Chapter 3 Protein Structure and Function

polymer

"many parts" when a large number of monomers are bonded together

monomer

"one-part" a molecular sub-unit such as an amino acid, a nucleotide, or a sugar

why are proteins not considered to be good candidate for the first living molecule?

The cannot serve as a template for replication

molecular chaperones

folding is often facilitated by specific proteins

cell theory step 4

life became possible when one of these large, complex molecules acquired the ability to replicate itself. By increasing in copy number, this molecule would then emerge from the pool of chemicals. At that point, life had begun-- chemical evolution gave way to biological evolution

transport

proteins allow particular molecules to enter and exit cells or carry them throughout the body. Hemoglobin is a particularly well studied transport protein, but virtually every cell is studded with membrane proteins that control the passage of specific molecules and ions.

a major theme in this chapter is that the structure of molecules correlates with their function. Use this theme to explain why proteins can perform so many different functions in organisms and why enzymes are such effective catalysts

proteins are highly variable in overall shape and chemical properties due to variation in the composition of R-groups and the array of secondary through quaternary structures that are possible. This variation allows them to fulfill many different roles in the cell. Diversity in the shape and reactivity of active sites also makes them effective catalysts.

signaling

proteins are involved in carrying and receiving signals from cell to cell inside the body. If sugar levels in your blood are low, a small protein called glucagon will bind to receptor proteins on your liver cells, triggering enzymes inside to release sugar into your bloodstream.

defense

proteins called antibodies and complement proteins attack and destroy viruses and bacteria that cause disease

substrates

reactant molecules

beta-pleated sheet

segments of a peptide chain bend 180 degrees and then fold in the same pleane

you should be able to provide the characteristics of proteins that make them especially useful for the following cellular activities: catalysis, defense, and signaling.

Catalysis- proteins are made of amino acids, which have many reactive functional groups, and can fold into different shapes that allow the formation of active sites. Defense- similar to catalysis, the chemical properties and capacity for different shapes allows proteins to be made that can attach to virtually any type of invading virus or cell. Signaling- the flexibility in protein structure allows protein activities to be quickly turned on or off based on binding to signal molecules or ions.

IFU- you should be able to explain how you could use the structural formula of an amino acid to determine if it is acidic, basic, uncharged polar, or nonpolar

Look at the R-group of the amino acid. If there is a positive charge, then it is basic. If there is a negative charge, then its an acid. If it has no charge, but there is an oxygen atom, then it is polar uncharged. If there is no charge or oxygen, then it is nonpolar

provide an example of how a specific shape of a protein is correlated with its function

Many possible correct answers, including 1) the prescence of an active site in an enzyme that is precisely shaped to fit a substrate or substrates in the correct orientation for a reaction to occur 2) the doughnut shape of porin that allows certain substances to pass through it 3) the cable shape of collagen to provide structural support for cells and tissues.

disulfide "two sulfurs" bonds

are frequently referred to as bridges, because they create strong links between distinct regions of the same polypeptide or two separate polypeptides

By convention, biologists write the sequence of amino acids in a polypeptide in which direction?

b

in a polypeptide, what bonds are responsible for the secondary structure called an alpha helix?

b

explain how water participates in the development of of the interactions that glue non-polar amino acids together in the interior of globular proteins.

because the non polar amino avid residues are not able to interact with water solvent, they are crowded together in the interior of a protein and surrounded by a network of hydrogen-bonded water molecules. This crowding leads to the development of van der Waals interactions that help glue the non polar side chains together

active site

catalysis usually occurs

cell theory step 1

chemical evolution began with the production of small organic compounds from reactancts such as H2, N2, NH3, and CO2.

what 2 functional groups are present on every amino acid?

d

hydrophobic

do not interact with water

Quarternary structure is based on tertiary structure which is based in part on secondary structure which is based on primary structure

...

you should be able to identify one way the process of folding in calmodulin and infectious prions is similar

Both calmodulin and infectious prions require some form of induction to achieve their active conformations. Calcium ions are required for calmodulin to fold into its functional structure while prions are induced to change their shape by other, improperly folded prion proteins

if proteins folded only into rigid, inflexible structures, how might this affect the cell's ability to regulate protein function

In many proteins, especially those involved in cell signaling, their structure is affected by binding to other molecules or ions. Since the Shape of the protein is directly involved in its function, the protein's activity is regulated by controlling how it is folded. If proteins were inflexible, this type of control could not occur.

