2. Protein Structure

Question 1

Example of primary protein structure

Answer 1

AA sequence

Question 2

Example of secondary protein structure

Answer 2

Local scaffolding (alpha helix & beta sheet)

Question 3

Example of tertiary protein structure

Answer 3

long-range folding (3D structure)

Question 4

Example of Quaternary protein structure

Answer 4

multimetric organization (more than 1 peptide chain)

Question 5

Example of multiprotein complexes (molecular machines)

Answer 5

multiprotein complexes & molecular machines

Question 6

Major categories of amino acids:

Answer 6

• Acidic
• Basic
• Uncharged polar
• Nonpolar

Question 7

What determines the type amino acid

Answer 7

the R group

Question 8

The 3 parts of amino acids

Answer 8

1. Alpha carbon
2. Amino group
3. Carboxyl group

Question 9

A unique amino acids

Answer 9

CYSTEINE (DISULPHIDE BONDS/ DISULPHIDE BRIDGE)

Question 10

how are peptide bonds formed?

Answer 10

there is a reaction between the carboxyl group on the lysine & the amino group on the phenylalanine

Question 11

Residue

Answer 11

amino acids within a peptide chain (not a full amino acid anymore- because of the loss of H20)

Question 12

what are the 2 ends of an alpha helix called?

Answer 12

N terminal end
C terminal end

Question 13

what are the 2 ends of a DNA double helix called?

Answer 13

5’
3’

Question 14

What is the difference between protein & DNA

Answer 14

• *Protein is single stranded- bases point outwards of helix
• *DNA is double stranded- bases point into centre of helix

Question 15

What is DNA synthesised from?

Answer 15

deoxyribonucleoside triphosphates (dNTPs)

Question 16

What is RNA is synthesized from

Answer 16

ribonucleoside triphosphates, or:
➢ NTPs

Question 17

Ionic bonds, interactions between oppositely charged atoms, happens within a molecule or between

Answer 17

Electrostatic attractions

Question 18

much weaker than covalent bonds, fond in water, also found when and H+ comes close to an electronegative atom ie: O or N

Answer 18

Hydrogen bonds

Question 19

whenever atoms are close together, are transient fluctuations in electron distributions

Answer 19

Van der Waals attractions

Question 20

pushing nonpolar parts of molecules out of H-bonded water network)- ie. Hydrophobic interior of cell membrane

Answer 20

Hydrophobic force

Question 21

A-T have ___bonds

Answer 21

2 hydrogen

Question 22

G-C have ____ bonds

Answer 22

3 hydrogen

Question 23

3 Forces that keep DNA strands Together

Answer 23

1. Hydrogen bonds
2. Hydrophobic interactions
3. Van der Waals attractions

Question 24

__________ covalently link nucleotides together to make DNA or RNA

Answer 24

Phosphodiester bonds

Question 25

____________ covalently link together amino acids into polypeptides

Answer 25

peptide bonds

Question 26

Beta Sheets

Answer 26

- Not as compact as alpha helix - R groups not involved but notice they alternately project up and down Beta sheet typically contains 4-5 beta strands but can have 10+!

Question 27

Bonds within beta sheets

Answer 27

H -bonding between carbonyl oxygen (C=O) of 1 aa and amide hydrogen (N -H) of aa in neighboring strand

Question 28

2 types of beta sheets

Answer 28

1. anti-parallel 2. parallel

Question 29

Hydrogen bonds are ____ to axis to actual helix

Answer 29

parallel

Question 30

Which atoms are H-bonded?

Answer 30

- Carbonyl oxygen - amide hydrogen in peptide backbone

Question 31

Where are hydrogen bonds located in alpha helices?

Answer 31

4 AA’s apart and within the same segment of pp chain

Question 32

Where are hydrogen bonds located in beta sheets?

Answer 32

Between AA’s in different segments or strands of pp chain (is one polypeptide-3 beta strands- parallel or anti-parallel)

Question 33

Amphipathic

Answer 33

contain both hydrophobic & hydrophilic parts

Question 34

Amphipathic alpha helix

Answer 34

coiled coils (in myosin motor proteins, skin & hair)

Question 35

3 Ways Protein structures are held together by

Answer 35

- hydrophobic interactions - non-covalent bonds - covalent disulfide bonds

Question 36

Proteins generally fold into the conformation that is the most ________

Answer 36

energetically favorable.

Question 37

Proteins will fold into the shape dictated by their amino acid sequence, but _________ help make the process more efficient and reliable in living cells

Answer 37

chaperone proteins

Question 38

Protein Domains

Answer 38

are often specialized for different functions - Portion of a protein that has its own tertiary structure, often functioning in semi- independent manner (one part of the protein can function independent of the other protein)

Question 39

Eukaryotic proteins often have_____domains connected by intrinsically disordered sequences (connecting sequences of amino acids)

Answer 39

2 or more

Question 40

Protein Families

Answer 40

are groups of proteins with a common evolutionary origin (clear that overtime, proteins that have evolved to a stable structure- the DNA sequence has copied & passed on with new structure & function)

Question 41

Protein Families have similar...

Answer 41

sequences & tertiary structures

Question 42

Quaternary Structures are made of

Answer 42

- More than 1 polypeptide chain (example: hemoglobin)

Question 43

Examples of multi protein complexes & molecular machines

Answer 43

- mixtures of different proteins and DNA/RNA— e.g. viruses and ribosomes - very dynamic assemblies of proteins to form molecular machines—e.g. machines for DNA replication initiation or for transcription

Question 44

Scaffold

Answer 44

an entity that Is used to bind proteins by putting them in close proximity (usually RNA)

Question 45

Interactome

Answer 45

Protein-protein interactions - Abundance & turnover