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bio120 > week 2 > Flashcards

week 2 Flashcards

1
Q

What is the primary sequence of protein structure?

A

This is the most simple level of protein organization; the linear amino acid sequence

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2
Q

What is the secondary sequence of protein structure?

A

This allows for local folding, specific and more common structures include the alpha helix and the beta sheet

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3
Q

What is the tertiary protein sequence

A

This concerns the long-range folding, and the 3D structure of the protein

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4
Q

What is the quaternary structure of protein?

A

This is when there is more than one polypeptide chain

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5
Q

Describe an amino acid structure

A
  • Proteins are comprised of amino acids
  • They have an amino group, a carboxylic acid group, and a side chain/R group all attached to an alpha carbon
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6
Q

What is an R group?

A

The R group can have a multitude of variations depending on the acid. It is what differentiates each of the 20 amino acids

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7
Q

What are the 4 major categories of amino acids?

A
  • Acidic
  • Basic
  • Nonpolar
  • Uncharged polar
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8
Q

Where are polar amino acids found?

A

These are important for enzymatic amino acids

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9
Q

Where are nonpolar amino acids found?

A

They are found in the interior of proteins, and sometimes in lipid bilayers

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10
Q

Describe the structure of cysteine

A

Cysteine is considered nonpolar; it has sulfhydryl groups and can form disulphide bonds

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11
Q

What is a disulphide bond?

A

These are bonds that can form between polypeptides or intrachain. They are also found in the keratin in your hair/skin, due to the fact that they can be exposed to external physical/chemical stress

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12
Q

Where does the peptide bond occur?

A

They occur within the ribosome, there occurs a reaction between the carboxyl group of the first amino acid, and the amino group of the second one

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13
Q

What are the terminus’ of proteins?

A

There is the N-Terminus, which is the amino group, and the C-Terminus, which is the carboxylic end. The peptide bond formation can be shown through C-C-N

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14
Q

What is a residue?

A

An amino acid when is it connected to another amino acid by a peptide bond/peptide chain
- Since they’ve lost a water molecule through the formation of the peptide bond, they are no longer a full amino acid

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15
Q

What is Leu-Enkephalin?

A

It is a pentapeptide, in which its reversed composition does not have any pharmacological effect. This is demonstrated to show that the linear orientation of a
peptide is essential for the function of an amino acid

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16
Q

What is the alpha helix in terms of structure?

A

The alpha helix is found in cell membranes with a strong cylindrical structure, and it is about 10 residues long with an amino and carboxyl end

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17
Q

What makes the cylindrical form of the alpha helix?

A

The hydrogen bonding within other molecules (NOT THE R GROUPS) in the molecule. There is hydrogen bonding between the H from the amino and the O from the carboxyl group.

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18
Q

How does bonding occur in the helix?

A

It occurs like position n with n+4
The second residue bonds with the 6th residue, and so on.

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19
Q

What are the differences between the alpha helix and DNA?

A
  • DNA is usually double stranded, whilst protein is single stranded
  • In DNA, the bases are also usually inward, whilst the amino acid bases are pushed to the outside in the alpha helix, and the R groups are pushed to the inside
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20
Q

How are beta sheets formed?

A

Hydrogen bonding occurs between the carbonyl oxygen and the amide hydrogen in neighbouring strands, whilst in Alpha helices it occured 4 residues away

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21
Q

Why is it now carbonyl and amide in the beta sheet/alpha helix?

A

Due to the condensation reaction done to form the polypeptide, it turns carboxyl to carbonyl, and amino to amine

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22
Q

What is a similarity between beta sheet and alpha helix?

A

Their bonding both occurs between non-adjacent molecules

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23
Q

What are the two types of beta sheets?

A

Parallel and Anti-Parallel
- Depends on the configuration of the amino acid and carboxyl ends and their orientations

24
Q

What is an amyloid?

A

Beta sheets can form strong rigid structures, such as ribbon diagrams where the sheets are stacked ontop of one another

25
Q

What is a coiled coil?

A

It is an amphipathic type of alpha helix; and it has both hydrophilic and hydrophobic parts to it

26
Q

What is the purpose of a coiled coil?

A

These coils wrap around each other so that they can minimize the exposure of the hydrophobic parts, and increase exposure of the hydrophilic

27
Q

What is the tertiary structure?

A

This is the overall 3D structure of the protein, and it is held together by hydrophobic interactions, non-covalent bonds, and covalent disulfide bonds

28
Q

What ensures that proteins can fold into the most energetically favourable conformations?

A
  • In the backbone, hydrogen bonds are between atoms of peptide bonds, and they can also be present within the side chains
29
Q

What are chaperone proteins?