If amino acids were mixed together in a solution, resembling the prebiotic soup, would they spontaneously polymerize into polypeptides? why or why not?

No, polymerization is a non-spontaneous reaction because the product molecules have lower entropy than the free form of the reactants and there would be nothing to prevent hydrolysis from reversing the reaction

tertiary structure

a polypeptide results from interactions between R-groups or between R-groups and the backbone.

enzyme

a protein that functions as a catalyst

macromolecule

a very large molecule that is made up of smaller molecules joined together

flexibility

although the peptide bond itself canot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate.

macromolecular machines

groups of multiple proteins that assemble to carry out a particular function

hydrogen bonding

hydrogen bonds form between polar R-groups and opposite partial charges either in the peptide backbone or other R-groups

hydrophilic

interact readily with water

secondary structure

is created in part by hydrogen bonding between components of the peptide-bonded backbone

cell theory step 3

mid-sized, building block molecules linked to form the types of large molecules found in cells today, including proteins, nucleic acids, and complex carbs. Each of these large molecules is composed of distinctive chemical sub-units that join together: proteins are composed of amino acids, nucleic acids are composed of nucleotides, and complex carbs are composed of sugars.

amino acids

most of these molecules are composed of just 20 different building blocks

movement

motor proteins and contractile proteins are responsible for moving the cell itself, or moving large molecules and other types of cargo inside the cell.

you should be able to predict where nonpolar amino acid residues would be found in a globular protein, such as trypsin molecule.

nonpolar amino acid residues would be found in the interior of a globular protein, grouped with other nonpolar residues due to hydrophobic interactions

van der Waals interactions

once hydrophobic side chains are close to one another, their association is further stabilized by electrical attractions

prions

proteinaceous infectious particles

catalyze

speed up

structure

structural proteins make up body components such as fingernails and hair, and define the shape of individual cells. Structural proteins keep red blood cells flexible and in their normal disc-like shape.

peptide bond

the C-N covalent bond that results from this condensation reaction

twenty different amino acids are found in the proteins of cells. what distinguishes these molecules?

the atoms and functional groups found in the side chains

quaternary structure

the combination of polypeptides, referred to as subunits

Where is the information stored that directs different polypeptides to fold into different shapes?

the order and type of amino acids contains the information that directs folding

alpha helix

the polypeptide's backbone is coiled

What is an active site?

the position in an enzyme where substrates bind

polymerization

the process of linking monomers together

R-group orientation

the side chains present in each residue extend out from the backbone, making it possible for them to interact with each other and with water

primary struture

the unique sequence of amino acids in a protein

directionality

there is an amino group on one end of the backbone and a carboxyl group on the other. The end sequence that has the free amino group is called the N-terminus, or amino-terminus, and the end with the free carboxyl group is called the C-terminus, or carboxy-terminus. By convention, biologists always write amino acid sequences from the N-terminus to the C-terminus, because the N-terminus is the start of the chain when proteins are synthesized in cells.

cell theory step 2

these small, simple organic compounds reacted to form mid-sized molecules, such as amino acids, nucleotides, and sugars.

denatured

unfolded

protein

used to describe any chain of amino acid residues, but formally protein refers to the complete, functional form of the molecule

oligopeptide

when feweer than 50 amino acids are linked together in this way

condensation reactions or dehydration reactions

when monomers polymerize, the newly formed bond results in a loss of a water molecule

polypeptides

when more than 50 amino acids are linked together in this way