Week 2: Intro to Protein Structure

Question 1

What are the levels of protein structure?

Answer 1

Primary > Secondary > Tertiary > Quaternary > Multiprotein complexes

Question 2

Which levels of proteins do only SOME proteins have?

Answer 2

Quaternary and multiprotein complexes

Question 3

What are proteins composed of?

Answer 3

Amino acids

Question 4

What differentiates amino acids from each other?

Answer 4

The side-chain/R group

Question 5

What are the major categories of amino acids?

Answer 5

Acidic, basic, uncharged polar, nonpolar

Question 6

What are the parts of an amino acid?

Answer 6

Amino group, alpha carbon, carboxyl group, R-group

Question 7

True or False: The grouping of genetic codes is perfect

Answer 7

False

Question 8

What makes cysteine stand out?

Answer 8

Its ability to create disulfide bonds

Question 9

Where are regular cysteine (no disulfide bonds) regularly found?

Answer 9

In reduction conditions in the cytosol

Question 10

Where are the cysteine that form disulfide bonds regularly found?

Answer 10

In oxidation conditions in the ER outside the cell

Question 11

What is an important property of disulfide bonds?

Answer 11

They have strong covalent bonds

Question 12

Disulfide bonds act as braces, which helps to hold the _________ in proper configuration

Answer 12

Protein shape

Question 13

What kind of bond holds amino acids together?

Answer 13

Peptide bond

Question 14

What are examples of more proper names for the components of an amino acid, post-peptide bond?

Answer 14

R-group + main parts = reisdue
Carboxyl carbon = carboNYL carbon
Amino group nitrogen = amiDE nitrogen

Question 15

What happens when a peptide bond forms (besides the joining of two amino acids)? What kind of reaction is this?

Answer 15

The OH from one AA’s carboxyl group and the hydrogen from another AA’s amino group make water. This is a condensation reaction

Question 16

What is considered a polypeptide chain?

Answer 16

2 or more AA together

Question 17

What is lies at the end of polypeptide chains?

Answer 17

An amino end (N-terminus) and Carboxyl end (C-terminus)

Question 18

True or False: Differences in primary AA sequence DO NOT matter

Answer 18

False

Question 19

True or False: The order of AA acids are important

Answer 19

True

Question 20

How many residues do you need to create an alpha helix?

Answer 20

> 4 residues

Question 21

What properties differentiate alpha-helices from DNA double-helices?

Answer 21

Alpha-helix:
- R-groups OUTWARD
- R-groups DO NOT hold it together (No H-bonds)
- SINGLE strand
- N-end, C-end

DNA double helix:
- Base pairs face INWARDS
- Base pairs HELP hold it together
- DOUBLE strand
- Anti-parallel

Question 22

What bonds stabilizes the beta sheet?

Answer 22

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

Question 23

True or False: R groups are involved in the stability of beta sheets

Answer 23

False

Question 24

What are the two types of beta sheets?

Answer 24

Anti-parallel and parallel

Question 25

What is the difference between the two types of beta sheets?

Answer 25

Anti-parallel face the opposite directions while parallel face the same directions

Question 26

True or False: A coiled coil is a tertiary protein structure

Answer 26

False!!!!!!!!

Question 27

What does it mean when an alpha helix is amphipathic?

Answer 27

Two different biochemical/biophysical properties on two different sides. One side is hydrophobic while the other is hydrophilic.

Question 28

Where can coiled coils be found?

Answer 28

alpha-keratin of skin, hair, and myosin motor proteins

Question 29

Why does the hydrophobic strand coil inwards?

Answer 29

There is H2O all around the cell, the hydrophobic strand coils inward to get away from the water.

Question 30

What is the tertiary structure of a protein?

Answer 30

The overall 3D structure of the protein

Question 31

What is the tertiary structure of a protein held together by?

Answer 31

Hydrophobic bonds, non-covalent bonds, covalent disulfide bonds

Question 32

Proteins generally fold into the conformation that is the most __________ _________

Answer 32

energetically favourable

Question 33

Proteins will fold into the shape dictated by their amino acid sequence. What makes this process more efficient and reliable in living cells?

Answer 33

Chaperone proteins

Question 34

What are protein domains in tertiary structures?

Answer 34

Domains are portions of a protein that has its OWN tertiary structure, often functioning in a SEMI-INDEPENDENT manner

Question 35

Eukaryotic proteins often have 2 or more domains connected by ___________ ____________ ____________

Answer 35

intrinsically disordered sequences

Question 36

True or False: Connectors are not really part of the domain

Answer 36

True

Question 37

What makes protein families alike?

Answer 37

Similar sequences and tertiary structures

Question 38

What makes protein families different?

Answer 38

They often evolve to have different structures

Question 39

What subunits make up the hemoglobin protein?

Answer 39

2 alpha helices, 2 beta sheets

Question 40

True or False: 1 polypeptide chain can make up one protein

Answer 40

True

Question 41

What makes up multiprotein complexes & molecular machines?

Answer 41

Many identical subunits, mixtures of different proteins and DNA/RNA, and very dynamic assemblies of proteins to form molecular machines

Question 42

What are examples of multiprotein complexes & molecular machines?

Answer 42

Actin filaments, viruses and ribosomes, machines for DNA replication initiation or for transcription

Question 43

What are the steps for studying a single or a few proteins?

Answer 43

1. Purify protein or proteins of interest (i.e. various types of electrophoresis & affinity chromatography 2. Determine amino acid sequences (e.g. Mass spectrometry) 3. Discover precise 3D structure using techniques such as: x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, or cry-electron microscopy and other techniques

Question 44

What is proteomics?

Answer 44

Large scale study of proteins

Question 45

Researchers usually use a range of "____-____" and computational approaches to collect & analyze data on the set of proteins in a sample

Answer 45

Wet-lab

Question 46

What are some examples of the types of data of analyses performed?

Answer 46

- Protein-protein interactions, regulation of these interactions, & their position within a pathway - Abundance & turnover to protein - Location within a cell or tissue - Bioinformatics, statistics, & artificial intelligence (e.g. machine-learning-based algorithms), often in combination with other "omics" data sets