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91 Cards in this Set

  • Front
  • Back
Protein constitute most of the cell's what?
Dry mass
Proteins execute nearly all of the cell's what?
What is proteins fuction determined by?
by the protein's 3D structure
What are proteins?
Are linear chins of amino acids that are linked by peptide bonds.
What unique type of feature does each type of protein have?
Unique sequence of amino acids
When proteins fold into a particular 3 D structue what is it stabilized by?
Many noncovalent interactions
-hydrogen bonds,
-van der walls
-electrostatic attraction
What helps proteins fold into compact conformations?
Hydrophobic forces (contain nonpolar side chins)
Where are Hydrogen bonds found?
-forms on the polar side chins on the outside of the protein molecule

-between atoms of two peptide bonds (backbone+backbone)

-between peptide bond and amino acid side chain (backbone+sidechin)

-betwn 2 amino acid side chin (side chain+side chain)
Proteins spontaneously fold into a conformation of what?
lowest energy
when can protein conformatin change? And why is the change in shape crucial?
When interacting with other molecules in th cell.

Crucial for regulating protein activity
Prion diseases
when protein folding goes wrong
Prion protein can adopt what?
And abnormal misfolded form
What do misfolded prion proteins form?
aggregates that cause disease, plus othe neurodegenerative disorders
How can prion diseases be spread?
ingestion of a misfolded prion protein
prion converts normal into abnormal
converts more proteins until aggregate forms
Common folding patterns of proteins?
Alpha helix and Beta sheet
What bond do the common folding patterns of proteins have? And betwen what?
hydrogne bonds between N-H
and C=O groups in polypeptide backbone
In alpha helix, the N-H of ever peptide hond is hydrgon bonded to the C=O ___ amino acids away in the same side change
What is a segment of alpha helix often used for?
to span a lipid bilayer
What can beta sheets form at the core of many proteins?
rigid structures
Beta shets can be ---- or ----
parallel or aniparalll
what do dthe arrow ppoin to in beta sheets?
C termina end of the polypeptide chain
What protein domian is common among proteins involved in cell signaling and is 100 amiino acids long
SH2 domain
What domian comprimise a family of proteolytic enzymes
Serine proteases
What are examples of proteins with multiple copies of a single protein subunit?
CAP and neuraminidase
An example of protein that is formed as a symmetrical assmely of two different subunits
What is composed of identical protein subunits?
An actin filament
What can single protein subunits can pack to form?
A filament, tube, or a spherical shell
Example of spherical protein assemplies
viral capsids
What is the most abundant protein in animals?
Collagen (20-25% total protein)
What is collagent a component of?
extracellular matrix (a gel like material that binds cells together to from tissues)
What can mutations in collagen genes cause?
cuticle defects in C. elegans resulting in Dumpy, Blister or Roller pheinotypes
These are cross linked togeter to form rubberlike, elastic fibers.
Elastin polypeptide chains
What do elastin fibers do?
Allow skin and other tissues to stretch and recoil without tearing
What are extracellular protein structures stabilized by?
disulfide bonds
Where do disulfide bonds do not form? Why
in cyston becuse of high concnetration of reducing agens present
What are proteins?
strucutral supports
signal receptors
tiny motors
What do proteins fuctions depend on?
depend on the physical binding of a protein to another molecule
What can proteins bind to
small molecules (enzyme substrate, DNA)
The binding of a protein molecule is highly---- and requires the combined effect of many ---- ----- bonds
weak noncovalent
HOw is the biniding site formed?
1. Folding of the polypeptide chin creates a cervice or cavity on the surface

