Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BISC 312 > Lecture 6 > Flashcards

Lecture 6 Flashcards

1
Q

What are proteins and what are the different functions they can do?

A
  • they are the workhorses that “do” everything in life
  • they interact with other proteins in a precise and specific way
  • function as machines for muscle contraction, immune function and blood clotting
  • more complex than DNA - 20 building blocks instead of 4
  • also provide transport of molecules across membranes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is protein function dependent on? Why is the 3D structure important?

A
  • protein function is dependent on 3-D structure
  • protein will not be functional unless it folds into correct 3-D structure
  • changes in protein sequences can change protein structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the building blocks of proteins?

A

Amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the basic structure of an amino acid? And what are the pKa values of the groups of the basic structure?

A
  • An alpha carbon in the middle which is linked to a carboxyl group, a hydrogen, an amino group and an “R” group
  • this is the basic amino acid structure for all amino acids except proline
  • carboxyl –>pKa = 2
  • amino group –> pKa = around 9 to 10.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is an “R” group

A
  • It is the side chain and portion of amino acid that differs among 20 amino acids
  • gives amino acid it’s properties
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the Isoelectric point (pI) ?

A
  • it is the pH when positive and negative charges are the same on a protein
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is a zwitterion?

A
  • when a molecule carries both positive and negative charges

- hybrid and has a net charge of 0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How does ionization state vary with pH

A
  • because depending on the pKa levels and the pH levels both groups on the amino acid can be pronated, in the zwitterionic form or both groups could be depronated where one group has a negative charge (carboxyl) and one group is neutral as its depronated (amino group)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What defines carbon as a stereocenter?

A
  • When a carbon atom has four different substituents attached to it –> aka a asymmetrical carbon
  • glycine does not have a stereocenter cause it is bound to two H2s on opposite ends
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What happens when a carbon contains one asymmetric carbon?

A
  • two distinguishable stereoisomers exist

- non super imposable mirror images of each other or enantiomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is an example of an enantiomer?

A

Alanine
- can be distinguished from one another experimentally because their solutions rotate plane - polarized light in opposite directions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What confirmation do amino acids tend to be in?

A
  • L- confirmation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are properties of Glycine?

A
  • smallest and simplest amino acid (has two hydrogens bound to central alpha)
  • hydrophobic/nonpolar in character
  • sometimes found on a surface of protein due to its ability to make tight turns
  • aliphatic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What are properties of Alanine

A
  • hydrophobic and alipathic

- no charge on methyl R group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the definition of Alipathic?

A

Alipathic means hydrogen and carbons of R group are in linear or branched chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are properties of Valine?

A
  • also non polar like Glycine and Alanine
  • non polar side chain (much of hydrocarbons and methyl group)
  • often found in core of protein where they are shielded from interactions w/ water
  • non cyclic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are properties of Leucine?

A
  • nonpolar
  • often found in core of protein where they are shielded from intereactions with water
  • also has a bunch of hydrocarbons
  • has two methyl groups
  • non cyclic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the properties of Isoleucine

A
  • also non polar
  • also has a bunch of hydrocarbons and methyl groups
  • non cyclic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What are properties of methionine?

A
  • apart of the thioether group due to the Sulfur it has
  • sulfur containing amino acid
  • not technically an alipathic group but Sulfur has the same electronegativity as carbon
  • non cyclic
  • nonpolar
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the properties of Proline?

A
  • alipathic ring
  • the one amino acid that doesn’t have the standard basic structure of amino acid
  • unique cause its side chain is covalently bonded to both nitrogen and alpha Carbon
  • this has a large effect on protein structure, causing kinks cause there isn’t free rotation in the bond between nitrogen and the alpha carbon
  • can be on surface of proteins like Glycine
  • would cause too much strain for secondary alpha helix
21
Q

What are the properties of Phenylalanine ?

A
    • has a phenyl ring –> aromatic ring
    • this is the most hydrophobic
    • non polar
    • Phe, F
22
Q

What are the properties of Tyrosine ?

A

– also hydrophobic in nature even though it has polar groups (the hydroxyl) on its side chains

– can even ionize at a high pH –> weakly acidic at high pH

    • absorption of aromatic amino acids around 280 nm allows quantitation of proteins with UV light
    • non polar
    • Tyr, Y
    • aromatic ring

– pKa = 10.1

23
Q

What are the properties of Tryptophan

A
  • has an indole group joined to a methylene -CH2
  • it can also form a weak hydrogen bond but it is mostly hydrophobic
  • strong UV absorption of light @280 nm –> absorption of aromatic amino acids around 280 nm allows quantitation of proteins with UV light
  • non polar
  • Trp, W
    • aromatic ring
24
Q

What are the properties of Asparagine ?

A
  • Asn, contains a terminal carboxamide
  • can form interactions with water and hydrogen bonds
    • Asn, N
    • neutral, non ionizable
    • polar
25
Q

What are the properties of Glutamine?

A
  • also contains a terminal carboxamide
  • can form interactions with water and hydrogen bonds
    • Gln, Q
    • neutral, non ionizable
26
Q

What are the properties of Serine?

