Lecture 1 Flashcards
All proteins are enzymes
True or false
False
Many different functions
Transcription Regulators
Turn things on and off
Signal Proteins
Signal transduction
_______ drives function
Structure
Structure is MUCH more conserved than sequence data
The shape of a protein is specified by __________-
Its amino acid sequence
proteins fold into a conformation of ________ energy
Lowest
proteins come in a wide variety of complicated shapes
True
The alpha helix and Beta sheet are
Common folding patterns
Helices form ___________________-
Readily in biological structures
Beta sheets form ___________________________-
Rigid structures at the core of many proteins
Misfolded proteins can form _____________ that cause disease
Amyloid structures
proteins have _______ level(s) of organization
Several
Amino acids are linked together by __________ bonds
Peptide
Polarity
Has direction
i.e. DNA
Peptide bonds form by ___________-
Dehydration (removal of water)
A protein is made of amino acids linked together into a ___________
Polypeptide chain
Side chains of amino acids are
Different
i.e. can have negatively or positively charged, polar uncharged, nonpolar
The amino acids present in a chain will dictate how a protein will fold
Given interactions
3 types of noncovalent bonds help proteins fold
1) Electrostatic - held by charges
2) van der Waals attractions - close together
3) Hydrogen bonds - attachment b/w H and O, F, or N
Noncovalent interactions have a __________ effect
Additive
The more that’s there, the stronger the structure will be
Hydrophobic forces help the proteins fold into compact conformations
Hydrophobic forces will be w/in folds, protected from liquid environment
Hydrogen bonds w/in a protein help _________ its folded shape
Stabilize
Backbone to backbone
H-bond b/w atoms of 2 peptide bonds
Backbone to side chain
H-bond b/w atoms of a peptide bond and an amino acid side chain
Side chain to side chain
H-bond b/w atoms of 2 amino acid side chains
proteins fold in lowest energy conformation; dictated by amino acid sequence
Protein folding is an energetically favorable interaction
Most proteins need help fodling
Chaperones
Type of protein
Guide the folding of a newly synthesized polypeptide chain
Help proteins fold correctly; MOST assist in protein folding by keeping everything else in the cell AWAY during folding, it doesn’t know how the protein needs to be folded; SOME may prevent proteins from folding too early; SOME may create a chamber to isolate protein from everything else so it can fold correctly, then be released from this chamber
Found in ALL cellular life
Some chaperone proteins act as ________- that help a polypeptide fold
Isolation chamber
Proteins put in chaperone that is like a container to keep all other junk away while the protein folds
Proteins come in a ____________ of shapes and sizes
Wide variety
Secondary structures
Core elements of protein architecture
Stable arrangments of segments of a polypeptide chain held together by H-bonds b/w backbone amide and carbonyl groups
Propensity of a segment ot form any given secondary structure depends on its amino acid sequence
Alpha helices and Beta sheets
Formed STRICTLY with noncovalent H-bonding
In an average protein:
–60% of the chain = alpha helices and beta sheets with the remainder of the molecules existing as irregular structures, coils and turns
Primary structure
Amino acid sequence
Alpha helix
Some polypeptide chains fold into an orderly repeating form
Side chains protrude outward
Helix structure is very coordinated
Every amino acid is bound to another structure 4 residues down
Every amino acid in alpha helix takes part in H bonding EXCEPT those at N- and C-terminal ends
Held together STRICTLY by H bonds
Seen frequently in cells that cross the plasma membrane
Backbone forms a spiral structure stabilized by H bonds b/w the carbonyl oxygen atom to the amide hydrogen atom of the amino acid 4 residues downstream
ALL backbone amino and carboxyl groups are hydrogen-bonded (except at the beginning and the end of the helix)
Many membrane-bound proteins cross the lipid bilayer as an alpha helix
Form a stiff coiled-coil: join w/ other alpha helices to form this; alpha helices start reacting and twisting around each other to form coiled coild
Collagen is a coiled coil (strictly made of alpha helices)
Beta Sheets
Formed STRICTLY by H bonds
Can form single polypeptide chain OR in multiple chains
Run parallel (connected via loops that come out) or antiparallel
Backbone forms laterally packed strands stabilized by H bonds b/w backbone amino and carboxyl groups of separate, but adjacent strands
Distinct Beta strands may be:
- W/in a single polypeptide chain
- Different polypeptide chains
