WEEK 2

Question 1

DNA is synthesized from

Answer 1

dNTPs (deoxyribonucleoside triphosphates)

Question 2

RNA is synthesized from

Answer 2

NTPs (ribonucleoside triphosphates)

Question 3

Difference between peptide and phosphodiester bonds

Answer 3

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)

Question 4

What forces keep DNA strands together?

Answer 4

1. Hydrogen bonds between bases
2. Vander waals attractions
3. Hydrophobic interactions (bases are hydrophobic thus want to stay on inside)

Question 5

Which base pairing is stronger?

Answer 5

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.

Question 6

Whats the backbone of DNA

Answer 6

Sugar phosphate

Question 7

Is DNA one molecule or two molecules?

Answer 7

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.

Question 8

One complete turn of DNA is…

Answer 8

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.

Question 9

DNA has both major and minor…

Answer 9

grooves. Most protein contact is made in the major grooves because the minor ones are too narrow.

Question 10

Strands in double helix are…

Answer 10

antiparallel and complementary

Question 11

Denaturation

Answer 11

Destroys natural structure of DNA by separating the two strands. This is a natural, reversible process.

Question 12

Why does a DNA sequence with more G and C require more heat to denature?

Answer 12

G and C base pairs are held together by three hydrogen bonds so more heat is required to denature the strands.

Question 13

What other than heat can denature DNA?

Answer 13

High pH environment (excess of hydroxide, OH- ions) will disrupt the H-bonding and cause DNA to unzip.

Question 14

Stages of protein structure (examples of each)

Answer 14

• primary - amino acid sequence
• secondary - alpha helix or beta sheet
• tertiary - 3D structure (long range folding)
• quaternary - Multiple polypeptide chain (multimeric organization)
• multiprotein complexes

Question 15

Stages of protein structure (examples of each)

Answer 15

• primary - amino acid sequence
• secondary - alpha helix or beta sheet
• tertiary - 3D structure (long range folding)
• quaternary - Multiple polypeptide chain (multimeric organization)
• multiprotein complexes

Question 16

Four major categories of amino acids

Answer 16

• polar charged
• polar uncharged
• non polar
• those with unique properties

Question 17

Cysteine

Answer 17

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.

Question 18

Examples of reduced and oxidized conditions in the nature

Answer 18

reduced (gaining electrons) - in the cytosol

oxidized (losing electrons) - inside lumens of organelles (lumen is the space enclosed by a membrane)

Question 19

genetic code

Answer 19

set of rules specifying the correspondence between nucleotide triplets (codons). Tells you which bases make up which amino acids.

Question 20

The genetic code table is…

Answer 20

degenerate (most amino acids can be coded in multiple ways) and almost universal (almost every living thing has this code)

Question 21

Start codon

Answer 21

AUG

Question 22

Amino end of chain is called… and carboxyl end of chain is called…

Answer 22

• amino-terminus

- carboxyl-terminus (or c-terminus)

Question 23

R-Groups

Answer 23

Vary between amino acids and are what distinguish the acids. They do NOT contribute to stabilizing secondary structures.

Question 24

What hydrogen bonding exists in secondary structures

Answer 24

• 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)

Question 25

How long do you need a peptide chain to be before you form an alpha helix?

Answer 25

Typically you need 6 residues in a chain to form an alpha helix

Question 26

What’s a super secondary structure?

Answer 26

Compact three-dimensional structure of several adjacent elements of a secondary structure that is smaller than a protein domain.

Question 27

What are protein domains?

Answer 27

Units of tertiary protein structure that often function in a semi-independent manner. Have own specific function.

Question 28

Examples of supersecondary structures?

Answer 28

hairpin alpha helix - two alpha helixes that are coiled together (one hydrophobic and one hydrophilic)

Question 29

amphipathic

Answer 29

Two different biochemical properties on two different sides. Chemical compound that contains both non polar and polar regions. Hydrophobic regions coil together to get away from water.

Question 30

Helix-Turn-Helix

Answer 30

2 alpha helices joined by a short chain of amino acids

Question 31

Tertiary Structure

Answer 31

3D overall structure of a protein

Question 32

What holds together a tertiary structure

Answer 32

hydrophobic interactions, non-covalent bonds, covalent disulphide bonds

Question 33

Eukaryotic proteins often contain…

Answer 33

Two or more domains

Question 34

How many n-terminus and c-terminus ends in a tertiary structure?

Answer 34

Trick question!! There’s only one of each even though there are different domains

Question 35

Quaternary structures

Answer 35

made up of multiple folded protein subunits in a multi-subunit complex

Question 36

Hemoglobin is an example of…

Answer 36

a quaternary structure made of four polypeptide subunits in 1 “protein”?

Question 37

A virus shell is an example of…

Answer 37

a multiprotein complex