Cells, Small Molecules, Macromolecules, and Proteins

Question 1

Do prokaryotic cells have a nucleus?

Answer 1

No

Question 2

Diagram of eukaryotic cell

Answer 2

Question 3

Do eukaryotic cells have a nucleus?

Answer 3

Yes

Question 4

Diagram of prokaryotic cell

Answer 4

Question 5

Diagram of animal cell

Answer 5

Question 6

Micro- and macro-molecules

Answer 6

Question 7

Cells contain ___ major families of small organic molecules that are the building blocks for macromolecules

Answer 7

Four

Question 8

Diagram showing how macromolecules are composed of subunits

Answer 8

Question 9

Disruption to stable protein conformation

Answer 9

• Proteins and RNAs can fold into stable conformations or structures
• The folded structure is stabilized by multiple weak, noncovalent intermolecular bonds

Question 10

Macromolecules can assemble into macromolecular assemblies

Answer 10

Both covalent and non-covalent bonds are required to form a macromolecular assembly such as the ribosome

Question 11

What types of bonds are required to form a macromolecular assembly like a ribosome?

Answer 11

Both covalent and non-covalent bonds

Question 12

What are nucleotides?

Answer 12

The subunits of DNA and RNA

Question 13

How are phosphates attached to the sugar?

Answer 13

By a covalent bond

Question 14

Phosphates in nucleotides

Answer 14

Question 15

Bases in DNA and RNA

Answer 15

Question 16

What are the bases in DNA and RNA?

Answer 16

Nitrogen-containing ring compounds, either pyrimidines or purines

Question 17

DNA and RNA contain different sugars

Answer 17

Question 18

Differences between DNA and RNA

Answer 18

• DNA contains the bases G, C, A, T
• RNA contains the bases G, C, A, U
• DNA is double-stranded
• RNA is single-stranded

Question 19

How are nucleotides linked?

Answer 19

By phosphodiester bonds

Question 20

Nucleotides are linked by ___ to form ___

Answer 20

Phosphodiester bonds to form nucleic acids

Question 21

Diagram of nucleotides in nucleic acids

Answer 21

Question 22

The 5’ end has a ___

Answer 22

Free phosphate group

Question 23

The 3’ has a ___

Answer 23

Free hydroxyl group

Question 24

Nomenclature and abbreviations

Answer 24

Question 25

What is the difference between a nucleoside and a nucleotide?

Answer 25

Nucleoside = base + sugar Nucleotide = base + sugar + phosphate

Question 26

General structure of proteins

Answer 26

Question 27

20 amino acids

Answer 27

Question 28

Each amino acid has a distinct ___

Answer 28

Side chain (R group)

Question 29

Protein nomenclature

Answer 29

- Full name - 3-letter abbreviation - 1-letter code

Question 30

Diagram of amino acids in polypeptide chain

Answer 30

Question 31

What are peptide bonds?

Answer 31

Covalent amide linkages

Question 32

___ and ___ help proteins fold

Answer 32

- Noncovalent bonds - Hydrophobic forces

Question 33

Noncovalent bonds in proteins

Answer 33

Question 34

Hydrophobic forces in proteins

Answer 34

Question 35

Stable 3D conformation of proteins

Answer 35

- Note the variety of shapes and sizes - Both non-covalent and hydrophobic forces stabilize the folded structures

Question 36

Common depictions of protein structure

Answer 36

Question 37

⍺-Helix

Answer 37

- The ⍺-helix is a common polypeptide fold - The N-H of each peptide bond is hydrogen bonded to the C-O bond four amino acids away

Question 38

Bonding in ⍺-helix structure

Answer 38

The N-H of each peptide bond is hydrogen bonded to the C-O bond four amino acids away

Question 39

β-Sheets

Answer 39

- β-sheets are a common feature of polypeptide chains

Question 40

Structure of β-sheets

Answer 40

- β-strands are held together by hydrogen bonds to form a structure called a β-sheet - Note the anti-parallel configuration

Question 41

β-strands are held together by ___ to form a β-sheet

Answer 41

Hydrogen bonds

Question 42

What are the two varieties of β-sheets

Answer 42

Anti-parallel and parallel

Question 43

⍺-helices and b-sheets are elements of the ___ structure

Answer 43

Secondary

Question 44

Separate functional domain of a protein

Answer 44

- Many proteins are composed of separate functional domains - A protein domain is a polypeptide chain that can fold independently

Question 45

Examples of protein domains

Answer 45

Question 46

Can many proteins contain multiple copies of the same protein subunit?

Answer 46

Yes, e.g. dimer and tetramer

Question 47

How are dimers formed?

Answer 47

By interaction between a single, identical binding site on each monomer

Question 48

How are tetramers formed?

Answer 48

By interactions between two non-identical binding sites on each monomer

Question 49

Hemoglobin

Answer 49

- Hemoglobin is an example of how many proteins contain two or more different protein subunits - Hemoglobin contains two copies of each ⍺-globin and β-globin subunits

Question 50

Disulfide bonds

Answer 50

- Covalent bonds that help stabilize a protein fold

Question 51

What kind of bond is a disulfide bond?

Answer 51

Covalent

Question 52

How do proteins bind to other molecules?

Answer 52

- Binding sites allow proteins to interact with specific molecules - The binding of a protein to another molecule - termed ligand - is highly selective

Question 53

Antibodies as an example of how proteins work

Answer 53

- Antibodies are proteins that bind very tightly to their ligands (antigens) - Each antibody molecule is made up of two identical heavy chains and two identical light chains - The two antigen-binding sites are thus identical

Question 54

Specificity of antibody antigen-bind sites

Answer 54

- Each antibody has a distinct antigen-binding site, which recognizes its antigen with high specificity - An individual human can make billions of different antibodies

Question 55

In what ways can antibodies be used as a tool?

Answer 55

- They can be used to purify molecules - They can be used as molecular tags

Question 56

How can antibodies be used to purify molecules?

Answer 56

Question 57

How can antibodies be used as molecular tags? (Biochemical)

Answer 57

Question 58

How can antibodies be used as molecular tags? (Microscopy)

Answer 58

Question 59

Steps of protein purification for studying proteins

Answer 59

- Release the cellular contents - Centrifugation allows the separation of cellular components & separates components on the basis of size and density - Proteins are often separated by column chromatography - Major approaches to determine protein structure: * NMR spectroscopy * Cryo-electron microscopy * X-ray crystallography

Question 60

Releasing cellular contents for protein purification

Answer 60

Question 61

Centrifugation

Answer 61

Question 62

Differential centrifugation

Answer 62

Question 63

Protein separation by column chromatography

Answer 63

Question 64

Three kinds of column chromatography

Answer 64

- Ion-exchange chromatography - Gel-filtration chromatography - Affinity chromatography

Question 65

Major approaches to determining protein structure

Answer 65

Major approaches to determine protein structure: * NMR spectroscopy * Cryo-electron microscopy * X-ray crystallography