Can STACK to form an amyloid structure: misfolded proteins are beta sheets; can fold on top of each other to form these amyloid structures; have been found in MANY neurodegenerative diseases, recently found in type II diabetes
Prion diseases
Caused by proteins whose misfolding is infectious
Induce misfolding of a protein
Amyloid fibers commonly found in these structures
Prions make protein go to a different kind of protein
Levels of Protein hierarchy
Primary
Secondary
Tertiary
Quaternary
Primary structure
Amino acid sequence
Secondary structure
Alpha helices and Beta sheets
Tertiary structure
Combination of different secondary structural elements (several alpha helices, several beta sheets)
Get DOMAINS in tertiary
Quaternary structure
If protein interacts with another protein (2 or more polypeptide chains)
Some act as a monomer
NOT all proteins have quaternary structure
Many proteins are composed of separate functional _______
Domains
Domain
Section of a protein that serves specific function (part or section of protein)
Proteins can have many different domains
Dimers
2 identical polypeptide chains must interact in order for this protein to be functional
Many protein molecules contain multiple copies of the same protein subunit
Terms like dimer, tetramer, trimer indicate that it is a _________ structure
Quaternary
Tetramer
Formed by interactions b/w 2 NONidentical binding sites on each monomer
Dimer
Formed by interaction b/w single, identical binding site on each monomer
Identical protein subunits can assemble into _____________
Complex structures
Transcription factors act as dimers: Have 1 domain that binds to DNA, one that binds to something else
SOmetimes proteins can form helix structures
Tubules
Made up of repeating dimers
Microfilaments/Actin
Part of cytoskeleton
VERY complex structure, repeat over and over
Made of one monomer that binds to another monomer over and over again
The primary structure of a protein determines how it will fold
Hypothetical protein-folding pathway:
Primary -> secondary -> secondary -> pretertiary (with domains) -> tertiary
Proteins are very dynamic, always moving
Proteins are often stabilized by ____________________
Covalent Cross-Linkages
Disulfide bonds help stabilize a favored protein conformation
-When you have an amino acid chain with CYSTEINE residues, potential for disulfide bonds to form
Reducing agent = breaks disulfide bonds = cysteine present
Disulfide bonds are ______ bones
Covalent
Oxidation
When disulfide bonds FORM
Reduction
When disulfide bonds BREAK
ALL proteins bind to
Other molecules
Enzymes are powerful and highly specific catalysts
Enzymes greatly accelerate the speed of chemical reactions
All proteins interact w/ other molecules in some way, VERY _________
Specific
Ligand
Something a protein binds to
If a protein binds to DNA, it will ____ bind to something else
NOT
The binding of a protein to another molecule is highly ________
Selective
If a protein has several functional domains, it can binds to numerous ligands
Exemplified by Lock and Key model
Binding sites allow proteins to interact with __________
Specific Ligands
Binding b/w a protein and its ligand is
Very specific
Side chains project into binding site; interact w/ _______________-
Noncovalent interactions
Enzymes convert substrates to _________ while ______________
Products; remaining unchanges
Hydrolase
General term for enzymes that catalyze a hydrolytic cleavage reaction
Nucleases
Break down nucleic acids by hydrolyzing bonds b/w nucleotides
Protease
Breaks down proteins by hydrolyzing peptide bonds between amino acids
Isomerase
Catalyzes the rearrangement of bonds w/in a single molecule
Polymerase
Catalyzes polymerization reactions such as the synthesis of DNA and RNA
Kinase
Catalyzes the addition of phosphate groups to molecules
Protein kinases are an important group of kinases that attach phosphate groups to proteins
Phosphatase
Catalyzes the hydrolytic removal of a phosphate group from a molecule
Oxido-reductase
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced; Enzymes of this type are often called oxidases, reductases, or dehydrogenases
ATPase
Hydrolyzes ATP
Many proteins have an energy-harnessing ATPase activity as part of their function, including motor proteins such as myosin and membrane transport proteins such as the NA+ pump
Enzymes can encourage a reaction in several ways:
1) Enzyme binds to 2 substrate molecules and brings them close enough to react
2) Binding of substrate to enzyme arranges electrons in substrate, creating partial negative and positive charges that favor a reaction
3) Enzyme strains the bound substrate molecule, forcing it toward a transition state that favors a reaction
- Changes bond angles