A

Proteins will fold into the shape dictated by their amino acid sequence, but chaperone proteins make the process more efficient and reliable in living cells – they make sure that proteins fold in a reliable way

30
Q

What is a protein domain?

A

These are regions of sequences that are able to fold up independently and create their own tertiary structure; they usually have their own specialized functions that can operate in a semi-independent matter

31
Q

How many domains do eukaryotic proteins have?

A

Two or more domains connected by intrinsically disordered sequences

32
Q

What are kinases?

A

These can phosphorylate proteins, and attached to them are kinase domains

33
Q

What is a protein family?

A

They are groups of proteins with a common evolutionary origin; overall their functions are very similar, but they have evolved to have slightly different functions within a cell

34
Q

What is the quaternary structure?

A

They consist of different polypeptide chains called subunits, and within a peptide, there can be a domain

35
Q

What differs between a subunit and a domain?

A

A domain is a discrete function and/or structural section of a polypeptide. These are regions of sequences with their own functions.
This differs from a subunit, which is a single polypeptide in a protein which is in turn composed of multiple polypeptides. It is important to note that subunits can have domains.

36
Q

What are scaffold proteins?

A

These are examples of multiprotein complexes; sometimes you need a scaffold protein as an entity that will bind different proteins and get them in close enough proximity for them to react

37
Q

What is proteomics?

A

This is the large-scale study of proteins; how they interact and their locations etc. etc.

38
Q

What exactly is a polypeptide?

A

The resulting chain of amino acids from linking them with peptide bonds

39
Q

What are the L & D isomers of amino acids?

A

These are two isomers of existing amino acids. In the L isoomer, the carboxyl is on the right and the amino is on the left, whilst it is the opposite in the D isomer.

40
Q

Which amino acids do proteins exclusively contain?

A

L-amino acids

41
Q

What is special about cysteine?

A

A disulfide bond can form between two cysteine side chains in proteins

42
Q

What is the polypeptide backbone made of?

A

A repeating sequence of C-C-N

43
Q

How do electrostatic attractions assist in polypeptide formation?

A

It aids in protein folding

44
Q

How does the hydrophobic force assist in determining the shape of a protein?

A

In an aqueous environment, hydrophobic molecules tend to be forced together to minimize their disruptive effect on the hydrogen bonded network of the surrounding water molecules; thus, a polypeptide is able to face polar amino acid side chains on the surface, whilst nonpolar ones are buried on the inside to form a tightly packed hydrophobic core on the inside

45
Q

What helps a molecule stabilize its folded shape?

A
  • Large numbers of hydrogen bonds within a protein molecule (backbone-backbone, backbone-sidechain, sidechain-sidechain)
46
Q

What is renaturation?

A

A process whereby denatured proteins can refold spontaneously into its original conformation once the denaturing solvent is removed from a denatured protein

47
Q

What is the role of an isolation chamber?

A

Some chaperone proteins act as isolation chambers that help a polypeptide fold; chamber caps are used so that the polypeptide chain can fold without aggregating with the crowded conditions of the cytoplasm

48
Q

What is the role of a chamber cap?

A

This provides an enclosed chamber in which the newly synthesized polypeptide chain can fold without the risk of aggregating with other polypeptides in the cytoplasm

49
Q

What are amyloid structures?

A

When proteins fold incorrectly, they sometimes form amyloid structures that can damage cells and even whole tissues; they are thought to contribute to a number of neurogenerative disorders such as Alzheimers

50
Q

What are prions?

A

These are misfolded proteins that are able to convert the properly folded version of a protein in an infected area into the abnormal folded version

51
Q

What is the difference between globular and fibrous proteins?

A

Globular proteins are which the polypeptide chain folds up into a compact shape, like a ball, with an irregular surface
Fibrous proteins have elongated, three dimensional structures that are long and narrow

52
Q

What is alpha keratin?

A

Keratin filaments are fibrous proteins that are extremely stable, they are dimers of coiled coil regions

53
Q

What are intermediate filaments

A

A component of the cytoskeleton that gives cells mechanical strength

54
Q

Describe the formation of collagen

A

Collagen molecules consist of three long polypeptide chains, each containing the nonpolar amino acid glycine at every third position.
This allows the chains to wind around one another to create a triple helix with glycine at the core.
Collagen fibrils are very strong and help tissues hold together

55
Q

What are covalent cross-linkages?

A

These linkages can either tie together two amino acids in the same polypeptide chain or join together many polypeptide chains in a large protein complex

56
Q

What is a disulfide bond?

A

The most common covalent cross-links in proteins are sulfur-sulfur; they form disulfide bonds
These bonds help stabilize a favoured protein conformation

bio120 (2 decks)

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