Chapter 4: Protein Structure and Function Flashcards
When we look at a cell in a microscope or analyze its electrical or _______, we are, in essence, observing the handiwork of proteins.
Biochemical activity
The main building blocks from which cells are assembled, and they constitute most of the cell’s dry mass.
Proteins
Proteins are the main building blocks from which cells are assembled, and they constitute most of the cell’s ______.
Dry mass
Enzymes promote _____ chemical reactions by providing intricate molecular surfaces contoured with particular bumps and crevices that can cradle or exclude specific molecules.
Intracellular
It catalyze covalent bond breakage or formation
Enzymes
It makes the alcohol in wine
Alcohol dehydrogenase
Degrades dietary proteins in the stomach
Pepsin
Helps convert carbon dioxide into sugars in plants
Ribulose bisphophate carboxylase
An enzyme that copies DNA
DNA polymerase
It adds a phosphate group to a protein molecule
Protein kinase
The common constituents of extracellular matrix and form fibers in tendons and ligaments
Collagen and elastin
It forms long, stiff microtubules inside cells
Tubulin
It forms filaments that underlie and support the plasma membrane
Actin
It forms fibers that reinforce epithelial cells and is the major protein in hair and horn
Keratin
It carries lipids in the bloodstream
Serum albumin
Proteins that provide mechanical support to cells and tissues
Structural proteins
Type of proteins that carry small molecules or ions
Transport proteins
Type of proteins that generate movement in cells and tissues
Motor proteins
Type of proteins that stores amino acids or ions
Storage proteins
Type of proteins that carry extracellular signals from cell to cell
Signal proteins
Type of proteins that detect signals and transmit them to the cell’s response machinery
Receptor proteins
Type of proteins that bind to DNA to swith genes on or off
Transcription regulators
It carries oxygen
Hemoglobin
Carries iron in thr bloodstream
Transferrin
A bacterial protein that is a light-activated proton pump that transports H+ ions out of the cell
Bacteriorhodopsin
Shuttle glucose into and out of cells
Glucose transporters
It clears Ca2+ from a muscle cell’s cytosol sfter the ions have triggered a contraction
Ca2+ pump
It provides the motive force for humans to move
Myosin
It interacts with microtubules to move organelles around the cell
Kinesin
It enables eukaryotic cilia and flagella to beat
Dynein
Iron is stored in the liver by binding to the small protein called
Ferritin
Iron is stored in the ____ by binding to the small protein ferritin
Liver
Found in egg white which is used as a source of amino acids for the developing bird embryo
Ovalbumin
Source of amino acids for baby mammals found in milk
Casein
A small protein that controls glucose levels in the blood
Insulin
It attracts growing nerve cell axons to specific locations in the developing spinal cord
Netrin
It stimulates some types of nerve cells to grow axons
Nerve growth factor (NGF)
It stimulates the growth and division of epithelial cells
Epidermal growth factor (EGF)
Found in the retina that detects light
Rhodopsin
Allows a cell to respond to the hormone insulin by taking up glucose
Insulin receptor
It increases the rate of heartbeat when it binds to epinephrine secreted by the adrenal gland
Adrenergic receptor
The adrenergic receptor on heart muscle increases the rate of heartbeat when it binds to _____ secreted by the adrenal gland
Epinephrine
The adrenergic receptor on heart muscle increases the rate of heartbeat when it binds to epinephrine secreted by the _____
Adrenal gland
Found in bacteria. Silences the genes for the enzymes that degrade the sugar lactose
Lac repressor
It acts as genetic switches to control development in multicellular organisms, including humans
DNA-binding proteins
From a ____ point of view, proteins are by far the most structurally complex and functionally sophisticated molecules known
Chemical
A protein molecule is made from a long chain of these amino acids, held together by ____
Covalent peptide bonds
Proteins are therefore referred to as
Polypeptides, or polypeptide chains
In each type of protein, the amino acids are present in a unique order, called the
Amino acid sequence
Each polypeptide chain consists of a backbone called ____ that is adorned with a variety of chemical side chains. It is formed from a repeating sequence of the core atoms (-N-C-C-) found in every amino acid
Polypeptide backbone
Proteins are typically made up of chains of several hundred amino acids, whose sequence is always presented starting with the _____, and read from ____ to ____.
N-terminus ; left to right
Amino group in a polypeptide chain is written as
NH3+, also written as NH2
Carboxyl group is written as
COO, or COOH
The end carrying the amino group (NH3+/NH2) is called _________
Amino terminus or N-terminus
The end carrying the free carboxyl group is the __________
Carboxyl terminus or C-terminus
Projecting from the polypeptide backbone are the ___________ - the part of the amino acid that is not involved in forming peptide bonds
Amino acid side chains
It gives each amino acid its unique properties
Side chains
Long polypeptide chains are very flexible, as many of the covalent bonds that link the carbon atoms in the polypeptide backbone allow free rotation of the atoms they join. Thus, proteins can fold in an enormous number of ways. The shape of these folded chains however, is constrained by many sets of ______ bonds that form within proteins that help protein fold up and maintain their shape.
