Lecture 1-Review

Question 1

in one sentance describe protien synthesis

Answer 1

DNA template produces mRNA (transcription), ribosomes then read mRNA and build protien polymers (translation)

Question 2

DNA is made up of nucleotides, what are the 4?

Answer 2

1. adenine (A)
2. thymine (T)
3. Cytosine (C)
4. guanine (G)

Question 3

what is the difference between DNA and RNA

Answer 3

thyamine is replaced by uracil and the sugar deoxyribose is replaced by ribose

Question 4

What is the first step of protien synthesis?

Answer 4

1. 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

Question 5

Why does transcription have to happen?

Answer 5

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.

Question 6

What is the role of ribosomes in translation

Answer 6

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

Question 7

what is the second step of protien synthesis?

Answer 7

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.

Question 8

what is a codon and what is an anticodon?

Answer 8

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

Question 9

how many codons are possible? and why is it way more than the number of AA?

Answer 9

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

Question 10

what is the start codon

Answer 10

AUG which is also methionine

Question 11

how many stop codons are there?

Answer 11

3

Question 12

why is there argument for the number of AA?

Answer 12

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

Question 13

what is the basic structure of an amino acid

Answer 13

Connected to the alpha carbon is 1. primary Amino group (NH2), 2. carboxyl group (COOH), 3. hydrogen and 4. R group, side chain

Question 14

what is the range of molecular weight of a AA?

Answer 14

75-204 Dalton depending on the side chain

Question 15

most amino acids are chiral, but what is the one exception?

Answer 15

glycine

Question 16

what isomer form are most amino acids?

Answer 16

L

Question 17

why are D-amino acids low in nutritional value?

Answer 17

it is because the body is used to L isomers and so D is not digested well

Question 18

what is special about proline?

Answer 18

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

Question 19

why is cystenine an important nucleophilic amino acid?

Answer 19

Because has S which is less electronegative and less stable therefore more powerful nucleophile and can protect from oxidation damage by reduction reactions

Question 20

Whats special about tryptophan?

Answer 20

has indole ring

Question 21

what is significant about lysine?

Answer 21

has ε-amino group

Question 22

what are derived amino acids?

Answer 22

come from post translation metabolite, hydroxyproline comes from proline and hydroxylysine derivied from lysine

Question 23

explain peptide bond

Answer 23

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

Question 24

what are the interchain assocations that can be formed between amino acids in order of strongest to weakest?

Answer 24

1. covalent (peptide, disulfide)
2. ionic
3. hydrogen (dipole-dipole attraction from a hydrogen atom that is bonded to a very electronegative atom and another electronegative atom)
4. hydrophobic (clump together)
5. van der waals force (weak electrostatic forces which attract neutral molecules together)

Question 25

how are AA sequence in a peptide chain read?

Answer 25

from N terminus (free amino group) → to C terminus which has free carboxyl group

Question 26

briefly describe the 4 levels of structure

Answer 26

1. primary: amino acid
2. secondary: folding polypeptide chain
3. tertiary: folding of secondary structures into 3D
4. quaternary: assembly of 2 or more protiens in 3D structures into a superstructure

Question 27

what is a primary sructure?

Answer 27

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

Question 28

what is a secondary structure

Answer 28

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/

Question 29

describe alpha helix

Answer 29

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

Question 30

describe beta sheets

Answer 30

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)

Question 31

describe beta barrel

Answer 31

when beta strands forming a sheet are twisted so r groups are above or below sheet

Question 32

describe beta turns

Answer 32

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)

Question 33

what is the tertiary structure?

Answer 33

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

Question 34

what is the quaternary structure?

Answer 34

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

Question 35

in terms of bond polarity what number is non-polar and hydrophobic and which is polar and hydrophylic

Answer 35

above o.4 is polar
below 0.4 is non polar

Question 36

why is glycine said to be hydrophilic

Answer 36

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