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Cell Physiology > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

What is the shape of proteins determined by?

A

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

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2
Q

What determines the flexibility or rotation of proteins?

A

Covalent bonds between amino acids

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3
Q

What role do hydrophobic forces play in protein structure?

A

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

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4
Q

Lowest energy protein confirmation

A

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.

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5
Q

Molecular chaperone

A

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.

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6
Q

Clinical examples of misfolded proteins

A

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

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7
Q

Types of folding patterns and their location

A

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

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8
Q

Alpha helix

A

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

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9
Q

Beta sheets

A

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

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

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10
Q

Levels of protein organization

A

Primary, secondary, tertiary, quaternary, protein domain

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11
Q

Primary

A

Amino acid sequence

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12
Q

Secondary

A

Alpha helices and beta sheets

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13
Q

Tertiary

A

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

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14
Q

Quaternary

A

More than one polypeptide chain

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15
Q

Protein domain

A

Independently folding polypeptide chain from which other proteins are constructed

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16
Q

Define unstructured protein regions

A
  • Larger proteins w/ multiple domains connected by polypeptide chains
  • disordered sequences
  • tether one protein to another to provide movement
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17
Q

Define and give examples of protein families

A

Groups of proteins w/ similar amino acid sequences

Ex.- serine proteases (trypsin, elastase)

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18
Q

Aggregate

A

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

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19
Q

Forms the backbone of DNA

A

Sugar and phosphate

20
Q

mRNA vs. rRNA vs. tRNA

A

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

21
Q

RNA structure is

A

Single stranded

22
Q

Promoter vs. terminator

A

signals RNA polymerase where to begin/end transcribing on DNA

23
Q

Post-transcriptional processing

A

Process where primary RNA transcript is converted to mRNA

  • 5’ capping (modified guanine)
  • 3’ polyadenylation
  • RNA splicing
24
Q

RNA splicing

A

Removal of introns, remaining extrons joined together

25
Q

Subunits of RNA and their function

A
  • Small subunit — put mRNA w/ tRNA and provide a binding site for them
  • Big subunit - enzyme that makes peptides that will become proteins
26
Q

Aminoacyl tRNA synthetases

A
  • link tRNA to amino acid

- each RNA has its own synthetase

27
Q

How does protein synthesis begin?

A

With AUG - methionine

  • small ribosomal subunit binds to 5’ cap and moves along RNA
  • at AUG, large subunit translates to mRNA
28
Q

Stopping translation

A
  • Stop codons (UAG, UAA, UGA)
  • if tRNA does not match those, water is added
  • water terminates the end of the protein
29
Q

Results of reading frame being off

A

Creates nonsense proteins

30
Q

Polyribosomes

A

Multiple ribosomes that simultaneously translate the same mRNA into a protein

31
Q

Protein synthesis inhibitors include

A

Antibiotics

32
Q

Proteolysis

A
  • Proteases break proteins down into peptide bonds
  • then into amino acids
  • used on proteins w/ short life spans or improperly folded
33
Q

Proteasomes and ubiquitin

A

Breakdown proteins in cytosol

34
Q

Factors that determine protein shape

A
  • Amino acid sequence
    (Proteins, side chain, polar/nonpolar, polypeptides)
  • lowest energy confirmation
  • molecular chaperones`
35
Q

Hydrophobic forces

A
  • role in shaping proteins

- pushes hydrophobic molecules together

36
Q

Diseases as a result of improperly folded proteins

A

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

37
Q

Unstructured protein regions

A
  • 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
38
Q

Flexible tethers

A
  • provide movement and flexibility
  • help scaffold proteins bring proteins together in intracellular signaling pathways
  • assist elastin in forming fibers
39
Q

Function of disulfide bonds in extracellular proteins

A

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

40
Q

Functions of proteins

A
  • Enzymes as catalysts
  • antibody binding sites
  • protein binding
41
Q

Antibody binding sites

A
  • specific between antibody and antigens
  • due to looped ends on antibody
  • binding triggers an immune response
42
Q

How proteins are controlled

A

Allosteric enzymes, phosphorylation, GTP binding

43
Q

Allosteric enzymes

A
  • have 2 binding sites

- shift confirmations to inactive enzymes

44
Q

Phosphorylation

A
  • attachment of a phosphate group to an amino acid side chain
  • protein kinases: adds phosphate
  • phosphotases: removes phosphate
45
Q

GTP binding

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

Cell Physiology (1 decks)

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