Weak noncovalent bonds
The non covalent bonds that help proteins fold up and maintain their shape include
Hydrogen bonds
Electrostatic attractions
Van der Waals attractions
The stability of each folded shape is largely determined by the combined strength of large numbers of
Noncovalent bonds
Protein folding has been studied in the laboratoru using ___
Highly purified proteins
A process where proteins gets unfolded by treatment with solvents that disrupt the noncovalent interactions holding the folded chain together
Denaturation (denatured protein)
Under the right conditions, when the denaturing solvent is removed, the protein often refold sponaneously into its original conformation , a process called
Renaturation
The final folded structure of a protein is called
Conformation
Although a protein chain can fold into its correct conformation without outside help, protein folding in a living cell is generally assisted by a large set of special proteins called ____ that bind to partly folded chains and help them to fold along the most energetically favorable pathway. The function of thede chaperones requires ATP binding and hydrolysis
Chaperone proteins
Others form ____ in which single polypeptide chains can fold without the risk of forming aggregates in the crowded conditions of the cytoplasm
Isolation chambers
The conformation of a protein is determined solely by its
Amino acid sequence
A model that shows the overall organization of the polypeptide chain and provides a straightforward way to compare the structures of related proteins
Backbone model
A model that shows the polypeptide backbone in a way that emphasizes its most conspicuous folding patterns
Ribbon model
A model that includes the positions of all the amino acid side chains; this view is essentially useful for predicting which amino acids might be involved in the protein’s activitiy
Wire model
A model that provides a contour map of the protein surface, which reveals which amino acids are exposed on the surface and shows how the protein might look to a small molecule such as water or to another macromolecule in the cell
Space-filling model
The first folding pattern discovered that was found in the protein a-keratin which is abundant in skin and hair, nails, and horns
a helix
A second folded structure that was found in the protein fibroin, the major constituent of silk
B sheet
The two folding patters (a helix and B sheets) are particularly common because they result from ____ bonds that form between N-H and C=O groups in the polypeptide backbone
Hydrogen
True or false. The helix is not a channel: no ions or small molecules can pass through it
true
It is generated simply by placing many similar subunits next to one another, each in the same strictly repeated relationship to the one before
helix
A hydrogen bond is made between every ____ amino acid, linking the C=O of one peptide bond to the N-H of another. This pattern gives rise to a regular right-handed helix with a complete turn every 3.6 amino acids
Fourth
Sometimes two (or three) α helices will wrap around one another to form a particularly stable structure called
coiled-coil
A folding structure that form the basis of amyloid structures, in
which they are stacked together in long rows with their amino acid
side chains interdigitated like the teeth of a zipper
B sheets
It can convert the properly
folded version of the protein in an infected brain into the abnormal conformation. This allows the to form aggregates which can spread rapidly from cell to cell, eventually causing the death of
the affected animal or human
misfolded prion form of a protein
a protein’s structure begins with its amino acid sequence, this is considered its
primary structure
The next level of organization includes the α helices and β sheets that form within certain segments of the polypeptide chain; these folds are elements of the protein’s
secondary structure
The full, three-dimensional conformation formed by an entire polypeptide chain—including the α helices, β sheets, and all other loops and folds that form between the N- and C-termini—is sometimes referred to as the
tertiary structure
It is defined as any segment of a polypeptide chain that can fold
independently into a compact, stable structure. It usually contains between 40 and 350 amino acids—folded into α helices and β sheets and other elements of structure—and it is the modular unit from
which many larger proteins are constructed
protein domain
Any region on a protein’s surface that interacts with other molecule through sets of noncovalent bonds is termed as
Binding site
Two protein subunits
Dimer
These proteins generally have a relatively simple, elongated three-dimensional structure and are commonly referred to as
Fibrous proteins
Fibrous proteins are especially abundant outside the cell, where they form the gel-like ______ that helps bind cells together to form tissues
Extracellular matrix
It enables skin and other tissues, such as arteries and lungs, to stretch and recoil without tearing
Elastic fibers (produced by elastin molecules)
A component of the cytoskeleton that gives cells mechanical strength
Intermediate filaments
Any substance that is bound by a protein- whether it is an ion, a small organic molecule or a macromolecule is referred to as
Iigand
The ability of a protein to bind selectively and with high affinity to a ligand is due to the formation of
Weak noncovalent interactions
These are immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those in the surface of an invading microorganism.
Antibodies
The target molecule that the antibody recognizes
Antigen
This generates an enormous diversity of antigen-binding sites by changing only the length and amino acid sequence of this thing which is how the wide variety of different antibodies is formed
Hypervariable loops
It gives hemoglobin and blood its red color
Heme
It is a form of negative regulation that prevents an enzyme from acting
Feedback inhibition
Large molecules that contain binding sites recognized by multiple proteins. It allows proteins to be assembled and activated only when and where they are needed
Scaffold proteins
The resulting slurry of breaking open the cells to release their contents
Cell homogenate or extract
The standard approach involves purifying the protein through a series of _____ steps to separate the individual components of a complex mixture into portions or fractions
chromatography
The most efficient forms of protein chromatography separate a polypeptides on the basis of their ability to bind to a particular molecule - a process called
Affinity chromatography
A technique where an electric field is applied to a solution or a polymer gel containing protein molecules and migrate them in a direction and at a speed that reflects their size and net charge
Electrophoresis
A technique that determines the exact mass of peptide fragment in a purified protein, which then allows the protein thought to be encoded by the genome of the relevant organism.
Mass spectrometry
After the peptides pass through the first mass spectrometer, they are broken into even smaller fragments and analyzed by a second mass spectrometer
Tandem mass spectrometry
Not a question. The predominant way to discover the precise folding pattern of any protein is by experiment, using
X-ray crystallography,
Nuclear magnetic resonance spectroscopy
Cryoelectron microscopy
