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Biochemistry 1 > Protein Structure (midterm) > Flashcards

Protein Structure (midterm) Flashcards

1
Q

Peptide bonds are ___________, strong and rigid

A

covalent

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2
Q

Peptide bonds are hydrolyzed by 6M HCL with ____________ or _____________

A

proteases, peptidases

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3
Q

Proteins are synthesized from _____ to ________

A

N, C terminal

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4
Q

Is 5’ the phosphate end or sugar end?

A

phosphate end

so 3’ end is the sugar end

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5
Q

What is primary DNA?

A

nucleotides held together by phosphodiester bonds

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6
Q

Are peptide bonds naturally in trans or cis form?

A

trans form

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7
Q

What is the primary structure of a protein?

A

AAs sequence

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8
Q

What is the most important determinant of protein 3D structure?

A

primary structure of protein

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9
Q

What are the 2 different types of secondary structure in proteins?

A

alpha helix (single stranded held together by hydrogen bonds) or beta pleated sheet

can be parallel or antiparallel

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10
Q

What is secondary structure in DNA?

A

double helix held together by hydrogen bonds, and is antiparallel

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11
Q

What is a tertiary structure in DNA?

A

nucleosome (weak connections)

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12
Q

What is tertiary structure in proteins?

A

-3D folding in space
-energetically favorable conformation
-some have disulfide bonds (-S-S-) which are covalently bonded if theres multiple cysteines (don’t have to be adjacent)
-held together by weak interactions (noncovalent bonds) like hydrogen bonds, hydrophobic interactions, electrostatic interactions (same as ionic bonding), and van der waals interactions

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13
Q

Can all proteins reach quaternary structure?

A

no

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14
Q

What are quaternary structures of protein?

A

association of multiple polypeptide chains/subunits

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15
Q

Protein function is dependent on what?

A

proper 3D structure

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16
Q

Proline creates rigid bends in AA chain, what can this do to secondary structure?

A

break it if theres a lot of kinks

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17
Q

What do charged R groups cause to happen within a protein?

A

electrostatic attraction or repulsion

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18
Q

Could bulky R groups cause a constraint on protein conformation?

A

yes, trp can do this

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19
Q

Which bond within proteins is rigid?

A

peptide bonds

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20
Q

T/F proteins can handle any temp or pH

A

FALSE, proteins cannot make ATP to function in extreme cold, and heat can cause denaturation, same goes with acidic or basic pH, neutral pH and room temp is usually best

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21
Q

What happens to DNA if it gets denatured? Can it be renatured?

A

DNA will go from double stranded to single stranded and can be renatured

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22
Q

What happens to denatured proteins?

A

-loss of secondary and tertiary structure
-peptide bonds are still there (primary structure)
-denaturation can result from heat, unfavorable pH or chaotropic agents

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23
Q

Can proteins be renatured?

A

NO, usually impossible

they would need to be correctly refolded/recreated

ribonuclease A (RNase A) can do this

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24
Q

What are simple proteins?

A

proteins that just contain AAs

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25
Q

What are complex proteins?

A

proteins that contain amino acids and something else (conjugated):

lipoprotein = lipid + protein

glycoprotein = sugar + protein

phosphoprotein= phosphate + protein

nucleoprotein = DNA or RNA + protein (like a ribosome)

metalloprotein= metal ion(s) + protein

chromoprotein= pigmented protein (like hemoglobin, heme is the pigment for red and has 4 chains 2 alpha and 2 beta chains)

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26
Q

What is a conjugated protein? What bond holds it together?

A

complex protein, its a protein interacting with other biomolecules by covalently bonding with a prosthetic group or weak interaction

this can affect protein location, structure and or function

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27
Q

What is heme?

A

consists of a Fe+2 ferrous ion that is contained in the center of a large heterocyclic organic ring called porphyrin

synthesizes RBCs, carries oxygen

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28
Q

Fibrous and globular proteins are based on their ____________ or ____________ structure

A

secondary, tertiary

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29
Q

fibrous proteins usually form what?

