2Protein Structure Flashcards
Secondary structure
Hydrogen bonding beta sheets or helical shape
Primary structure
Amino acid sequence held by covalent bonds
Tertiary structure
Poly peptide chain folding and held by covalent and non covalent bonds
Quarternary structure
Protein assembly- several subunits (2-4) come together to make functioning protein complex
Forming a peptide bond:
When 2 amino acids come together to kick out water. If we take C of one AA and N of another AA and bring them together. It kicks out two Hydrogen and 1 oxygen in between. This how we get peptide bonds.
Peptide bonds are:
Covalent
Partial double bond of a :
Peptide binds keeps it from freely rotating
Psi and phi angles are freely rotating
Backbone of a protein:
Repeating pattern of psy, peptide, phi, psy, peptide, phi
No free rotation around peptide bond
Why can’t we have 360° angles for the R groups on a molecule?
If we go 360 degree angles for phy and psi, we see R groups bump into each other, even carbonyls and nitrogen so it is not possible for rotation on the phy and psi angles.
What is Ramachandran Plot??
It shows a list of angles that are possible for phy and psi within a peptide.
From the Romachandran Plot, we can see that proteins will form:
Helix or Beta sheet- somewhere in domains within the protein
3 Types of Helices: Left handed alpha helix, Right handed alpha helix, or collagen triple helix
***most common is right handed alpha helix
3 Types of sheets: Antiparallel beta sheet, parallel beta sheets, right twisted beta sheets
Most restricted bond rotation:
Peptide bond
What percentage of amino acids are found in the right-handed alpha helix form?
25% of all amino acids that are found in proteins. This has the highest percent of any structures formed.
Who are the two scientist that were the biggest contributors to understanding the alpha helix?
Linus Pauling
Robert Corey
Alpha helix bonds are:
Phy angle is (-45 to -50)
Psi angle is (-60)
This minimizes steric interactions between amino acids and maximizes hydrogen bonds within the protein.
There is hydrogen bonding between every fourth amino acid in the helix.
Where are the R groups located on the alpha helix?
The R groups are pointed away from the center of the helix to the outside, so this makes a whole right down the middle of the helix.
Anti-parallel beta sheets are made by:
Looping of amino acid layers together- one running one direction and looping to run the amino acids Antiparallel. They have H bonding between them.
The angles of this sheet are (Psy:-139) and (Phi: +135)
Has pleating
Parallel beta sheet:
Has angles of (Psi: -119) and (Phi: +113)
These are alpha Helices flattened into sheets but have a cycle within the strong if amino acids…they run parallel to each other.
No looping
What factors determine if it will be an alpha helix or beta confirmation?
It is the R group that determines it.
Beta confirmation amino acids that determine structure:
Ile
Val
Leu
Phe
Trp
Tyr
Alpha helix amino acid determinants:
Glu
Met
Ala
Beta turn amino acid determinants:
when we change domains, these don’t fold as well as the others
Pro
Gly
Asn
Ser
Asp
Proline isomers
Beta turns commonly have Proline.
commonly domain breaker**
1/3 of all amino acids in the beta turns of globular proteins are prolines in cis form
The beta turn involves 4 amino acid and makes 180° turn.
Tertiary structure is:
Protein folding
Alpha keratin (fibrous protein) is made by:
Alpha right handed helix ⬇️ Coiled coil ⬇️ Pronto filament and protofibril
These are cross linked and held together by disulfide bonds.
- very strong, flexible, water insoluble
Alpha helix found at:
2° level of protein organization
Waving of hair is formed by:
The placement of disulfide bonds in the Keratin fibers.
It is chemically possible to restructure hair by using a reducing agent to break disulfide bonds between Alpha Keratin protein fibers, curl hair and then add oxidizing agent so it is possible to put disulfide bridges in other places.
Collagen triple helix:
L handed helix w/ 3 AA per turn
Superhelical twisting in triple helix is R handed
Gly, Ala, Pro, hydroxyproline
Stronger then steel of same thickness due to highly cross linked (2 lysines linked together to make powerful cross link)dehydrohydroxylyaibonorleucine
What is osteogenesis imperfecta/Ehlers – Danlos syndrome:
This is a loose joints.
