondary structure folding occurs because of interactions between amino acids that are fairly close together (4 apart)
whereas, folding in tertiary structure can be a result of interactions between R groups that have any distance between them
- ex. amino acid #3 can form an ionic bond with amino acid #140 and pull those regions together
Describe conformation
the final 3D arrangement of all the atoms in a protein molecule
Why is there only realistically a few specific conformations for a folded protein?
Because they need to maximize the number of weak interactions to stabilize the protein
T or F: the final conformation for a protein should be consistent each time it folds (and refolds)
true, the final shape is intrinsic to the molecule
Describe conformational changes
Every activity a protein engages in is accompanied by a conformational change
essential to the protein’s function
Why are conformational changes essential to protein function?
Because a protein may need one conformation when bound to something, but may need another when unbound
or may have active and inactive conformations depending on cell conditions
ex. ion channels - proteins will change conformations to allow ions to transport
Describe domains
Distinct regions within the tertiary structure that have separate functions and are connected by an unstructured portion of the polypeptide
Describe quaternary protein structure
the overall protein structure when the protein requires more than one polypeptide (aka sub unit)
Define monomer
a functional protein with one polypeptide
Define dimer
a functional protein with 2 polypeptide chains
Define tetramer
a functional protein with 4 polypeptide chains
T or F: quaternary structure only exists if proteins have 2+ polypeptides
TRUE
Give an example of a quaternary protein
Hemoglobin
Has two polypeptides with 4 subunits
the quaternary structure allows for O2 binding and release
What are the two general shapes for quaternary structure?
fibrous
globular
Describe fibrous shaped quaternary structures and give an example
fibrous proteins form long fibres, usually involved in structural support
ex. collagen is a fibrous trimer
Describe globular shaped quaternary structures and give an example
roughly spherical in shape
ex. hemoglobin is a globular tetramer
Describe denaturation
Occurs when the weak chemical bonds (ex. hydrogen bonds) that hold the protein together cannot form or are broken
the protein will unravel into a non-functional state and lose its 2/3/4 level structures and become primary
T or F: when a protein denatures it loses all structure
FALSE. it will never lose its primary structure!!
What can cause denaturation?
If chemical and physical conditions of the cell are outside of the range that’s tolerable for the protein to function
ex. pH, salt concentration, temperature
Can a denatured protein refold into the same protein if conditions are restored? what does this mean about the shape of the protein?
Yes
this means the shape is INTRINSIC to the protein - all the info needed to form a functional protein is located within the primary structure
What is a molecular chaperone? How do they work?
A protein that assists other proteins in folding if they cannot do it alone
Often they bind to the protein or create the conditions necessary for the protein to fold
Is there a difference between a polypeptide and a functional protein? what is it?
YES YES YES YES
Polypeptide = long string of amino acids that is not necessarily folded into a protein
protein = MUST BE FOLDED to be functional
proteins must be WHAT to be functional?
FOLDED