A

fibers

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30
Q

What do globular proteins usually form?

A

enzymes

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31
Q

What are the characteristics of fibrous proteins?

test q

A

-usually forms fibers
-made of either alpha helix or beta sheet
-has an elongated structure
-usually insoluble
-mostly a structural protein

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32
Q

What are the characteristics of globular proteins?

A

-usually forms enzymes
-made of BOTH an alpha helix and beta sheet
-tightly folded structure, looks like glob
-mostly soluble
-mostly a functional protein

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33
Q

What is a prosthetic group?

A

a non-protein (that is attached to a protein)

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34
Q

What is the prosthetic group of hemoglobin?

A

heme

heme is covalently bonded to hemoglobin

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35
Q

Myoglobin and hemoglobin are examples of _________ protein

A

globular

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36
Q

Does myoglobin have a high or low affinity for oxygen?

A

high (its an oxygen scavenger)

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37
Q

Where is myoglobin found in the body?

A

in myocytes (muscle cells)

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38
Q

Is myoglobin made up of one polypeptide or multiple?

A

1 polypeptide (1 heme, so can only carry one oxygen molecule)

39
Q

What is the highest protein level structure myoglobin can reach?

A

tertiary

40
Q

Where is hemoglobin found in the body?

A

RBCs

41
Q

Does hemoglobin have a high or low affinity for oxygen?

A

low affinity (its an oxygen transporter)

42
Q

Is hemoglobin made of one polypeptide or multiple?

A

4 polypeptides (also has 4 hemes, so can carry 4 oxygen molecules)

43
Q

What is the highest level of protein structure that hemoglobin can reach?

A

quaternary (made up of 2 alpha subunits and 2 beta subunits)

44
Q

What does percent saturation mean?

A

percentage of oxygen that is bound to either myoglobin or hemoglobin or another globin protein

45
Q

What shape is the myoglobin oxygen binding curve?

A

hyperbolic

46
Q

What shape is the hemoglobin oxygen binding curve?

A

sigmoidal (this is because of cooperativity)

47
Q

define cooperativity

A

when oxygen binds to the iron complex of one polypeptide in hemoglobin, it causes conformational changes and facilitates oxygen binding to other polypeptides

aka 1st oxygen is the most difficult one to bind to hemoglobin and then after that its easy for following oxygens to bind to heme

48
Q

Rate the following globin proteins from highest to lowest affinity
-myoglobin
-oxyhemoglobin
-deoxyhemoglobin
-HbF
-methemoglobin

A

1) myoglobin
2) HbF
3) oxyhemoglobin
4) deoxyhemoglobin
5) methemoglobin

49
Q

What can cause a left shift in hemoglobin oxygen binding curve? What happens here?

A

oxygen binding affinity increases, tissues will have less oxygen (this is bad because your tissues want oxygen!)

Left shift causes:
-high altitude
-decreased temp
-increased pH (so decreases H+ conc., becomes more basic)
-CO
-decreased 2,3 DPG

hemoglobin will not release oxygen to the tissues as much as it would normally, or in a right shift

50
Q

Why do some athletes train in high altitudes?

A

-train in high altitude will cause a left shift
-muscles will produce lactate which makes you tired (lactate is acidic and will cause right shift)
-body will adapt to less oxygen in tissues from the altitude and will increase RBCs which in turn creates 2,3 BPG
-lactate, RBCs and 2,3 BPG increase will result in a right shift, more oxygen in tissues= perform better

note: once you go back to sea level, the right shift will go back to normal after RBCs die (lifespan is 120 days)

51
Q

What is a right shift in the hemoglobin oxygen binding curve? What causes it?

A

reduced oxygen affinity, tissues will have more oxygen

Right shift causes:
-increase temp
-increased 2, 3 DPG
-increased H+ conc (decreased pH, this is also known as Bohr effect)
-increased 2, 3 BPG

52
Q

What is methemoglobin?

