IB: Proteins Flashcards
made of long unbranched chain of these amino acids
Protein
a linear chain of amino acids
polypeptides
repeating sequence of atoms along the core of the polypeptide chains
Polypeptide backbone
give amino acids its unique properties
side chains
involved in protein folding
weak covalent bonds
Types if if weak noncovalent bonds on protein folding
-Hydrogen bonds
-electrostatic attrations
- Van der Waals
contains all the information needed for specifying the three-dimensional shape of a protein
amino acid sequence
assist in protein folding
Molecular chaperones
Common folding patterns
- α helix
- β-sheet
Types of folding that leads to α-helix and β-sheet folding patterns?
Hydrogen bonding between N-H and C=O groups
Types of β-sheet structures
- Parallel chains
- antiparallel chains
form from neighboring segments of the polypeptide backbone that run in the same orientation
parallel chains
-from a
polypeptide backbone that folds
back and forth upon itself
-each section of the chain running in the direction opposite of that of its immediate neighbors
Antiparallel chains
Formation of α-helix
- when single polypeptide chain twist around on it self to form rigid cylinder
-Hydrogen bonds between every 4th peptide
-coiled-coil form
4 levels of protein structure
- Primary structure
- secondary structure
- tertiary structure
- Quaternary structure
amino acid sequence
primary structure
hydrogen
bonding of the peptide
backbone; α helices and β sheets
Secondary structure
full 3D
organization of a polypeptide chain
tertiary structure
protein
molecule formed as a complex of more than one polypeptide chain
Quaternary structure
How are protein classified?
Based on their tertiary structure
used to see structure of protein
X-ray crystallography
the basic units of proteins that can fold,
function, and evolve independently
Protein domains
process of
creating new combination of gene functional domains
domain shuffling
subset of protein domains, mobile during evolution
protein modules
only in humans, the reason why humans cant receive blood from other organisms
MHC (Major Histocompatibility Complex)
allow proteins to bind to each other to produce
structures in the cell
Weak noncovalent bonds
any region of a protein’s surface that can interact with another molecule
binding site
forming a symmetric complex of two protein subunits (dimer)
“Head-to-head” arrangement
two identical α-globin
subunits and two identical β-globin subunits, symmetrically arranged
Hemoglobin
long helical structure produced from many molecules of the protein actin
actin filament
a long chain comprised of identical protein molecule
Filaments
Why is alpha helix common?
All subunits are identical
- can only fit together in one way
Types of protein molecule shapes
-Fibrous protein
-Elongated protein
elongated three-dimensional structure
fibrous protein
example of fibrous protein
- keratin filaments
- a(alpha) keratin
ropelike structures;
important component of the cytoskeleton
intermediate filaments
consists of three long polypeptide chains
- each containing that nonpolar amino acid glycine at every 3rd position
collagen
Another abundant protein in ECM
- highly disordered polypeptide
Elastin
causes of disordered polypeptide chain
- To form specific binding sites for other protein
- Trigger cell signaling
- Restrict diffusion
- Serves as tether to hold two domains
act as atomic staple
stabilize monomeric and multisubunit proteins
S-S bonds (Disulfide bonds)
Advantages of subunits
-requires only small amount of genetic information
- assembly and disassembly
- error in synthesis can be avoided easily
example of subunit
capsid of viruses
made of identical protein subunits that enclose and protect viral nucleic acid
Capsid of viruses
Guide construction but take no part in the final assembled structure
Assembly factors
self propagating, stable β-sheet aggregates
amyloid fibrils
What dangers does amyloid cause?
- Alzheimers disease and other neurodegenerative illness
may be released from dead cells and accumulate as amyloid
Protein aggregates
caused by a misfolded, aggregate form of a particular protein called PrP (prion protein)
Prion diseases
What does misfolded protein do?
convert normal PrP into abnormal conformation
acts like a vesicle containing peptide and hormones
specialized “secretory granules” that consist of amyloid fibrils
Protein functions
- Contractile
- Hormonal
- Protection
- Transport
- Enzyme
- Storage
- Structural
- Receptor
each protein molecule can usually bind just one or a few molecules out of many thousands
Specificity
the substance that is bound by the protein
Ligand
Noncovalent bonds in proteins
- Hydrogen bonds
- Electrostatic attractions
- Van der Waals
the region of protein that associates with a ligand
Binding site
Determines the chemistry of protein
Surface Conformation
Types of Surface conformation
- Interaction of neighboring parts of polypeptide chain
- Clustering of neighboring polar amino acid chains
Types of Interfaces (Protein binding)
- Surface string interaction
- Helix-helix
- Surface-surface
Most common interface
Surface-surface
binds tightly to a particular target molecule (antigen), inactivating directly or making it for destruction
antibody or immunoglobulins
Shape of antibody molecules
Y-shaped
cause the chemical transformations that make and break covalent bonds in cells
Enzymes
speed up reactions, act as catalysts
Enzymes
the maximum rate of reaction divided by the enzyme concentration
Turnover number
unstable intermediate state
Transition state
the free energy required to attain the transition state
Activation energy
adds a molecule of water to a single bond between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break
Hydrolysis
Add Extra Functions to Proteins
Tightly Bound Small Molecules
key light-sensitive protein expressed exclusively in rod photoreceptor cells of the retina
Rhodopsin
tightly related to rhodopsin, helps it to carry reaction
Retinal
Gives red color in blood
heme group
- a large protein assembly
- allows the product of enzyme A to be passed directly to enzyme B, and so on
multienzyme complex
the factor that limits the reaction rate is the frequency wuth which the enzymes collides with its substrate
Diffusion-limited
a product produced late in a reaction pathways inhibits an enzyme that acts earlier in the pathway
feedback inhibition
prevent an enzyme from
acting
Negative regulation
regulatory molecule stimulates the enzyme’s activity rather than shutting the enzyme down
Positive regulation
have at least two binding sites on their surface
Allosteric enzymes
Two binding site of allosteric enzymes
- Active site
- Regulatory site
that recognizes the
substrates
Active site
that recognizes a regulatory molecule
Regulatory site
interaction between separated sites on a protein
conformational change
can occur in multimeric proteins, where each subunit of the protein has its own ligand binding site
cooperative allosteric
transition
Contains a Large Collection of Protein Kinases and Protein Phosphatases
Eukaryotic cell
transfer of the terminal phosphate group of an ATP molecule to the hydroxyl group
Protein phosphorylation
phosphorylates
Protein kinase
phosphate removal,
dephosphorylate
Protein phosphates
- phosphate is part of guanine nucleotide GTP
- addition and removal of phosphate
GTP-binding proteins
generate forces responsible for muscle contraction and the crawling and swimming of cells
Motor proteins
major function of motor proteins
Move other molecules, reversible
coupling one of the conformational changes to the hydrolysis of an ATP molecule that is tightly bound to the protein
unidirectional conformation changes
function to export
hydrophobic molecules from the cytoplasm
ABC transporters
are made up of individual proteins that collaborate to perform specific task
Protein machines
proteins binding sites for multiple other proteins
Scaffold proteins
What does scaffold proteins serve?
- both to link together specific sets of interacting proteins
- Position them at specific locations (inside a cell)
Computer based bioinformatics tools
Proteomics
protein is represented by a box or dot in two-dimensional network
Protein interaction map