2. Amino acids form differnt parts of the protein chain can come togeter in the binding site.
What are imoortant for proper folding and whre can they be found?
aminno acids
protein core
The binding sites of what are especially versatile?
What is the first step in enzymes function to catalzye chemical reactions?
How are enzymes grouped into fuction classes?
Based on the chemical reactions they catalyse
enzymes that catlyze a hydrolytic cleavage reaction
breaks down proteins by hydrolysing peptide bonds between amino acids
name used for enzymes that synthesize molecules in anabolic reactions by condensing two molecules together
catalyzes the rearrangement of bonds within a single molecule
catalyzes polymerization reactions such as the synthesis of DNA and RNA
adds phospahte groups to proteins
Lysozyme severs what that form what and is found in what?
polysacchride chain
bacterial cell walls (anitibiotic)
egg white, saliva, tears
What enzyme was the first structrurew to be determined by X-ray crystallography
HOw do enzymes lower activation energy?
1. enzyme binds to 2 substrate molecules and orients them precisely to encourage a reaction to occur between them

2. binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and postivie charges that favor reaction

3. enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction
Many proteins require what to peform theri fuciton? Give an example
bound smal moleucles

heme on hemoglobin
The number of molecules of each protein are regulated by what?
by regulation of gene expression
Proteins may be confined to what?
particular subcellular compartments
Proteins can be switched on or off very rapidly by what? and what does this do?
by a variety of mechinaism due to change of shpe

change funciton and tus the protein.
Feedback Inhibition
the end product of a reaction pathway inhibits the activity of an enzyme acting early in the pathway (megatove regulation)
In feedbakc inhibiton a molecule other than the normal substrate bind to the enzyme at a special ----- site not at the --- site, the molecule is what?
Postive reguulation
Uses a similar mechanism however the enzyme activity is timulated by binding of a regulatory molecule.

For ex. ADP stimulates enzymes invovlved in oxidation of sugars
What does feedback inhibition at multiple sites regulates
conncected metabolic reactions

ex. Foru amino acid biosynthetic pahtyways in bacteria and thier coordinated regulation
Allosteric proteins
proteins tha can adopt two or more slighly differnt conformations.
Allosteric proteins acitivy is regulated by what
by a shift from one conformation to another
A specific proteiin conformation is stablized by waht?
by the binding of a ligant to a site on the protein away from the active site.
The ligand might stabilize an ------ or an ----
inhibitor (inactive conformation) or activator (active confromation)
The bacterial protein CAP (catabolite activiating protein) has one large domain and one small domin what do each domin bind to to form a dimer
Small domin binds to DNA
Large domin binds to cyclic AMP
What does a CAP dimer do
Binds DNA (in presence of cAMP) which bends DNA and recruits RNA plymerase to the rpmoter
What does cAMP binding cause
rotation of the prtoen subunits so that the DNA binding helices are aligned with the major groove of the DNA
Protein phoshorylation is a very common means of what
of regulating protein activity
HOw many proteins in a typical mammalian cells are phosphoryalated at any one time
1/3 of the 10,000
Why can phosphorylation dramatically affect the conformation of the protein
because each phosphate group has two negative charges
Protein phosprhylation is
reversible and fast but energecialy costsly
THe phosphorylated form of the protein can be either the --- or --- form, depend on the particular protein
active or inactive
Phosphorylation is not used to simly turn protein activity on or of but to what?
to regulate the binding fo different proteins to each other
GTP binding proteinss are regulated by what?
cyclic gain or loss of a phosphate group.
GTP binding proteins act as a whoat
molecular switchers
GTP binding proteins play a crusial role in what?
intracelluar signalling pathways
What do motor proteins do to genrate movment
contrat muscles
move chormosomes druing mitosis
move organells along the cytoskeleton
move enzymes along a DNA strand
What allow proteins to walk along a filament such as a DNA molecule or a microtuble
Changes in conformation
How is walking in one direction made irreversible
by hydrolysis of ATP in every cycle
Once ATP is hydrolyzed what can a protein ono longer do
go back it can only go forward
What conrols the location and assemlby of protein machines?
covalent modifications
what fuction as molecular machines
large complexes formed by proteins
protein machines are assembled at ---locations within cells
protein machines are actived when and where
only needed
What protein controls how a cell responds to DNA damage
What determines how a protein binds to other molecules and its activity
the chemical proteris of the surfact of a protein
What deterimnes those surface proteities of a protein
the tree dimensinoal shape
How are proeins regulated?
by chainging thir shapes and surfaces