02 Flashcards
What is the structure of the amino acid
alpha carbon
amino group, carboxylic acid, hydrogen, unique side chain (R)
What are zwitterions
state when amino acids exist at physiological pH
- pH 7.35-7.45 in blood
- amino and carboxylic groups ar charged
- molecule is neutral
depending on pKa of each functional group, it may be charged or uncharged at physiological pH
Which part of the amino acids do peptide bonds form
How do they occur
between the carboxylic acid group of one amino acid and the amino acid of the amino group
- condensation reaction
- catalyzed by ribosomes
Backbone formed by nitrogens and carbons
What is a nonpolar, aliphatic molecule
have mostly hydrophobic side chains
- shared electrons, no charges to interact with the polar water molecules
What is an aromatic molecule
have aromatic rings in their side chains
- have different polarities (could be non polar or polar)
What is a polar, uncharged molecule
have side chains containing electronegative O and N atom
- electrons are not shared equally
- side groups are not charged at physiological pH
- can form hydrogen bonds and participate in chemical reactions
What is a sulfur-containing molecule
S bonded to C
methionine and cysteine (can form SS bonds)
What is a charged molecule
carry (or can carry) a charge on their side at physiological pH
When are buffers most effective
when pH=pKa
- equal amount of acid and base are present
(in blood, when pKa = ~7)
What are disulfide bonds
sulfhydryl groups of two cysteines are oxidized and bound together
- spontaneous, doesnt require an enzyme
Strong covalent bond because the sulfur atoms share the electrons equally
conformational stabilizer - holds different parts of a proteins molecule together or 2 or more chains that make up a protein molecule
What are electrostatic (ionic) interactions
charged groups on amino acids interact with each other
when pH changes, more H+ starts to bond –> no more charge, cannot participate in the interaction and starts to unfold
what are the types of post-translational modifications
can alter the structure or function of a protein –> allow other molecules to interact with them or altering the location of the protein in the cell
- accesorizing a protein to recognize self and doesn’t illicit immune response
- carbohydrate addition
- o-glycosylation (OH)
- N-glycosylation (NH2) - regulation (uncharged to charged or charged to uncharged)
- phosphorylation
- acetylation - modified amino acids
- oxidation
- carboxylation
What is the N and C terminus
N-terminus: has NH3
C terminus: has COOH
What is sickle cell disease
point mutation in the gene for B-globin protein
- mutation changes the 6th amino acid in the B-globin chain of hemoglobin from glutamate to valine
(changes the structure of the RBC –> changes function (more rigid))
What is the heterozygotic pattern of hemoglobin
1 good allele, 1 altered allele
- mixture of normal and altered hemoglobin
- usually asymptomatic unless under stress
- protects against malaria
What is a homozygotic pattern of hemoglobin
either 2 good allele or 2 altered alleles
- both copies encode the sickle cell allele (homozygous), all the hemoglobin will be the altered version
What does homologs mean
similar protein that have arisen from a common ancestor, often by gene duplication
What are the types of general protein structure
globular protein: balls of polypeptide
fibrous protein: long linear (repeating structures)
Transmembrane proteins: embedded in plasma membrane
DNA binding proteins: bind to DNA
What type of bonds hold protein shapes
non covalent bonds
- electrostatic (ionic) interactions
- hydrogen bonds
- hydrophobic interactions (non-polar amino acids)
What are the protein structure rules
3d structure must be flexible enough to function properly
stable enough that it will not convert to another conformation
exposed amino acids must be compatible with the environments the protein will function in
What is primary structure of protein
sequence of aa in the polypeptide chain determined by genetic code
- connected through peptide bonds
- rigid and stable
- Rchains are on opposite sides of the bond
- direction from n-terminal to c-terminal
What is secondary structure
a-helix
- maintained by h bonds
- H in N-H forms a Hbond with the O=C of the amino acids 4 residues away in the peptide chain
- no proline “helix breaker” because no hydrogen on nitrogen
- R groups radiate out to stabilize
B-sheets
- AA in a flat plane
- can be parallel or anti parallel
- more rigid than a-helix
- can form B-barrels –> transport hydrophobic substances or form pores in membranes
What is tertiary structure
secondary structures combine with irregular elements (loops and turns)
- AA from primary structure define which secondary structure will be adopted and which tertiary conformation every molecule of the protein will take
What is quarternary structure
proteins that are made up of more than one polypeptide subunit (eg. dimers, trimers, tetramers…)
