Chapter 4 Flashcards
What are proteins made up of?
Amino acids
Proteins are found in all living systems and are composed of amino acids, which are the building blocks specified by the genetic code.
What is a gene?
A specific stretch of nucleotides in DNA or RNA that contains information for making a particular RNA molecule
mRNA provides the information to make a particular protein.
What is the primary structure of a protein?
Amino acids joined together by peptide bonds
The amino group of one amino acid reacts with the carboxyl group of another in a condensation reaction.
What are residues in the context of proteins?
Amino acids joined by peptide bonds
A short sequence of amino acids is called a peptide; longer chains are referred to as polypeptides.
What is the role of the antisense strand of DNA during transcription?
Acts as the template for RNA polymerase
It is read in a 3’ to 5’ direction.
What is a codon?
A combination of 3 nucleotides in a row that specifies an amino acid
There are 64 different codons in the genetic code.
What is the significance of the degenerate code in genetics?
More than one codon can specify the same amino acid
This is referred to as synonymous codons.
True or False: The genetic code is universal.
True
The codon table is nearly universal across different organisms.
What is ‘wobble’ in the context of codons?
tRNAs specific to a particular amino acid recognize multiple codon triplets that differ only in the third letter
e.g., leucine is coded for by 6 different codons.
What are the three basic elements of protein secondary structure?
- alpha-helix
- beta-pleated sheet
- Unstructured turns
What stabilizes the alpha-helix structure in proteins?
Hydrogen bonding among near-neighbor amino acids
Proline cannot participate as a donor in hydrogen bonding, acting as a ‘helix-breaking residue’.
Describe the beta-pleated sheet structure.
Extended amino acid chains packed side by side to create a pleated appearance
It is stabilized by hydrogen bonding.
What is tertiary structure in proteins?
The folded three-dimensional shape of a polypeptide
Most interactions are stabilized by noncovalent bonds such as hydrophobic interactions and hydrogen bonds.
What types of interactions stabilize tertiary structure?
- Hydrophobic interactions
- Hydrogen bonds
- Charge pair interactions
- Van der Waals interactions
What are D- and L-amino acids?
Enantiomers that are mirror images of each other
Living organisms predominantly use L-amino acids.
What is the typical molecular weight range for polypeptide chains?
20 to 70 kDa
Molecular weights are often described in Dalton (Da) units.
What is the average molecular weight of an amino acid?
110 Da
What are the main interactions that stabilize the secondary structure of proteins?
Hydrogen bonds
Secondary structure may also depend on disulfide bridges, van der Waals interactions, hydrophobic contacts, and electrostatic interactions.
What are the three main categories of tertiary structure?
Globular proteins, fibrous proteins, membrane proteins
What is the overall shape of most globular proteins?
Roughly spherical
Example: The enzyme lysozyme folds up into a globular tertiary structure forming the active site.
What are fibrous proteins characterized by?
Long filamentous or rod-like structures
They serve as structural components of cells and tissues.
List three major designs of fibrous proteins.
- Coiled coils
- Triple helical arrangement
- Antiparallel beta-pleated sheets
What is a common motif in membrane proteins?
Seven transmembrane helix structure
What methods are used to predict protein structure?
- X-ray crystallography
- Nuclear magnetic resonance
- Cryo-EM
What is quaternary structure in proteins?
A functional protein composed of one or more polypeptide subunits
What types of subunits can quaternary structures have?
- Identical subunits
- Nonidentical subunits
What are dimers in the context of quaternary structure?
Two polypeptides
Types include homodimers and heterodimers.
What are multimers in protein structure?
- Hemoglobin
- Antibodies
What are macromolecular assemblages involved in?
- Cooperative binding of proteins
- Interactions
- Molecular machines
- DNA replication, repair, recombination, transcription, chromatin remodeling, RNA processing, translational processes
What defines intrinsically disordered proteins?
Lack a well-defined secondary or tertiary structure
What do intrinsically disordered protein regions contain?
Short segment(s) that are disordered
What is a common characteristic of proteins larger than about 20 kDa?
Often formed from two or more domains with specific functions
What is an example of a single domain in proteins?
DNA-binding domain
What is the role of enzymes?
Catalyze the hundreds of chemical reactions necessary for life
What do enzymes do to activation energies?
Lower the activation energies of chemical groups participating in a reaction
What is post-translational modification?
Proteins are joined covalently and noncovalently to other molecules after translation
Give an example of a type of modified protein.
- Lipoproteins
- Glycoproteins
- Metalloproteins
What is the most common regulatory mechanism for proteins?
Reversible phosphorylation of amino acid side chains
What do kinases do?
Catalyze the addition of phosphate groups
What are the two groups of protein kinases widely studied in eukaryotes?
- Those that phosphorylate serine or threonine side chains
- Those that phosphorylate tyrosine side chains
What do phosphatases do?
Remove phosphates
What is allosteric regulation of protein activity?
Ligand-induced conformational change affecting activity
What is molecular chaperones’ role in protein folding?
Increase the efficiency of protein folding and reduce aggregation
What are heat-shock proteins?
Molecular chaperones that promote protein folding and aid in destruction of misfolded proteins
What is the purpose of the endoplasmic reticulum in protein folding?
Quality control and folding of secreted proteins before secretion through the Golgi apparatus
What is the ubiquitin-proteasome system (UPS)?
Protein degradation pathway in eukaryotes
What triggers the degradation of a protein in the UPS?
Polyubiquitination at Lys48
What is chaperone-mediated autophagy (CMA)?
A protein degradation pathway where chaperones target misfolded proteins to the lysosome
What are protein misfolding diseases associated with?
Formation of protein aggregates linked to at least 20 different human diseases
What are amyloid fibrils?
Insoluble deposits formed from normally soluble proteins
What are prions responsible for?
Transmissible spongiform encephalopathies (TSEs)
What symptoms are associated with prion diseases?
- Progressive neurodegeneration
- Dementia
- Loss of muscle control of voluntary movements
What is the infectious agent in prion diseases?
A protein called PrPSc
How does PrPSc differ from the normal host protein PrPC?
PrPSc is misfolded into a different 3-D structure
What characteristics does PrPSc exhibit?
- Aggregated
- Insoluble
- Resistant to protease and heat
- Not deactivated by normal sterilization techniques
