Protein structures Flashcards
Functions of proteins (9)
Structured mechanics
Enzymes
Hormones
Signalling molecules
Antibodies
Fluid balance
Acid-base balance
Channels and pumps
Transport function
What is the definition of secondary structure?
Regular repeating interactions between amino acids that are close in primary sequence
Alpha-helix
Beta-pleated sheet
Are there proteins that contain only secondary structure?
Yes
Example of protein that only have secondary structure
Collagen
Definition of tertiary structure
Amino acids interaction that are far from each other in the cell
Globular and fibrous structures
Definition of quaternary structure
Interaction between two different sub units
Can you have both alpha-helix and beta-pleated sheet in the same protein structure?
Yes, complex protein typically have both
Can proline exist in the cis-configuration in peptides?
Yes
What is the rotation around the N-C bond called?
Phi
What is the rotation around the C-C’ bond called?
Psi
Why is rotation limited? and only few angles allowed when the amino acid is stable
The R groups. If they rotate more the two R groups will interact
What does the blank space on the Ramachan plot represent?
The angles where the amino acid isn’t stable
Does protein structure influence it’s function?
Yes very much so
What is the secondary structure due to? (1 type of bonding and 1 type of forces)
Hydrogen bonding and Van der Waals forces
What happens if you disrupt the structure of the protein?
It becomes inactive, denatured
Are the van der Waals attractions attractive or repulsive?
Both
What is residues/turn?
Same as amino acids per turn
Do aa/turn change in an alpha helix depending on the R group?
No, almost always 3.6 aa/turn
What model is used to study secondary structures?
Ribbon model
Which way does the R group point in the alpha- helix? inwards or outwards
Outwards
Are there more interactions between amino acids in the alpha helix or the beta pleated sheets
Not a big difference, if anything then more in the beta structures because multiple sheets can be close and cause additional interactions
Are the amino acids in beta-pleated sheets typically parallel or anti parallel?
Anti parallel, but can be both
It’s more stable typically
What decides wether it’s parallel or anti parallel? (beta-pleated sheets)
The space available
What makes the parallel beta pleated sheets less stable?
Longer hydrogen bonds and R groups close together
What does stable mean energetically?
Favourable
Does space have an influence on stability?
Yes, the less space the less stable
If there eis not enough space for a group they interact
Why is antiparallel more stable? (beta-pleated sheets)
Bonds are stronger, more aligned
Are proteins assembled random?
No very orderly way because of the beta sheets and alpha helix
Which kind of alpha helix is most stable, right handed or left handed?
Right handed
Are the R groups closer in alpha helix or beta pleated?
Beta pleated sheet
What gives silk it’s peculiar propert?
The long anti parallel beta sheets with simple amino acids
How many amino acids are involved in forming the beta-turn/hairpin loop?
4, typically small/simple amino acids
How many structures do proteins form?
Only 1 each
Which amino acids allow for beta turns?
Proline and glycine, other simple aa
What are random coils?
Longer connections between alpha helix and beta sheets
What are short connecting points called? 2 kinds
Loops and beta-turn
What are the longer connections called?
Random coil
What are ribbons diagrams useful for?
Studying interactions and protein structure
What differes in the insulin from humans and pigs? structure or amino acids?
Amino acids
Where does the arrow go when drawing beta pleated sheets
N->C
3 ways to classify proteins
Structure, composition and functions
3 structures of proteins
Fibrous
Globular
Intermediate
2 compositions of proteins
Simple
Conjugated
3 functions of proteins
Structural (enzymes and hormones)
Pigments, transport, contractile
Storage, toxins
How is collagen classified? (structure)
Fibrous
What do fibrous protein look like?
Long intertwined alpha helix
What can rigidt proteins function as?
Structural elements in cytoskeleton or connective tissue
What are flexible proteins important for?
They can change formations when for example binding to oxygen (haemoglobin)
The ability to respond with a conformational change
What does globular protein consist of?
Coiled and folded polypeptide chains forming spherical shape
Are fibrous proteins soluble in water?
No insoluable
Are globular proteins soluble in water?
Yes
Example of globular proteins
Enzymes and haemoglobin
Different name for fibrous protein
Scleroprotein
What is alpha keratin made up of?
Long alpha helix coiled together
Is kreatin able to go back to it’s own structure after being denatured (by heat)?
Yes
Is collagen a rigid structure?
Yes
Which is the only amino acid where the R groups form a bond with the amino group?
Proline
What is hydroxyproline?