A
  • has polar side chains that can form hydrogen bonds with water or other hydrogen bond donors or acceptors
  • tends to be on the surfaces of proteins where they can contact aqueous environment
  • can form hydrogen bonds, weak
    • Ser, S
    • neutral nonionizable
27
Q

What are the properties of Threonine ?

A
  • has polar side chains that can form hydrogen bonds w/ water or other Hydrogen bond donors or acceptors
  • tends to be on surface of proteins where they can contact aqueous environment
  • often sites of post translational modifications
  • has some hydrocarbons but they’re few so it is mostly classified as hydroxyl
  • polarity comes from hydroxyl groups
    • Thr, T
    • neutral, non ionizable
28
Q

What are the properties of Cysteine?

A
  • weakly acidic
  • R group is a sulfhydryl group
  • often at active site of enzymes
  • can form disulfide bonds
  • can ionize at pH = 8.3 –> pKa = 8.3
  • S- –> H+

– polar

29
Q

What are the properties of Lysine?

A
  • polar/hydrophilic
  • basic
  • R group is amino group –> modified by acetylation and methylation
    • pKa = 10.0
  • strongly polar so mainly found on the surface of proteins
  • can be found in substrate binding sites
  • can form ionic bonds (proton acceptor)
    • Lys, K
30
Q

What are the properties of Arginine

A
  • polar/hydrophilic
  • basic
  • R group is guandinium group –> pKa = 12.5
  • strongly polar so mainly found on the surface of proteins
  • found in substrate binding sites on enzymes
  • modified by acetylation and methylation
  • can form ionic bonds (proton acceptor)
    • Arg, R
31
Q

What are the properties of Histidine?

A
  • polar/hydrophilic
  • basic (least basic of 4 basic amino acids)
  • R group is imidazole group
  • strongly polar so mainly found on the surface of proteins
  • found in substrate binding sites on enzymes
  • can form ionic bonds (proton acceptor)
  • often involved in acid and base catalysis of enzyme reactions
    • His, H

– positively charged

pKa = 6.0

32
Q

Titration of Histidine

A
  • histidine loses the proton on its imidazole ring at about pH 6
33
Q

Why can Histidine exist both protonated and deprotonated in the body?

A
  • the pKa range for His is 6.5 - 7.4 when incorporate into proteins
  • this is near physiological pH there fore His is often involved proton transfers during enzyme catalysis
34
Q

What are the properties of Aspartate ?

A
  • highly acidic
  • hydrophilic
  • have carboxylic acid as an R group
  • at physiological pH lack proton (deprotonated) –> proton donor
  • can form ionic bonds
  • typically named based on if they are protonated or not
  • tend to be on the surface of proteins in contact w/ aqueous environment or other molecules
    • Asp, D

– negatively charged

– Aspartic acid pKa = 3.9

35
Q

What are properties in Glutamate ?

A
  • highly acidic
  • hydrophilic
  • have carboxylic acid as an R group
  • at physiological pH lack proton (deprotonated) –> proton donor
  • can form ionic bonds
  • typically named based on if they are protonated or not
  • tend to be on the surface of proteins in contact w/ aqueous environment or other molecules
    • Glu, E

– negatively charged

–> Glutamic acid pKa = 4.2

36
Q

what does pKa represent ?

A
  • it is the acid dissociate constant
  • pH at which the acid is 50% dissociated
  • large Ka –> smaller pKa value
37
Q

What does most peptide bond formation require?

A

Energy

38
Q

What is a peptide bond?

A

It is a bond between carboxylic acid group of one amino acid and amino group of the other

39
Q

What does the formation of a peptide bond result in?

A
  • water

- there’s two hydrogens removed from the amino group, while there’s an oxygen removed from carboxylic acid

40
Q

What are the negative amino acids?

A
  • Aspartic Acid
  • Glutamic Acid
  • both have acidic side chains
41
Q

What are the positive amino acids?

A
  • Histidine
  • Lysine
  • Arginine
  • all of which have basic amino acid chains
42
Q

What is the directionality of a peptide chain (polypeptide)

A
  • amino terminal to carboxyl terminal
43
Q

What is the double character bond of peptide backbone geometry?

A
  • double bond character of C-N bond

- results in a relatively short bond

44
Q

What are the benefits of the double bond resonance form of the peptide bond?

A
  • increases stability

- decreases rotation about the bond

45
Q

What are the two possible configurations of the peptide bond?

A
  • cis

- trans

46
Q

Which of the two configurations is favorable and why ?

A
  • the trans figuration, where alpha carbons are on opposite sides ; it is lower energy (more favored)
    - during translation R groups are on opposite sides
  • It is more favorable because on the cis configuration the R groups on adjacent alpha carbons can sterically interfere –> atoms cannot more around
47
Q

What direction are protein sequences always written?

A

From N to C terminal direction

48
Q

What are the ionizable groups on the peptide chain?

A
  • only ionizable (charged) groups are side chains (R groups) except for terminal amino and carboxyl groups
49
Q

What are the two rules of thumb for pKa

A
  • when pH is much higher than pKa group will be predominantly deprotonated
  • when pH is much lower than pKa group will predominantly protonated

BISC 312 (31 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions