Textbook 1.1

Question 1

in neutral aqueous solution…

Answer 1

the alpha carboxyl group loses its proton and exists as COO- and alpha amino group accepts a proton

Question 2

Amino acids exist as

Answer 2

stereoisomers except glycine

Question 3

How long is the average polypeptide chain?

Answer 3

450 amino acids

Question 4

Can proteins contain components other than amino acids?

Answer 4

Yes, after polypeptide has been synthesized other things like carbohydrates (to form glycoproteins), metal- containing groups (to form metalloproteins), and organic groups (to form flavoproteins).

Question 5

Polar charged amino acids

Answer 5

In physiologic pH, side chains of these amino acids are able to form ionic bonds with other charged species in the cell.
ex. aspartic acid

Question 6

Polar uncharged amino acids

Answer 6

side chains can have partial pos. or neg. thus can form H bonds with other molecules (including water)
ex. tyrosine

Question 7

Non polar amino acids

Answer 7

hydrophobic side chains, usually lack oxygen and nitrogen. Interactions are restricted to hydrophobic interactions and Van der Waals forces.
ex. Alanine

Question 8

Other amino acids

Answer 8

Glycine - only has one stereoisomer (side chain is just H)
Proline - doesn’t really fit into any secondary structures and its alpha amino group is part of a ring (produces kinks and folds)
Cysteine - forms disulfide bridges

Question 9

Post-translational modifications (PTMs)

Answer 9

proteins with different amino acids that arise from alteration of side chain of one of normal 20 amino acids AFTER its incorporation into a polypeptide chain

Question 10

How can a single polypeptide chain exist as a number of distinct biological molecules?

Answer 10

Post-translational modifications can alter its biological activity

Question 11

Examples of post-translational modifications

Answer 11

• reversible addition of phosphate group to a serine, threonine, or tyrosine residue
• lysine acetylation affects thousands of proteins in a mammalian cell

Question 12

Where are polar residues usually found?

Answer 12

Situated near the surface of molecule where they can associate with nearby water molecules and contribute to solubility.

Question 13

Primary Protein Structure

Answer 13

specific linear sequence of amino acids that constitute the chain

Question 14

Secondary Protein Structure

Answer 14

describes conformation (spatial arrangement) of portions of the polypeptide chain

Question 15

What did Linus Pauling and Robert Corey propose?

Answer 15

That polypeptide chains exist in preferred conformations that provide maximum number of possible H-bonds between neighbouring amino acids.
Alpha helix and beta sheet.

Question 16

Alpha helix

Answer 16

backbone lies on inside of helix, side chains project out. In water soluble proteins, the outer surface of the alpha helix often contains polar residues in contact with the solvent (inward facing contains non-polar side chains).

Question 17

Beta sheet

Answer 17

Consists of several segments of a polypeptide lying side by side. Backbone assumes folded or pleated conformation. Beta sheet also has hydrogen bonds but they are oriented perpendicular to the long axis of polypeptide chain and project across from one part of the chain to another.

Question 18

Silk has a lot of…

Answer 18

beta sheets which make it resistant to pulling

Question 19

Tertiary Structure

Answer 19

describes conformation of entire polypeptide. This kind of structure is virtually unlimited—many possible conformations.

Question 20

Tertiary structures are stabilized by…?

Answer 20

Non covalent bonds between side chains of protein.

Question 21

How is tertiary structure usually determined?

Answer 21

X-ray crystallography: crystal of protein is bombarded by thin beam of x-ray radiation that is scattered by electrons of the proteins which then strike radiation sensitive detector in an array of spots. Computer program is then used to convert the spatial arrangement of dots into protein structure.

Question 22

Fibrous proteins

Answer 22

elongated shape

Question 23

globular proteins

Answer 23

compact structure

Question 24

Where are fibrous and globular proteins found?

Answer 24

Fibrous proteins are usually the structural material outside the living cell (collagens and elastins of connective tissues, keratins of hair, skin, and silk). They resist pulling or shearing forces. Most proteins within the cell are globular proteins.

Question 25

Can proteins with different primary structure have similar biological functions?

Answer 25

Yes. Even if the primary linear sequence differs, structural similarity between the tertiary structure indicates the possibility that the functions of the proteins are similar. Function follows structure.

Question 26

How are x-ray crystallographic images of proteins not necessarily accurate?

Answer 26

They are static images and proteins are dynamic. Its like saying one resonance structure represents the molecule when really it represents only a portion of the true structure.

Question 27

Homodimer

Answer 27

protein complex of two identical subunits/chains

Question 28

heterodimer

Answer 28

protein complex of two nonidentical subunits

Question 29

conformational changes

Answer 29

predictable movements within a protein that are triggered by the binding of a specific molecule

Question 30

Proteome

Answer 30

the entire inventory of proteins that is produced by an organism. Also applies to inventory of proteins present in a particular tissue, cell, or cellular organelle.

Question 31

TAP-tag mass spectrometry

Answer 31

Used to study interactomics (protein interactions). DNA from gene of interest is fused to DNA encoding for protein tag (called a TAP tag) that is easily purified using affinity chromatography.

• TAP tagged gene is expressed in cell
• cell is lysed and tagged protein + interacting protein is purified
• set of accompanying proteins can be identified using mass spectrometry

Question 32

hub proteins

Answer 32

More likely to be of higher importance biologically. Have multiple binding partners. Some have multiple binding surfaces and can bind with many at once while others have one surface capable of binding with many different proteins (at different times).

Question 33

Distance between nucleotides on a strand of DNA

Answer 33

0.34 nm

Question 34

How frequently does a large structural repeat occur?

Answer 34

Ever 3.4 nm of helix or every 10 base pairs

Question 35

What about DNA is constant for a specific species?

Answer 35

base composition (proportion of each base)

Question 36

A nucleoside is a nucleotide without…

Answer 36

the phosphate

Question 37

What causes DNA to have a negative charge?

Answer 37

The phosphate groups

Question 38

What’s the width of the double helix?

Answer 38

2 nm

Question 39

Proteins can fit in…of DNA and can read the sequence without…?

Answer 39

• the major and minor grooves

- separating the strands

Question 40

Can PCR be used for RNA?

Answer 40

Yes, if RNA template strands are converted to complimentary DNA strands using reverse transcriptase

Question 41

Final product of PCR

Answer 41

(2^n double stranded DNA molecules)(however many strands you started with). For example if you started with ten and you did four rounds of PCR you would have
(2^4)(10) = 160