AA Proline with a hydroxyl group
What happens when your collagen lacks hydroxyproline?
Your collagen is weak
What can a vitamin C deficiency lead to?
Weak collagen (lack of hydroxyproline) -> scurvy
How many types of collagen?
3
Where is collagen 1 found?
Skin
Bones
Capsule of organs
Tendons
Cornea
Fascia
Where is collagen II found?
Elastic cartilage
Where is collagen III found?
Skin
Lungs
Intestinal walls
Walls of blood vessels
What is the dynamic structure of elastin called?
Beta spiral (loose held together by hydrophobic forces)
What is the overall shape which makes the polypeptide chain functional?
Tertiary structure
What interactions are in tertiary structures? (4)
Hydrophobic interactions
Disulphide bridges
Ionic bonds
Hydrogen bonds
What kind of reaction forms disulphide bonds?
Oxidation
How many disulphide bonds in insulin makes the protein stable?
3
What does the hydrophobic effect help determine?
Protein structure
What is a protein domain?
Region of the protein’s polypeptide chain that is self-stabalizing and that fold independently from the rest
Repetitive structure that can allow the protein to move
Can a single protein have different domain?
Yes
What is a dimeric protein?
Has two different chains, subunits
Does a mutation always effect the structure of protein?
No depends on the location of the amino acid replaced
What determines the folding and function of proteins?
Tertiary structure
What dictates the characteristics of a protein?
Th linear amino acid sequence (primary structure)
What kind of hindrance do we have in cis form amino acids?
Teric hindrance
Which isomers are more stable?
Trans
Are all rotations allowed?
No
Which structure determines how proteins fold and interacts with other molecules?
Primary structure
What creates the secondary structure?
Regular repeating interactions between amino acids that are close in primary sequence
What bonds create the alpha helixes and beta sheets?
Hydrogen bonds
Van der Waals forces
Between what does hydrogen bonds mainly occur?
H and O
Which bonding plays a big role in stabilising secondary structures?
Hydrogen bonding
Which Van der Walls control protein folding, repulsive or attractive?
Both
Van der Waals force are very weak, how do they are they still so significant?
Because there are so many of them
Can both parallel or anti-parallel beta sheets exist within the same protein?
Yes
What differentiates parallel and antiparallel beta sheets?
Different hydrogen bonding patterns
Where are random coil typically present?
At the end of the protein or in the middle of 2 alpha helices or beta structures
Are random coils conserved?
They can be but wast majority are not
What are loops?
Unstructured regions found between regular secondary structure elements
3 ways to classify proteins based on?
Structure
Composition
Function
What structure are fibrous proteins made by?
Secondary structure
What does fibrous protein consist of?
Long and parallel polypeptide chains forming helical structures or pleated sheets
What does globular protein consist of?
Coiled and folded polypeptide chains forming spherical shape
Are fibrous protein soluble in water?
No, insoluble
Are globular protein soluble in water?
Yes
Is the structure of fibrous protein stable or unstable?
Stable
Is the structure of globular protein stable or unstable?
Unstable
What does fibrous proteins play a big role in?
Mechanical and structural functions
What does globular proteins play a big role in?
Metabolite and chemical processes
2 examples of fibrous protein
Kreatin and collagen
2 examples of globular protein
Enzymes and haemoglobin
Are fibrous proteins strong or weak?
Strong
What is the characteristics of alpha helix?
Protective structures
What is the characteristics of beta sheets?
Soft and flexible filaments
What are fibrous proteins made up of?
elongated polypeptide chains of regular amino acid sequences that run parallel to one another
In what type of amino acids are there typically found many alpha helixes?
Hydrophobic amino acids
How much of the protein in your body is collagen?
About one quarter
Which is the only amino acid where the R group makes a bond with the amino group?
Proline
What does proline form when modified?
Hydroxylproline
What makes proline special?
The R group makes bond with the amino grojp
What does vitamin C deficiency do?
Slows the production of hydroxyproline and stops the construction of new collagen
What causes scurvey?
Vitamin C deficiency
Different name for vitamin C
Ascorbate
What is elastin?
Insoluble polymer which is rich in glycine. lysine and are hydroxyproline
What does elastin form when interacting with other proteins?
Reticulates
What kind of protein is elastin?
Fibrous (but very elastic)
What kind of protein is collagen?
Fibrous
How do membrane proteins fold in comparison to soluabl proteins?
Opposite way
What is the most important driving force for protein folding and assembly?
The hydrophobic effect
Can 2 different proteins have the same domain?
Yes
