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Biochem/ metab > lecture 6 > Flashcards

lecture 6 Flashcards

1
Q

what is a peptide bond?

A

bonds that hold peptides together

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2
Q

describe the rxn of a peptide bond

A

amides linkage that forms when the electron pair attack the alpha carbonyl carbon
*acyl sub rxn

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3
Q

what forms form the peptide bond

A
  1. h20 due to the dehydration rxn

2. residues–> linked amino acids

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4
Q

what is the N & C terminus?

A

N- amino group

C- carboxyl group

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5
Q

what is the direction of peptides and proteins?

A

natalie christine

N–> C

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6
Q

what makes peptide bonds?

A

ribosomes

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7
Q

what does peptidyl transferase do?

A

covalently links RNA to the peptide chain

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8
Q

what is native configuration

A

well defined 3-D structures of protein

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9
Q

what is derived from native configurations?

A

amino acid sequence

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10
Q

how are proteins classified and what do the classifications determine?

A
  1. shape and composition

- determine function

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11
Q

what is a common characteristic of proteins

A

they fold spontaneously into single biological active forms

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12
Q

what are 2 protein shapes?

A
  1. fibrous–> long rods

2. globular–> compact/ spherical

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13
Q

what are fibrous characteristics?

A
  1. insoluble in water and tough

found in hair, nails, skin

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14
Q

what are the characteristics of globular structures?

A
  1. water-soluble

- most enzymes are globular

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15
Q

what are the levels of structures?

A
  1. primary
  2. secondary
  3. tertiary
  4. quaternary
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16
Q

what is the primary structure?

A

amino acid sequence

specific to the genetics

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17
Q

what are homologs

A

proteins with similar primary sequences

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18
Q

what are variations in proteins?

A

mutations- *can be transcribed and translated

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19
Q

what are the 3 types of effects of mutations

A
  1. lethal
  2. minimal
  3. none
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20
Q

what are secondary structures?

A

primary structures stabilized by hydrogen bonds (peptide backbones)

  • a-helix
  • beta-pleated sheets
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21
Q

what are the shapes and interactions of secondary structures?

A

alpha- rigid- rodlike structure twisted

bonds: hydrogen bonds, N-H groups, N-C groups
* 4 residues always*

beta-sheets- 2 or more polypeptide chains line up side by side
bonds: hydrogen bonds are adjacent

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22
Q

what is a tertiary structure?

A

unique 3-D configuration of polypeptide

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23
Q

what is protein folding?

A

unorganized–> organized

*interactions between side chains residues are brought closer

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24
Q

How do proteins handle water?

A

excluded from protein interior

depending on the polarity

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25
Q

what is the specific to globular

A

the contain domains

26
Q

list the interactions involved in tertiary structures

A
  1. hydrophobic
  2. electrostatic
  3. hydrogen bonds
  4. covalent
27
Q

what is the role of hydrophobic interactions?

A

driving force to folding and exclude H2O

28
Q

what is the role of electrostatic interactions?

A

salt bridges

+ & - charges

29
Q

what is the role of hydrogen bonds?

A

lone pairs

30
Q

what is the role of covalent bonds?

A

disulfide bridges help stabilize against changes in

  1. pH
  2. salt
31
Q

what is the strongest of the 4 interactions of the tertiary structures?

A

covalent bonds

32
Q

Is protein spontaneous?

A

yes, it is thermodynamically favored

change in G <0 = - spontaneous

33
Q

what is cysteine oxidation?

A

when 2 amino acids come together and a covalent bond forms and there is a loss of electrons

forms a disulfide bond

34
Q

what is a quaternary structure?

A

each peptide chain folds and forms subunits and multiple subunits interact and fold together to form 1 large complex

oligomers

35
Q

what types of interactions are found in quaternary structures?

A
  1. hydrophobic
  2. electrostatic
  3. hydrogen
  4. covalent
36
Q

how are proteins viewed?

A 
x-ray crystals 
steps: 
1. crystalize proteins 
put in solution dehydrate hope for crystalization 
2. x-ray, look for diffracted pattern 
3. map pattern 
4. use math to discover other half
37
Q

what is denaturing?

A

when the structure is disrupted to the point of irreversibility

38
Q

what bonds are disrupted from denaturing and which are not?

A

non-covalent bonds are disrupted

  1. hydrogen
  2. electrostatic
  3. hydrophobic

*peptide bonds are not bothered

39
Q

what are types of denaturation?

A
  1. strong acid/ bases
  2. organic solvents
  3. detergents
  4. reducing agent
  5. salt concentration
  6. heavy metal ions
  7. temp changes
  8. mechanical stress–> pulled apart
40
Q

how are misfolded proteins handled?

2 methods

A

tagged for degradation and destroyed

  1. selective: UPS (ubiquitin-proteasome system)
  2. non-selective: autophagy
    - macro
    - micro
    - chaperone-mediated
41
Q

what is ubiquitin?

A

tagging proteins for trash–> proteasome

42
Q

describe allostery

A

when each subunit affects adjacent subunits

43
Q

how does allostery impact function

A

through ligand binding

  • on
  • off
44
Q

how is hemoglobin unique?

A

when one oxygen binds to hemoglobin it opens all the hemoglobin binding sites

45
Q

how are protein compositions (based on what is included) classified?

A
  1. simple: contain only amino acids

2. conjugated: simple + non-protein components (MAJORITY)

46
Q

what are prosthetic groups

A

non-protein components

47
Q

what are examples of simple proteins?

A
  1. albumin

2. keratin

48
Q

what are examples of conjugate amino acids?

A
  1. metalloprotein
  2. phosphoprotein
  3. glycoprotein
  4. lipoprotein
49
Q

what is PTM and when does it occur?

A

post-translational modification
Happens: after translation
adding molecules to modify

50
Q

where can PTM occur?

A

nucleus

cytoplasm

51
Q

what is phosphorylation?

A
  • addition of phosphates to specific amino sites, turns on or off
  • takes from ATP*
52
Q

what are the specific amino acids that are able to phosphorylate?

A

She Taste Tea

  • serine
  • tyrosine
  • threonine
53
Q

what enzymes add phosphate?

A

kinase can also add biomolecules

54
Q

what does phosphatase do?

A

use water to remove phosphate from an amino group

55
Q

what are the effects of protein phosphorylation?

A
  1. can impact function due to pH change

2. turn on and off which increases or decreases interaction with other proteins

56
Q

what is an example of protein phosphorylation?

A

phosphorylation cascade in metabolism

57
Q

what is sumoylation?

A

new member of ubiquitin

58
Q

what is acetylation?

A

open chromatin to initiate transcription

59
Q

what is HAT and its function?

A

histone acetyltransferase *push apart histones (on)

60
Q

what is HDAC?

A

histone deacetylase closes histones off

61
Q

what is methylation?

A

closes chromatin by using heterochromatin

Biochem/ metab (4 decks)

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