A

-oxygen temporarily and reversibly oxidizes Fe+2 to Fe+3
-the iron in the heme group is in the Fe+3 ferris state not the Fe+2 ferrous of normal hemoglobin
-methemoglobin cannot bind to oxygen like oxyhemoglobin
-has the lowest affinity for oxygen

53
Q

What is fetal hemoglobin (also known as hemoglobin F or HbF)?

A

-main oxygen transport protein in human fetus
-higher oxygen affinity than adult form of hemoglobin

54
Q

What is sickle cell anemia? What are the signs and symptoms? How is it treated?

A

-genetic mutation causes glutamate to be swapped for a valine
-this is a misense mutation
-this causes a different protein structure

S&S:
-sickle shaped RBCs
-ability to carry oxygen is greatly reduced
-hard to workout and breathe in general
-SOB
-RBCs can crystallize into fibrous structure and this causes pain
-anemia

tx:
-blood transfusions frequently
-BM transplant
-gene therapy/modification to BM

55
Q

What are 4 examples of fibrous protein?

A

1) alpha keratin
2) beta keratin
3) collagen
4) elastin

56
Q

Where is alpha keratin found?

A

-hair
-nails
-skin
-wool/cashmere

57
Q

What is the predominant secondary structure for alpha keratin? What other features does it have?

A

-alpha helix, has disulfide bridges
-rich in cysteine and hydrophobic AAs

58
Q

Where is beta keratin found?

A

spinder webs and silk

59
Q

What is the predominant secondary structure for beta keratin? What other features does it have?

A

-antiparallel beta sheet with hydrogen bonds
-soft but high tensile strength
-highly compact with ala and gly (bc of small R group)
-rich in ala/gly

60
Q

Where is collagen found?

A

connective tissue

61
Q

What is the predominant secondary structure for collagen? What other features does it have?

A

-left handed beta triple helix structure
-has lysine-hydroxy-lysine bonds
-has repeated glycine- X-X with proline, hydroxyproline, and/or hydroxylysine

62
Q

Which vitamin is needed for hydroxylation?

A

vitamin C

63
Q

Where is elastin found?

A

elastic connective tissue

64
Q

What is the predominant secondary structure for elastin? What other features does it have?

A

-alpha helix with lysine islands
-made up of desmosine (4 lysines crosslinked)

65
Q

What is collagen I?

A

-fibril forming collagen
-high tensile strength
-found in skin, tendons, vascularity, scars, bone (main component of the organic part of bone)

66
Q

What is collagen II?

A

cartilage (collagen II is the main component of cartilage)

67
Q

What is collagen III?

A

-reticular fibers
-found in blood vessels and granulation tissue
-commonly found alongside type I collagen

68
Q

Where is is collagen IV found?

A

-forms basement membrane
-found in eye lens

69
Q

Where is collagen V found?

A

found on cell surfaces, hair, and the placenta

70
Q

T/F: all tissues have the collagen gene

A

true, but not all tissues will use gene and express it

fibroblasts will synthesize collagen as needed

71
Q

How is collagen synthesized?

A

-fibroblasts will undergo DNA replication, transcription and translation
-protein is created and undergoes post translational modification which can include cutting, hydroxylation of lysines and prolines (vit C dependent), and/or glycosylation
-then the triple helix structure forms and will be released into the ECM
-oxidiation of OH-lys enables collagen cross linking and is done with lysyl oxidase and copper
-collagen is fully formed and functional

72
Q

What disease can occur if something goes wrong during DNA replication of fibroblasts for collagen synthesis?

A

osteogenesis imperfecta

73
Q

What 2 diseases can occur if something goes wrong during the post translational modification step during collagen synthesis, specifically hydroxylation of lysines and prolines?

A

Ehlers Danlos and Scurvy

74
Q

What disease can occur if something goes wrong during the crosslinking step of collagen synthesis?

A

menkes disease

75
Q

What is scurvy? What are the S&S?

A

-disorder related to collagen synthesis
-common in sailors, pirates, smokers
-generates oxidative stress and depletes vitamins and minerals
-issue with coenzyme
-has a deficient hydroxylation secondary to vitamin C deficiency
-need to eat fresh fruits and veggies like peppers, blueberries, raspberries

S&S:
-petechiae
-ecchymoses
-loose teeth and bleeding gums (most common in adults)
-poor wound healing and poor bone development (most common in children)

76
Q

What is osteogenesis imperfecta? What are its S&S?

