Protein Structure

Question 1

What is the shape of proteins determined by?

Answer 1

Noncovalent bonds (hydrogen, van der Waals interactions, ionic)

Question 2

What determines the flexibility or rotation of proteins?

Answer 2

Covalent bonds between amino acids

Question 3

What role do hydrophobic forces play in protein structure?

Answer 3

They push hydrophobic molecules together and keep hydrophilic together, therefore shaping the protein to accommodate these attractions.

Question 4

Lowest energy protein confirmation

Answer 4

Proteins will do they least they can to fold. If something like urea is introduced, it will only effect or break the noncovalent bonds.
This way, only side chains are broken and the backbone of the protein remains.
When the urea is washed away, proteins fold back to original shape.

Question 5

Molecular chaperone

Answer 5

Help protein to fold properly

Molecular chaperones place a chamber cap on to a protein and do not release it until the protein is correctly folded.

Question 6

Clinical examples of misfolded proteins

Answer 6

Alzheimer’s, Huntington’s, Creuzfeldt-Jakob Disease

Question 7

Types of folding patterns and their location

Answer 7

Alpha helix - found in keratin; examples = hair, nails, horns; found all over the membrane
Beta sheets - fibroin; first discovered in silk; example = antifreeze proteins

Question 8

Alpha helix

Answer 8

Curled ribbon
Hydrogen bond every 4th peptide bond
Can be right- or left-handed
In the membrane, hydrophobic particles curl around hydrophilic core

Question 9

Beta sheets

Answer 9

Laying side-by-side with hydrogen bonds between each peptide

Parallel (longer to loop around) or anti-parallel (relatively short)

Question 10

Levels of protein organization

Answer 10

Primary, secondary, tertiary, quaternary, protein domain

Question 11

Primary

Answer 11

Amino acid sequence

Question 12

Secondary

Answer 12

Alpha helices and beta sheets

Question 13

Tertiary

Answer 13

Polypeptide with a-helices, b-sheets, and random coils

Question 14

Quaternary

Answer 14

More than one polypeptide chain

Question 15

Protein domain

Answer 15

Independently folding polypeptide chain from which other proteins are constructed

Question 16

Define unstructured protein regions

Answer 16

• Larger proteins w/ multiple domains connected by polypeptide chains
• disordered sequences
• tether one protein to another to provide movement

Question 17

Define and give examples of protein families

Answer 17

Groups of proteins w/ similar amino acid sequences

Ex.- serine proteases (trypsin, elastase)

Question 18

Aggregate

Answer 18

If a protein folds onto itself, it is called an aggregate and is dangerous.

Question 19

Forms the backbone of DNA

Answer 19

Sugar and phosphate

Question 20

mRNA vs. rRNA vs. tRNA

Answer 20

mRNA - messenger RNA
rRNA - ribosomal
tRNA - brings protein to mRNA as an adaptor

Question 21

RNA structure is

Answer 21

Single stranded

Question 22

Promoter vs. terminator

Answer 22

signals RNA polymerase where to begin/end transcribing on DNA

Question 23

Post-transcriptional processing

Answer 23

Process where primary RNA transcript is converted to mRNA

• 5’ capping (modified guanine)
• 3’ polyadenylation
• RNA splicing

Question 24

RNA splicing

Answer 24

Removal of introns, remaining extrons joined together

Question 25

Subunits of RNA and their function

Answer 25

- Small subunit — put mRNA w/ tRNA and provide a binding site for them - Big subunit - enzyme that makes peptides that will become proteins

Question 26

Aminoacyl tRNA synthetases

Answer 26

- link tRNA to amino acid | - each RNA has its own synthetase

Question 27

How does protein synthesis begin?

Answer 27

With AUG - methionine - small ribosomal subunit binds to 5’ cap and moves along RNA - at AUG, large subunit translates to mRNA

Question 28

Stopping translation

Answer 28

- Stop codons (UAG, UAA, UGA) - if tRNA does not match those, water is added - water terminates the end of the protein

Question 29

Results of reading frame being off

Answer 29

Creates nonsense proteins

Question 30

Polyribosomes

Answer 30

Multiple ribosomes that simultaneously translate the same mRNA into a protein

Question 31

Protein synthesis inhibitors include

Answer 31

Antibiotics

Question 32

Proteolysis

Answer 32

- Proteases break proteins down into peptide bonds - then into amino acids - used on proteins w/ short life spans or improperly folded

Question 33

Proteasomes and ubiquitin

Answer 33

Breakdown proteins in cytosol

Question 34

Factors that determine protein shape

Answer 34

- Amino acid sequence (Proteins, side chain, polar/nonpolar, polypeptides) - lowest energy confirmation - molecular chaperones`

Question 35

Hydrophobic forces

Answer 35

- role in shaping proteins | - pushes hydrophobic molecules together

Question 36

Diseases as a result of improperly folded proteins

Answer 36

Alzheimer’s, Huntington’s, Creuzfeldt-Jakob disease

Question 37

Unstructured protein regions

Answer 37

- the loops on beta sheets - allows larger proteins to fold around one another - tether one protein to another to provide movement (flexible tethers) - targets for proteases

Question 38

Flexible tethers

Answer 38

- provide movement and flexibility - help scaffold proteins bring proteins together in intracellular signaling pathways - assist elastin in forming fibers

Question 39

Function of disulfide bonds in extracellular proteins

Answer 39

To fortify and protect the protein shape between 2 cysteine side chains

Question 40

Functions of proteins

Answer 40

- Enzymes as catalysts - antibody binding sites - protein binding

Question 41

Antibody binding sites

Answer 41

- specific between antibody and antigens - due to looped ends on antibody - binding triggers an immune response

Question 42

How proteins are controlled

Answer 42

Allosteric enzymes, phosphorylation, GTP binding

Question 43

Allosteric enzymes

Answer 43

- have 2 binding sites | - shift confirmations to inactive enzymes

Question 44

Phosphorylation

Answer 44

- attachment of a phosphate group to an amino acid side chain - protein kinases: adds phosphate - phosphotases: removes phosphate

Question 45

GTP binding

Answer 45

- GTP binds - becomes GDP when it loses a phosphate - leaves when a new GTP approaches