Biology Chapter 3: Protein Structures And Functions

Front 1

Describe the assumptions of Miller's famous experiment

Back 1

Assumed the early atmosphere was full of high energy molecules when chemical evoution occured, making redox reactions possible.

Front 2

Describe the set-up of Miller's experiment

Back 2

The microcosm of the atmosphere contained CH4, NH3, and H2, which were carried by water vapor through the cycle; elecric impulses sparked chemical evolution

Front 3

Name some of the problems later found with Miller's chemical evolution experiment

Back 3

Volcanic gases would have had lowe energy forms (CO2 and CO) which are less reactive; Chemical evolution may take place in the ocean, not atmosphere

Front 4

Describe the basic structure of the 20 protein-forming amino acids

Back 4

1st bond- NH2 the amino func. group
2nd bond- COOH the carboxyl group
3rd bond- H atom
4th bond- the 'R' group (side chain); distinguishes the amino acids from each other

Front 5

What happens to amino acids in water?

Back 5

The concentration of proteins causes the amino acids to act like bases, forming NH3+ and COO-.

Front 6

Describe the difference hydrophobic and hydrophilic R groups

Back 6

Hydrophobic- Non-polar side chains that cannot form H bonds in water
Hydrophiliac- Polar side chains that interact with water and dissolve easily

Front 7

Describe the reaction patterns of side chain composed of mostly C and H atoms

Back 7

These R groups rarely react chemically.

Front 8

Explain the importance of R groups containing S

Back 8

These R groups help link larger proteins.

Front 9

Isomers

Back 9

Molecules that have different structures, but the same molecule formulas.

Front 10

Describe the 3 types of isomers

Back 10

1. Structural Isomers- same atoms, different order due to covalent bonds
2. Geometric Isomers- differ in ring or double bond
3. Optical isomers- carbon atoms with 4 different groups attached

Front 11

T/F in cells, the 'left handed' isomer is interchangable with the 'riight handed' version

Back 11

False- the right handed version causes malfunctions.

Front 12

Monomer

Back 12

A molecular subunit such as a sugar, amino acid, or a nucleotide.

Front 13

Polymer

Back 13

The result of several monomers linked together.

Front 14

Polymerization

Back 14

The process of linking monomers.

(Amino Acids polymerize to form proteins)

Front 15

Protein

Back 15

The linear macromolecule of linked amino acids monomers.

Front 16

Why are proteins technically not expected to form spontaneously?

Back 16

Complex and highly organized molecules are not expected to form spontaneously because they result in decreased entropy; Delta G is positive for all temperatures.

Front 17

Condensation Reactions (Dehydration Reactions)

Back 17

A reaction in which the new molecule reults in the loss of a water molecule.

Front 18

Hydrolysis

Back 18

A reaction that breaks polymers apart by adding water molecule; dominates because it increases entropy and is energeticallt favorable.

Front 19

How do polymers escape hydrolysis?

Back 19

Adsorption to mineral particles protects polymers from hydrolysis.

Front 20

Peptide Bond

Back 20

A bond that forms between the carboxyl group of one amino acid and the amino group of another vi a condensation reaction.

Front 21

Describe a polypeptide

Back 21

*Side chains extend out from the-
*Backbone, which has direction and flexibility (due to single bonds); the peptide is always N terminus to C.

Front 22

How are amino acids referred to in a polypeptide?

Back 22

The amino acids are referred to as residuals.

Front 23

Primary Structure

Back 23

The sequence of amino acids of a protein; each protein has a unique sequence and structure ( Fred Sanger & insulin).

Front 24

Secondary Structure

Back 24

This structure is created by the H bonds that form between carboxyl and amino groups in the backbones ONLY; either alpha helices or beta pleated sheets.

Front 25

Tertiary Structures

Back 25

This structure is responsible for the overall shape of the protein; results froom interacts between R groups and backbones.

Front 26

What are some of the possible interactions at the tertiary level?

Back 26

1. Covalent bonds can form between the S atoms (disulfide bridges)
2. In H2O, hydrophobic regions form vn der Waals interactions; inc. stability and create glob structure
3. Ionic bonds can form between ionized amino and carboxyl groups
4. H bonds

Front 27

Quaternary Structures

Back 27

Not present in every protein; this structure is due to the combination of polypeptide subunits.

Front 28

Why is folding both spontaneous and important?

Back 28

Folding is spontaneous because van der Waals interactions make folded proteins more energetically stable, releasing free energy; folding is essential for protein function.

Front 29

How is a denatured protein different from regular proteins?

Back 29

Denatured proteins are unfolded.

Front 30

Molecular Chaperones

Back 30

Molecules that facilitate protein folding which belong to a group of proteins known as heat shock proteins.

Front 31

Heat Shock Proteins

Back 31

Proteins that are produced in large quantities in a cell after the cell experiences high temps. or other situation that make them lose 3rd struc.

Front 32

Prions

Back 32

Infectious proteins that are improperly folded forms of regualr proteins; they differ in shape and can induce normal proteins to change as well (fatal disease).

Front 33

What are the 6 main functions of proteins?

Back 33

1. Defense (antibodies), 2. Movement (motor/ contractile proteins), 3. Catalysis (enzymes), 4. Signaling (peptide hormones bind to receptors), 5. Structure (mechanical support), 6. Transport (carry compounds through body/ allow enterance into cells)

Front 34

Catlalyst

Back 34

A substance that lowers the activation energy of a reaction and increases the rate of the reaction; it is not consumed in the reaction.

Front 35

Enzymes

Back 35

Proteins that catalyze reactions;
often end in -ase.

Front 36

Lock and Key Model

Back 36

Enzymes are ridgid structures analogous to a lock; substrates bind to this lock and react;
However, enzymes are really flexible.

Front 37

Activation Sites

Back 37

The locations on the enzymes where the substrates bind to and react.

Front 38

Describe the process of catalyzing an enzyme

Back 38

1. Initiation- Reactants bind to the activation sites in a specific orientation
2. Transition Site- Activation energy lowered by the interaction between the enzyme and substrate
3. Termination- Products have lower affinity for activation sites and are released; enzyme remains unchanged.

Front 39

Enzyme Cofactor

Back 39

Atoms or molecules that are not part of the enzymes primary structure; they are either metal ions or coenzymes.

Front 40

Competitive Inhibition

Back 40

Catalysis is inhibited when a molecule similar in shape and size to the substrate competes for the enzyme activation site.

Front 41

Allosteric Regulation

Back 41

Molecule changes enzyme shape to activate/inactivate it.

Front 42

Enzyme Kinetics

Back 42

The rate of enzyme action; at a certain point, the rate tapers off because all of the enzyme is being used; affected by pH and temperature ( and population).

Front 43

How do endergonic reactions take place?

Back 43

1. Most reactions are endergonic
2. Adding a phosphate group (PO4 3-) adds 2 negative charges and adds enough free energy for polymerization -- phosporization occurs (exergonic).