Caused by a substitution of Cysteine or Serine for glycine. This substitution can be lethal because we don’t have the right 3-D structure of proteins and can’t form the right helices to function properly.
What factors can denature proteins?
Denature – unfolding protein so that the protein loses its function
Heat-liquid to solid Microwaves UV radiation Violent whipping or shaking Soaps Organic solvents Strong acids and bases – pH Salts Heavy metals – Mercury, lead, cadmium
Once proteins are unfolded, they very rarely can go back.
How can we measure the denaturing of a protein?
We can measure the protein unfolding by heating up the protein and measuring the amount of aromatic amino acids released from inside the proteins that are released to the outside. Proteins will start to absorb more UV light the more that it denatures.
Salt have the ability to;
Denature proteins. The increasing concentration of salt it will have then the increase the rate the protein unfolds.
What is a good example of a protein that can re-fold into its original form?
Ribonuclease that has disulfide bonds. Wendy’s bonds are reduced any in time is denatured using urea it loses activity. When urea is dialyze away in the disulfide bonds are permitted to reform the enzyme regains its activity.
Refolding of proteins steps:
Most proteins refold and assume the lowest energy confirmation possible.
Are are some proteins that do not do this and instead, they form a more stable confirmation that is not the lowest energy confirmation. If some of these proteins refold and go to the lowest energy confirmation, they become in active and even toxic. This is an example of mad cow disease.
Prion disease:
These proteins are not in the most stable confirmation. If a chaperone protein helps it refold into a more stable protein it loses its function. The theory is that this new more stable protein is also a chaperone and refolds other proteins that start a domino effect. This means that the infected prion will corrupt all of the similar proteins. It is infectious.
Degeneration of the brain.
What do you chaperone proteins do?
30% of our proteins do not fold themselves, so we need chaperone proteins that will influence how the protein will fold and to put it in its proper confirmation. Some chaperones need ATP to correctly fold the target protein.
Which level of protein organization is held together only by hydrogen bonding?
Secondary
Which of the following bonds has the most restrictive rotation compared to the others?
Peptide
The alpha helix is found at what level of protein organization?
Secondary
In mad cows disease, what is taking place?
The prion protein is re-folded into an alternate confirmation
Which of the following types of hemoglobin has the highest affinity for oxygen?
HbF
As the pH drops from pH 7.4 to pH 7.2, what changes for hemoglobin?
Oxygen binding decreases
What happens to oxygen binding to hemoglobin as BPG concentrations increase?
Decrease
As CO concentrations increase, what happens to oxygen binding to hemoglobin?
Decrease
If the partial pressure of carbon dioxide increases, the oxygen binds to hemoglobin
Decreases
Hemoglobin a increases oxygen binding when
Blood becomes more alkaline
Hemoglobin F
As a higher affinity for oxygen then hemoglobin a
Which of the following amino acids are positively charged?
K
When hemoglobin is oxygenated, what state is it prefer??
R
Which amino acids are switched in sickle cell disease?
Beta 6 glu becomes a Val
Which of the following is not correct concerning BPG?
Increases the affinity of hemoglobin for oxygen
The amino acid substitution of Val for glu and hemoglobin S results in aggregation on the protein because of ________ interactions between molecules
Hydrophobic
Which of the following hemoglobin varianctswould have the least pathological symptoms?
Hb Memphis
Primary structure:
Amino acid sequence
Secondary structure
Alpha helix and data sheet
Tertiary structure
Protein folding
Which level of protein organization is held together only by hydrogen bonding?
Secondary
The primary force that holds the most tertiary structures together are
Hydrophobic forces
Which of the following bonds has the most restrictive rotation compared to the others?
Peptide
Mad cow disease is caused by
Prion proteins that have refold it
Which the following amino acids is aromatic?
F
Hey peptide with the following one letter sequence will be closest to what charge at pH 7.4?
RSMAAPHCYTEARST
+1
And sickle cell anemia, why does the HbS cause signaling of the cell?
It has lost negative charges on it causing it to form rod shaped crystals inside the cell
How does hemoglobin F compared to hemoglobin a?
It has a higher affinity for oxygen because it binds BPG weaker
How does hemoglobin F compared to hemoglobin A?
It has a higher affinity for oxygen because it binds BPG weaker
