WEEK 2 Flashcards
(37 cards)
DNA is synthesized from
dNTPs (deoxyribonucleoside triphosphates)
RNA is synthesized from
NTPs (ribonucleoside triphosphates)
Difference between peptide and phosphodiester bonds
peptide bonds are used in the primary protein structure to link together amino acids while phosphodiester bonds link together nucleotides (help make the sugar phosphate backbone of DNA)
What forces keep DNA strands together?
- Hydrogen bonds between bases
- Vander waals attractions
- Hydrophobic interactions (bases are hydrophobic thus want to stay on inside)
Which base pairing is stronger?
G and C, which have three hydrogen bonds linking them, is a stronger pair than A and T, which only have two hydrogen bonds between them.
Whats the backbone of DNA
Sugar phosphate
Is DNA one molecule or two molecules?
Depends who you ask…
DNA could be two molecules because each strand is connected by covalent bonds and the strands are connected by non covalent bonds. BUT some people also say it is one molecule with two strands.
One complete turn of DNA is…
10.5 base pairs. Count from anywhere and then 10.5 bps down, it includes one major groove and two minor grooves. Kind of like a unit cell.
DNA has both major and minor…
grooves. Most protein contact is made in the major grooves because the minor ones are too narrow.
Strands in double helix are…
antiparallel and complementary
Denaturation
Destroys natural structure of DNA by separating the two strands. This is a natural, reversible process.
Why does a DNA sequence with more G and C require more heat to denature?
G and C base pairs are held together by three hydrogen bonds so more heat is required to denature the strands.
What other than heat can denature DNA?
High pH environment (excess of hydroxide, OH- ions) will disrupt the H-bonding and cause DNA to unzip.
Stages of protein structure (examples of each)
- primary - amino acid sequence
- secondary - alpha helix or beta sheet
- tertiary - 3D structure (long range folding)
- quaternary - Multiple polypeptide chain (multimeric organization)
- multiprotein complexes
Stages of protein structure (examples of each)
- primary - amino acid sequence
- secondary - alpha helix or beta sheet
- tertiary - 3D structure (long range folding)
- quaternary - Multiple polypeptide chain (multimeric organization)
- multiprotein complexes
Four major categories of amino acids
- polar charged
- polar uncharged
- non polar
- those with unique properties
Cysteine
A particularly important amino acid — the R group is
CH2-SH. Two Cysteines may form disulphide bonds together under oxidized conditions forming braces for protein structure.
Examples of reduced and oxidized conditions in the nature
reduced (gaining electrons) - in the cytosol
oxidized (losing electrons) - inside lumens of organelles (lumen is the space enclosed by a membrane)
genetic code
set of rules specifying the correspondence between nucleotide triplets (codons). Tells you which bases make up which amino acids.
The genetic code table is…
degenerate (most amino acids can be coded in multiple ways) and almost universal (almost every living thing has this code)
Start codon
AUG
Amino end of chain is called… and carboxyl end of chain is called…
- amino-terminus
- carboxyl-terminus (or c-terminus)
R-Groups
Vary between amino acids and are what distinguish the acids. They do NOT contribute to stabilizing secondary structures.
What hydrogen bonding exists in secondary structures
- atoms that are H bonded like the carbonyl oxygen and the amide hydrogen
- hydrogen bonding within the alpha helice (n and n+4 AAs)
- beta sheet (between beta sheets)
