Lecture 1-Review Flashcards
in one sentance describe protien synthesis
DNA template produces mRNA (transcription), ribosomes then read mRNA and build protien polymers (translation)
DNA is made up of nucleotides, what are the 4?
- adenine (A)
- thymine (T)
- Cytosine (C)
- guanine (G)
what is the difference between DNA and RNA
thyamine is replaced by uracil and the sugar deoxyribose is replaced by ribose
What is the first step of protien synthesis?
- The first step is transcription which is the copying of genetic infromation from DNA to RNA
- mRNA will then leave through the pores of the nucelus with the DNA code and will attach to the ribosome
Why does transcription have to happen?
DNA is needed because it has the genetic code for the protiens to be made but it is too large to leave the nucleus and protiens are made outside the nucleus at the ribosomes, so we need RNA which is single stranded and smaller to leave and give the info.
What is the role of ribosomes in translation
ribosomes have subunits that during translation assemble on the strand of mRNA like a sandwhich, they attract tRNA molecules and a long chain of amino acid emerges as the ribosome decordes the mRNA sequence
what is the second step of protien synthesis?
Translation: which is the decoding of mRNA into a protien. mRNA attaches to ribosome and carries codons. tRNA have anticodons which are complemntary to the codons on mRNA. these tRNA code for an amino acid and the chain is made.
what is a codon and what is an anticodon?
codon: series of 3 bases in a row in an mRNA molecule which code for a specific amino acid
anticodon: 3 nucelotides which are complentary to the codon in mRNA
how many codons are possible? and why is it way more than the number of AA?
64 (4x4x4), it is more since some amino acids are associated with more than one codon so its not like each codon is for a different amino acids and some are for start and stop
what is the start codon
AUG which is also methionine
how many stop codons are there?
3
why is there argument for the number of AA?
20 is common, but recently it was discorvered that there are 21, this amino acid is found in human and animals. Sometimes people say there are techincally 22 because another was found but it is super rare and only found in bacteria
what is the basic structure of an amino acid
Connected to the alpha carbon is 1. primary Amino group (NH2), 2. carboxyl group (COOH), 3. hydrogen and 4. R group, side chain
what is the range of molecular weight of a AA?
75-204 Dalton depending on the side chain
most amino acids are chiral, but what is the one exception?
glycine
what isomer form are most amino acids?
L
why are D-amino acids low in nutritional value?
it is because the body is used to L isomers and so D is not digested well
what is special about proline?
The R group is attached to the amino group forming a secondary amine since N is connected to 2 carbons and has one H. It forms a ring shape
why is cystenine an important nucleophilic amino acid?
Because has S which is less electronegative and less stable therefore more powerful nucleophile and can protect from oxidation damage by reduction reactions
Whats special about tryptophan?
has indole ring
what is significant about lysine?
has ε-amino group
what are derived amino acids?
come from post translation metabolite, hydroxyproline comes from proline and hydroxylysine derivied from lysine
explain peptide bond
A peptide bond is a strong covalent bond that forms between the amino group of one amino acid and the carboxyl group of another, releasing a molecule of water in the proces
what are the interchain assocations that can be formed between amino acids in order of strongest to weakest?
- covalent (peptide, disulfide)
- ionic
- hydrogen (dipole-dipole attraction from a hydrogen atom that is bonded to a very electronegative atom and another electronegative atom)
- hydrophobic (clump together)
- van der waals force (weak electrostatic forces which attract neutral molecules together)
how are AA sequence in a peptide chain read?
from N terminus (free amino group) → to C terminus which has free carboxyl group
briefly describe the 4 levels of structure
- primary: amino acid
- secondary: folding polypeptide chain
- tertiary: folding of secondary structures into 3D
- quaternary: assembly of 2 or more protiens in 3D structures into a superstructure
what is a primary sructure?
linear polypeptide chain of amino acids linked together only by peptide bonds. It is the backbone of a protien. It will have a single primary amine at one end and a carboxyl group at the other end
what is a secondary structure
folding of the polypeptide chain of the primary structure into alpha-helix, beta-sheet, beta-truns or random coil structure. These are stabilized by hydrogen bonds/
describe alpha helix
Coiling of a peptide chain, hydrogen bonds form between an NH group on one amino rediue and C=O of another AA. In a alpha helix the hydrogen bonds are weaker since far away. R group points out from helix. It is important to know that any large or small AA can destablize and so does proline cause of its weird shape
describe beta sheets
NH groups in the backbone of one strand create hydrogen bonds with C=O of a backbone in an adjacent strand which can form anti parrel (N terminus beside C terminus of other strand) or parrellel (N terminus in same direction)
describe beta barrel
when beta strands forming a sheet are twisted so r groups are above or below sheet
describe beta turns
are disorganized segments of peptide which connect beta strands and are made of only 3-4 amino acids normally glycine (small) and proline(does not bend cause of geomtry)
what is the tertiary structure?
is a 3D structure that is stablized by interaction between amino acid side chains:
- cysteine form disulfide bonds
- ionic bonds form between charged AA
- hydrogen bonds form between hydrophilic amino acids
- van der waals force can also stablize
- hydrophobic inside and hydrophilic on the outside tends to be the norm
what is the quaternary structure?
is the structure that is formed by some protiens that consit of more than one 3D protien, and these will fit together with a specified geomtry, these are stabilized by the same interactions of tertiary structyre
in terms of bond polarity what number is non-polar and hydrophobic and which is polar and hydrophylic
above o.4 is polar
below 0.4 is non polar
why is glycine said to be hydrophilic
C-H is borderline at 0,35 and because it is so small, the H2N and COOH have more of an affect making it hydrophilic
