Elements Of A Cell & Proteins

Front 1

What are the most common elements that make up a cell?

Back 1

Hydrogen, Carbon, Nitrogen, and Oxygen make up 99% of the cell.

Na, Mg, P, S, Cl, K, and Ca make up 0.9%.

Front 2

Life uses elements that are ______, ________, and ________.

Back 2

Common, reactive, and form strong bonds.

Front 3

Which of the elements most common in living organisms makes especially stable bonds? Known as the "backbone of life."

Back 3

Carbon

Front 4

What are macromolecules?

Back 4

Large molecules containing a large number of atoms. Key structural and functional components of cells.

Front 5

What are the four main classes of macromolecules?

Back 5

Polysaccharides: Sugar is the subunit, and they have 2 structural types (Branched and linear)

Proteins: Amino acids are the subunit

Nucleic Acids: Nucleotides are the subunits. DNA and RNA

Lipids: many structural types. Not a polymer like the other 3

Front 6

What is a polymer?

Back 6

A chain of the same or similar molecules. Ex: Proteins

Front 7

What are the two classes of peptides, and how are they categorized?

Back 7

Oligopeptides: 2-20 aa.

Ex: di-, tri-, and tetrapeptide, cell-to-cell signals, neuropeptides (opiate peptides, substance P, vasopressin)

Polypeptides/Proteins: 30+ aa. Typically several hundred aa.

Categorized by size

Front 8

What 3 traits do proteins share?

Back 8

1. All adopt at least 2 stable conformations.

2. All bind to at least one molecular target. Highly specific.

3. All perform at least 1 cellular function.

Front 9

Describe the structure of proteins

Back 9

The positively charged N-terminus is where the amino group (NH2) is. The negatively charged C-terminus is where the carboxy (COOH) is. These create the protein backbone.

The alpha carbon sits in the middle

The R group (or side chain) determines the type of amino acid

Front 10

What kinds of bonds connect amino acids?

Back 10

Peptide bonds, which are catalyzed by the ribosome during translation.

Front 11

How many classes of amino acids are there, and what determines the class?

See Pp for images of each side chain type.

Back 11

The Side chain (R group) determines the class.

1. Nonpolar, aliphatic side groups. Ex: Methionine

2. Aromatic side groups. Ex: Phenylalanine

3. Polar, uncharged side groups. Ex: Threonine

4. Positively charged side groups. Ex: Lysine

5. Negatively charged side groups. Ex: Glutamate

Front 12

What are the 4 levels of protein structure?

Back 12

1. Primary: aa sequence

2. Secondary: Alpha helix, beta pleated-sheets, and random coils. Based on the primary structure, but not easily predictable

3. Tertiary: The 3D conformation of the protein. Local structure: motifs and global/overall structure.

4. Quaternary: When the protein molecule is formed as a complex of more than one polypeptide chain

Front 13

What is the tertiary local structure?

Back 13

The combo of several individual secondary structures together into a characteristic motif structure seen in many proteins.

Ex: helix-loop-helix motif and hairpin turn motif (2 head-to-tail beta-sheets).

Front 14

What is tertiary overall structure?

Back 14

The shape of the entire protein for a single polypeptide.

Front 15

What are different models used to depict secondary, tertiary, and quaternary structure?

Back 15

1. Ribbon model (makes it easy to see alpha helices and beta sheets)

2. Space-filling model (emphasizes overall shape)

3. Backbone model

Front 16

How many types of overall tertiary structure are there?

Back 16

Two: globular and fibrous (long rod-shaped proteins made from parallel, cross-linked polypeptide chains)

Front 17

What protein is this?

Back 17

Aspartate transcarbamoylase. Globular structure

Front 18

What protein is this?

Back 18

Catalase. Globular structure

Front 19

What are these two proteins?

Back 19

Yellow one is lysozyme

Red one is myoglobin

Globular structures

Front 20

What protein is this?

Back 20

Porin. Globular structure

Front 21

What is this protein?

Back 21

Collagen. Fibrous structure

Front 22

How is the quaternary structure defined?

Back 22

By arrangement of polypeptide subunits in multimeric proteins.

Ex: Antibodies, which have two light chains connected by disulfide covalent bonds to two heavy chains

Front 23

What are some of the quaternary structures?

Back 23

Homodimers, helices, rings, spheres, and hollow tubes.

Front 24

What are the 5 types of chemical bonds that fold and stabilize protein structure?

Back 24

1. Disulfide bond. Only covalent bond, and by far the most stable.

Non-covalent

2. Hydrogen bond. Occur with alpha helices and beta sheets.

3. Electrostatic interactions. Can neutralize charged residues when they occur in the interior, which makes interior hydrophobic.

4. Hydrophobic interactions. Usually occur in the interior of protein, leaving polar/ionic residues at surface to interact with water.

5. Van der Waals forces. Only act at very short distances.

Front 25

True or false, reorganization of a few non-covalent bonds allows proteins to switch conformations?

Back 25

True

Front 26

What was the Anfinsen in vitro experiment?

Back 26

A test using Ribonuclease A to see if all necessary information for proper folding of a protein is contained in its primary sequence. Proved that yes, it does.

Front 27

How do cells fold proteins so quickly?

Back 27

Chaperone proteins. Some prevent misfolding by destabilizing weaker conformations using energy of ATP hydrolysis. Others create chambers to isolate nascent proteins.

