Lecture 4

Question 1

What are the types of DNA strands?

Answer 1

1. Sense/coding/non-template
2. Anti-sense/template

Question 2

What does an amino acid look like and what part determines what amino acid it is?

Answer 2

It’s a carbon bound by 4 functional groups. The R group determines what amino acid it is.

Question 3

What is the primary protein structure?

Answer 3

linear amino acid sequence held by covalent peptide bonds

Question 4

What is the secondary protein structure?

Answer 4

local folding (alpha helices and beta sheets) formed by hydrogen bonds in the polypeptide backbone

Question 5

What is the tertiary protein structure?

Answer 5

overall 3D shape of a single polypeptide resulting from R group interactions

Question 6

What is the quaternary protein structure?

Answer 6

assembly of multiple folded polypeptides (subunits) to form a functional protein complex

Question 7

How do 2 amino acids make a bond and what type of bond is it?

Answer 7

through dehydration synthesis they make a peptide bond

Question 8

What is a special feature of a peptide bond?

Answer 8

partial double-bond character due to resonance which makes it rigid and planar

Question 9

Proteins vs Peptides

Answer 9

Proteins: long polymers of amino acids linked by peptide bonds, always written with the N terminus toward the left
Peptides: shorter, usually fewer than 50 amino acids long

Question 10

Where does the flexibility of the peptide backbone come from?

Answer 10

rotations around the single bonds on either side of the alpha carbon… the peptide bond itself is rigid

Question 11

How is the alpha helix made?

Answer 11

formation of hydrogen bonds such that the oxygen of the carbon group is making a H bond with the amide group (4 conformations apart)

Question 12

What destabilizes secondary, tertiary, and quaternary structures?

Answer 12

Oxidation: causes damage to the amino acid side chains or interferes with the formation of stabilizing disulfide bonds

Question 13

Heterodimer

Answer 13

protein complex where 2 protein subunits (tertiary structures) that are different from each other form a 2-subunit quaternary structure

Question 14

Homotetramer

Answer 14

protein quaternary structure composed of 4 identical polypeptide subunits that are not covalently bonded

Question 15

How does the enzyme’s active site form?

Answer 15

amino acids that come together through the protein’s folding process, bringing together residues from different parts of the polypeptide chain into a specific 3D structure

Question 16

What has to happen to most proteins after folding and before becoming fully functional?

Answer 16

Post translational modifications

Question 17

What do post translational modifications do? Example?

Answer 17

They help with the conformational change of the protein… if phosphates are added the charge could cause repulsion causing the protein to fold

Question 18

What do phosphatase’s do?

Answer 18

enzymes that remove phosphate groups from molecules (primarily proteins and carbs) and it (most of the time) turns off the activity of the target molecule

Question 19

What do Kinase’s do?

Answer 19

enzymes that add phosphate groups (phosphorylation) to specific proteins which alters the structure and function of the protein making it active or inactive

Question 20

What does phosphorylation do?

Answer 20

Shape change; unmask or mask a catalytic or functional domain
Binding motif to help form a multi-protein complex
Promotes dissociation of a multi-protein complex by a shape change

Question 21

What are Intrinsically disordered proteins?

Answer 21

proteins that lack a well defined secondary or tertiary structure so they have more flexibility which allows them to bind to multiple partners, adapt to their environment, and transition from disordered to ordered state

Question 22

What are prions?

Answer 22

they are misfolded proteins that have an abnormal structure…
proteins that adopt alternative conformations that become self-propagating

Question 23

What are intrinsically disordered proteins/regions more prone to?

Answer 23

misfolding and aggregation

Question 24

What is fatal infectious transmissible spongiform encephalopathies (TSEs) and their primary cause?

Answer 24

Neurodegenerative disease where nerve cells are destroyed causing a sponge like appearance of brain tissue

PrP^Sc prions (misfolded proteins)… and these convert normal proteins into misfolded proteins forming plaques in the brain

Question 25

What is multiple system atrophy and what is it caused by?

Answer 25

the progressive loss of autonomic nervous system function misfolded alpha-synuclein protein glial cytoplasmic inclusions (clumps of misfolded proteins inside glial cells) that consist of filaments (abnormal) of alpha synuclein protein