Cells, Small Molecules, Macromolecules, and Proteins Flashcards
Do prokaryotic cells have a nucleus?
No
Diagram of eukaryotic cell
Do eukaryotic cells have a nucleus?
Yes
Diagram of prokaryotic cell
Diagram of animal cell
Micro- and macro-molecules
Cells contain ___ major families of small organic molecules that are the building blocks for macromolecules
Four
Diagram showing how macromolecules are composed of subunits
Disruption to stable protein conformation
- Proteins and RNAs can fold into stable conformations or structures
- The folded structure is stabilized by multiple weak, noncovalent intermolecular bonds
Macromolecules can assemble into macromolecular assemblies
Both covalent and non-covalent bonds are required to form a macromolecular assembly such as the ribosome
What types of bonds are required to form a macromolecular assembly like a ribosome?
Both covalent and non-covalent bonds
What are nucleotides?
The subunits of DNA and RNA
How are phosphates attached to the sugar?
By a covalent bond
Phosphates in nucleotides
Bases in DNA and RNA
What are the bases in DNA and RNA?
Nitrogen-containing ring compounds, either pyrimidines or purines
DNA and RNA contain different sugars
Differences between DNA and RNA
- DNA contains the bases G, C, A, T
- RNA contains the bases G, C, A, U
- DNA is double-stranded
- RNA is single-stranded
How are nucleotides linked?
By phosphodiester bonds
Nucleotides are linked by ___ to form ___
Phosphodiester bonds to form nucleic acids
Diagram of nucleotides in nucleic acids
The 5’ end has a ___
Free phosphate group
The 3’ has a ___
Free hydroxyl group
Nomenclature and abbreviations
What is the difference between a nucleoside and a nucleotide?
Nucleoside = base + sugar
Nucleotide = base + sugar + phosphate
General structure of proteins
20 amino acids
Each amino acid has a distinct ___
Side chain (R group)
Protein nomenclature
- Full name
- 3-letter abbreviation
- 1-letter code
Diagram of amino acids in polypeptide chain
What are peptide bonds?
Covalent amide linkages
___ and ___ help proteins fold
- Noncovalent bonds
- Hydrophobic forces
Noncovalent bonds in proteins
Hydrophobic forces in proteins
Stable 3D conformation of proteins
- Note the variety of shapes and sizes
- Both non-covalent and hydrophobic forces stabilize the folded structures
Common depictions of protein structure
⍺-Helix
- 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
Bonding in ⍺-helix structure
The N-H of each peptide bond is hydrogen bonded to the C-O bond four amino acids away
β-Sheets
- β-sheets are a common feature of polypeptide chains
Structure of β-sheets
- β-strands are held together by hydrogen bonds to form a structure called a β-sheet
- Note the anti-parallel configuration
β-strands are held together by ___ to form a β-sheet
Hydrogen bonds
What are the two varieties of β-sheets
Anti-parallel and parallel
⍺-helices and b-sheets are elements of the ___ structure
Secondary
Separate functional domain of a protein
- Many proteins are composed of separate functional domains
- A protein domain is a polypeptide chain that can fold independently
Examples of protein domains
Can many proteins contain multiple copies of the same protein subunit?
Yes, e.g. dimer and tetramer
How are dimers formed?
By interaction between a single, identical binding site on each monomer
How are tetramers formed?
By interactions between two non-identical binding sites on each monomer
Hemoglobin
- 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
Disulfide bonds
- Covalent bonds that help stabilize a protein fold
What kind of bond is a disulfide bond?
Covalent
How do proteins bind to other molecules?
- Binding sites allow proteins to interact with specific molecules
- The binding of a protein to another molecule - termed ligand - is highly selective
Antibodies as an example of how proteins work
- 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
Specificity of antibody antigen-bind sites
- Each antibody has a distinct antigen-binding site, which recognizes its antigen with high specificity
- An individual human can make billions of different antibodies
In what ways can antibodies be used as a tool?
- They can be used to purify molecules
- They can be used as molecular tags
How can antibodies be used to purify molecules?
How can antibodies be used as molecular tags? (Biochemical)
How can antibodies be used as molecular tags? (Microscopy)
Steps of protein purification for studying proteins
- 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
Releasing cellular contents for protein purification
Centrifugation
Differential centrifugation
Protein separation by column chromatography
Three kinds of column chromatography
- Ion-exchange chromatography
- Gel-filtration chromatography
- Affinity chromatography
Major approaches to determining protein structure
Major approaches to determine protein structure:
* NMR spectroscopy
* Cryo-electron microscopy
* X-ray crystallography