Front 28

What do proteins need to be functional?

Back 28

They must be able to be activated and inactivated. The two states are reflected by different conformations.

Front 29

How many mechanisms (at least) are there for controlling protein activity?

Back 29

1. Chemical modification of amino acids

2. Binding of small molecules to allosteric sites

3. Binding of regulatory proteins

4. Protein degradation

Front 30

What are the 7 common types of covalent protein modifications?

Back 30

1. Disulfide bonds (Cystine)

2. Ubiquitination (Lysine)

3. Sugars (glycosylation, Asparagine, serine, threonine)

4. Lipids (ex: farnesyl, cystine)

5. Phosphate groups (phosphorylation, tyrosine, serine, threonine)

6. Methyl groups (methylation, lysine, arginine)

7. Acetyl groups (acetylation, lysine)

Front 31

True or false: protein modifications do not depend on context (surrounding amino acids).

Back 31

False. They do depend on context, and because of this, only a few particular residues undergo modifications.

Front 32

True or false: many chemical modifications of proteins are not reversible.

Back 32

False. Proteins can switch between active and inactive many times.

Front 33

With small molecule modifications, why are active or inactive states relatively short lived?

Back 33

Proteins bind and release small molecules extremely quickly from allosteric sites. Costs the cell a lot of energy to maintain a steady supply of them.

Front 34

What is an allosteric site?

Back 34

The place on an enzyme where a molecule that is not a substrate may bind, thus changing the shape of the enzyme, affecting whether it's active or inactive.

Front 35

What is the only non-reversible protein regulatory mechanism?

Back 35

Protein degradation

Front 36

How can protein expression levels be regulated? (Meaning at what levels)

Back 36

Transcription, translation, and protein stability

Front 37

What are the 3 degradation mechanisms?

Back 37

1. Proteasomes (source is nucleus and cytosol)

2. Lysosomes (source is plasma membrane and Golgi apparatus)

3. Soluble proteases (source is extracellular matrix/ECM)

Front 38

What is the signal for protein degradation by the proteasome?

Back 38

A poly-ubiquitin tag.

Front 39

Describe the 20S proteasome structure.

Back 39

It has a cap on either end, which unfolds targeted proteins. The core is made of two alpha and two beta units in this order: abba. These rings are each 7 proteins. The target protein is degraded within these rings (which create the core).

Front 40

What do enzymes do?

Back 40

Bind substrates and convert them into products by speeding up a chemical reaction. They are catalysts.

Front 41

What are motor proteins?

Back 41

Proteins that generate force to move cells or cellular components within cells.

Front 42

What are response proteins?

Back 42

They detect signals inside or outside of cells and transduce these signals to activate cellular changes. Often regulate other proteins or gene expression.

Front 43

What are structural proteins?

Back 43

They provide scaffolds for the cell or for structures within the scaffold.

Front 44

What are transport proteins?

Back 44

They move material in/out and within the cell.

Front 45

True or false: proteins work in complexes

Back 45

True

Front 46

What holds protein complexes together?

Back 46

Multiple non-covalent bonds between protein surfaces. They are weak individually, but strong when there are many of them.

Front 47

What determines how a protein works?

Back 47

Side chains and spatial organization. Side chains don't need to be next to each other to bond.

Front 48

What is X-ray crystallography, and how does it work in general?

Back 48

A way of determining protein structure.

1. Purify single protein

2. Crystallize protein

3. Obtain X-ray diffraction pattern

Front 49

What is SDS PAGE and how does it basically work?

Back 49

A method for separating proteins based on size.

1. Separate proteins of different size using sodium dodecyl sulfate and polyacrylamide gel in gel electrophoresis.

2. Follow up with a western blot because cells have so many proteins, need some way to distinguish them.

SDS has a hydrophobic tail with a negative charge, coating the protein to maintain a denatured shape so shape doesn't affect test

Front 50

What is a Western Blot? What is the procedure?

Back 50

A procedure used to detect a specific protein from a mixture of proteins. Uses antibodies as probes. 1. Dissolve and isolate proteins in Sodiumdodecyl Sulfate and then boil (helps unfold proteins and coats them with a negative charge for gel electrophoresis)2. Separate protein by SDS-PAGE (Sodiumdodecyl Sulfate - Polyacrylamide gel electrophoresis). PAGE works better for proteins than agarose.3. Transfer proteins onto nylon membrane. 4. Add primary antibody that binds to protein of interest. Wash off excess. 5. Add secondary antibody, which binds to primary, and is covalently linked to a report enzyme. 6. Add enzyme substrate linked to secondary antibody to produce color or luminescence. 7. Expose to X-ray film to find target protein.

Front 51

Name the class of amino acid and an example.

Back 51

Nonpolar, aliphatic side group

Methionine.

Front 52

Name the class of amino acid and an example.

Back 52

Aromatic side group

Phenylalanine

Front 53

Name the class of amino acid and an example.

Back 53

Polar, uncharged side group

Threonine

Front 54

Name the class of amino acid and an example.

Back 54

Negatively charged side group

Glutamate

Front 55

Name the class of amino acid and an example.

Back 55

Positively charged side group

Lysine

Front 56

Describe the amino acid peptide bond formation

Back 56

Front 57

What are these two structures?

Back 57

1. Alpha helix

2. Beta pleated sheet

Both are secondary protein structures. The third major 2⁰ structure is the random coil