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