A

-disorder of collagen synthesis
-due to mutation in collagen genes-> can be either the coding or promotor
-can lead to spontaneous abortions

S&S:
-skeletal deformities
-fractures
-blue sclera (due to bleeding blood vessels)
-body is unable to carry its weight

77
Q

What is ehlers danlos? What are its S&S?

A

-disorder of collagen synthesis
-due to mutations in collagen genes and lysine hydroxylase genes
-mutation happens during post transitional modification

S&S:
-hyper-extensible fragile skin (skin can be pulled easily)
-hypermobile joints
-dislocations
-varicose veins
-ecchymoses
-intestinal ruptures

78
Q

What is Menkes disease? What are its S&S?

A

-disorder of collagen synthesis
-due to deficient cross-linking secondary to functional copper deficiency (note: copper is involved heavily with iron, its a cofactor)

S&S:
-depigmented hair
-arterial tortuosity/ ruptures
-cerebral degeneration
-osteoporosis
-anemia

79
Q

What is amino acid sequencing? How is it done?

A

determines the primary structure
1) protein denaturation occurs and makes primary structure with extreme pH, heat, or salt
2) disulfide bonds are cleaved/reduced by adding a proton back (these are seen in tertiary structures) with performic acid
3) determine the number of each amino acid by breaking peptide bonds with HCL for at least 24 hours
4) determine the N and C terminal amino acids with the use of carboxypeptidases in edman degradation
5) cleavage of the polypeptide into fragments, each peptide is sequenced separately, this is known as enzymatic fragmentation and edman degradation and then undergoes liquid chromatography mass spec
6) reconstruct the sequence from the sequences of overlapping fragments

80
Q

Insulin is made up of how many AAs?

A

51

81
Q

What are the 2 types of peptide enzymes?

A

exopeptidase and endopeptidase

82
Q

What are exopeptidases?

A

-cleaves the end of chain
-amino-peptidases cleave the N terminal residues of oligopeptides
-carboxypeptidases cleave C terminal AA

83
Q

What are endopeptidases?

A

cleaves AA in the middle of chain/within protein

examples:
-trypsin
-chromotrypsin
-pepsin
-elastase

84
Q

Trypsin is an endopeptidase. What are its cleavage points?

A

carboxyl end of lys, arg, and his

85
Q

Chromotrypsin is an endopeptidase. What are its cleavage points?

A

phe, trp, tyr (aromatic AAs)

86
Q

Pepsin is an endopeptidase. What are its cleavage points?

A

-phe, trp, tyr (aromatic AAs)
-met, glu, asp

87
Q

Elastase is an endopeptidase. What are its cleavage points?

A

ala, gly, ser

88
Q

What are the suffixes for enzymes?

A

-ase or -in

89
Q

This structural protein is the most abundant:
A) collagen
B) insulin
C) hemoglobin
D) glycogen

A

A) collagen

90
Q

Which type of bond is essential to the formation of a quaternary structure of a protein?

A

hydrogen bond

91
Q

If you are discussing the sequence of amino acids in a polypeptide chain then you are talking about a proteins ___________ structure

A

primary

92
Q

Denaturation of protein changes:
A) primary structure
B) secondary structure
C) tertiary structure
D) B and C

A

D) B and C

93
Q

Which protein has a higher affinity for oxygen?
A) hemoglobin
B) elastin
C) myoglobin
D) collagen

A

C) myoglobin

94
Q

Scurvy is a condition characterized by general weakness, anemia, bleeding gums and skin hemorrhages resulting from a lack of ascorbic acid in the diet. Ascorbic acid plays a crucial role in which of the following processes in collagen synthesis?
A) hydroxylation
B) glycosylation
C) transcription
D) C peptide cleavage

A

A) hydroxylation

Biochemistry 1 (12 decks)

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