Proteins
Amino acids
What determines the categorization of amino acids?
R group = side chain
Dehydration reactions ______ water and _____ polymers
Hydrolysis reactions _____ water and ______ polymers
Dehydration reactions release water and make polymers
Hydrolysis reactions use water and break polymers
What is the monomer of nucleic acids?
Nucleotides
What are the components of a basic nucleotide?
Draw a basic nucleotide on the board
Pentose sugar = 5 carbon sugar ring
Phosphate group at the 5' carbon
Nitrogenous base at the 1' carbon
A dehydration reaction, aka polymerization, of two amino acids results in a __________ bond.
Peptide = covalent
What is the difference between the N terminus and the C terminus? How does this differ from the amine group and the carboxyl group?
The N terminus and C terminus applies only to polypeptides, where the exposed amine group is called the N terminus and the exposed carboxyl group is the C terminus
Amine group and carboxyl group are used to describe an amino acid
What determines protein function?
The shape of the protein
The sequence of amino acids and their subsequent R groups
What is the main difference in the pentose sugar of DNA and RNA?
DNA has a deoxyribose sugar which lacks an oxygen on the 2' carbon
RNA has a ribose sugar has an oxygen on the 2' carbon
Describe a purine and a pyrimidine. Which purines/pyrimidines occur in DNA, RNA, or both?
Purines are larger with 2 rings while pyrimidines are smaller with 1 ring.
Adenine and guanine are purines that exist in both DNA and RNA
Cysteine, thymine, and uracil are pyrimidines where thymine is found in DNA and uracil is found in RNA
How does protein polymerization occur?
The amine group (NH3+) of one amino acid and the carboxyl group (COO-) of different amino acid interact to release water while forming a peptide bond
How many amino acids are there? What are the categories that they can be sorted into?
There are a total of 20 amino acids
There are 3 categories of amino acids:
Nonpolar
Polar and uncharged
Polar and charged
How does a protein gain its shape?
Spontaneously when immersed in water
With the use of chaperonins (proteins that help proteins fold)
What is complementary base pairing? Why is it important?
Given that DNA strands are antiparallel, the nitrogenous bases need to be complementary to each other in order to properly interact
Purine A can only bond with pyrimidines T and U
Purine G can only bond with pyrimidine C
What is Chargaff's rule?
Provide an example on the board
States that the number of purines (A and G) must equal the number of pyrimidines (T, C, and U)
What are the levels of protein? Which are 2D and which are 3D?
Primary structure is a 2D linear structure (just a chain of amino acids)
Secondary structure is 2D structure and can either be an alpha helix or a beta pleated sheet
Tertiary structure is a 3D structure and is the most common form of proteins
Quaternary structure is a 3D structure comprised of 2 or more polypeptides
What are the interactions in primary and secondary structures? Describe the interactions.
Primary structures are stabilized by peptide bonds which are covalent bonds
Secondary structures are stabilized by hydrogen bonds between amino acids and the backbone; it is the polar chargers of the amino acids that are involved in the hydrogen bonding
Denaturation is caused by what two factors? What is the resulting structure of denaturation?
High temperatures and low (acidic) pH
Denaturation results in the reversion back to the primary structure (chain of amino acids)
Describe the process of polymerization of nucleotides
This is a dehydration reaction which joins two monomers while releasing water
The connection results in a covalent bond known as a phosphodiester bond that is between the phosphate group of one and carbon 3 (OH) of the other
This is how the backbone is made (sugar-phosphate backbone)
There is a polarity (direction) of 5' and 3', the 3' is where a nucleotide can be attached
Where do components attach to on the pentose sugar?
The nitrogenous base attaches to carbon 1
The phosphate group attaches to carbon 4
When another nucleotide is bound to the other, the phosphate group of one attaches to carbon 3 of another
Tertiary and quaternary structures are stabilized by what types of interactions? Describe them.
Van der Waals - tiny interactions bc atoms close to each other
Hydrogen bonding - bonds between R groups of amino acids
Hydrophobic effect - between nonpolar R groups and is typically on the inner side of the protein
Disulfide bonds - a covalent bond between two sulfurs
Ionic bonds - between two polar and charged amino acid R groups
What is the amino acid involved in disulfide bonding in tertiary and quaternary structures?
Cysteine
Recall some of the functions of proteins
Movement intracellularly (cytoskeleton) and extracellularly (cell accessories like flagellum)
Catalysts/enzymes
Defense as antibodies
Cell to cell communication
Membrane proteins
What are the levels of DNA and, if applicable, how are they stabilized?
Nucleotides - stabilized by covalent bonds
Single Stranded DNA (ssDNA) - sequence of nucleotides and are stabilized by phosphodiester bonds
Double helix (dsDNA) - stabilized by hydrogen bonds between complementary nitrogenous bases
Chromosomes - DNA + histone proteins
Genome - all the genetic information of a species (nucleic, mitochondrial, chloroplasts)
What are the levels of RNA? What are the 3 types of RNA and their functions?
Nucleotides -> single strand -> hairpin -> 3D
Hairpin - when a ssRNA folds in on itself and stabilized by H bonds
3D - stabilized by H bonds
Decoding:
rRNA - found in ribosomes and assembles proteins
tRNA - delivers amino acids for protein synthesis
mRNA - copies the genes of DNA to give instructions for protein synthesis