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Molecular Biology > 3-Protein Structures & Functions > Flashcards

3-Protein Structures & Functions Flashcards

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1
Q

Which is the initiation codon and which the stop ones?

A

Initiation: AUG (methionine)

Stop:

  • UGA
  • UAG
  • UAA
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2
Q

Where are the ribosomes in the rough ER located?
What connectvity does it have with the nucleus?
What does ER ‘provide’?

A
  • They are encrusted on their outer surface of their membranes
  • Rough ER is continuous with the outer nuclear membrane (meaning that those two membranes are ‘stucked’ together)
  • They provide a large surface for chemical reactions and it is a pathway for transport of material
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3
Q

How molecules are travelling from ER to Golgi

A

They travel in vesicles.

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4
Q

What do we mean when we say that Golgi ‘modifies’ proteins, name an example.

A

For example Golgi adds a carbohydrate

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5
Q

Describe the ‘Exocytosis’ process

A

A vesicle that contains finished product (digestive enzyme,hormone etc) is pinched off at the end of Golgi Apparatus and fuses with cell membrane. Finally the vesicle discharges the content to the outside environment.

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6
Q

Which are the elements of a protein?

A 
-Carbon
• Hydrogen
• Oxgen
• Nitrogen
• (sulphur)
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7
Q

Does methionine containes sulphur?

A

yes

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8
Q

what is the percentage of a cell that is made of protein?

A

It is about 15%

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9
Q

Name some protein functions

A 
-Enzymes
– Structural
– Transport
– Motor
– Storage
– Signaling
– Receptors
– Gene regulation
– Special functions
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10
Q

How the final shape of a protein is caleed what is special about it?

A

The final shape is called the conformation

and has the lowest free energy possible

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11
Q

What is denaturation and how is that possible to happen?

A

Denaturation is the process of unfolding
the protein

– By heat, pH or chemical compounds

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12
Q

What molecular chaperones are?

A

Molecular chaperones are small proteins
that help guide the folding and can help
keep the new protein from associating with
the wrong partner

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13
Q

Name a chemical compound that can be used in order to denaturate a protein.

A

Urea

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14
Q

Which are the two folding patterns that proteins follow?

A

α-helix – protein turns like
a spiral
• β-sheet – protein folds
back on itself as in a ribbon

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15
Q

In which proteins can α-helix and β-sheet forms be found?

A

α-helix- fibrous proteins (hair, nails, horns)

β-sheet-globular protein

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16
Q

How many and which type of proteins can be found?

A

3 different types

  • fibrous proteins
  • globular proteins
  • conjugated protein
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17
Q

What are the characteristics of fibrous proteins?

A
  • Linked in parallel by disulphide bridges

* Protein has a rope-like structure

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18
Q

Fibrous protein: ELASTIN
Structural property?
Tissue rich in this protein?
Function of this protein?

A
  • Strong and elastic
  • Wall of large arteries
  • Flexible support
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19
Q

Fibrous protein: COLLAGEN
Structural property?
Tissue rich in this protein?
Function of this protein?

A
  • Strong and inelastic
  • Bone,Tendon and ligament
  • Rigid support, attachment
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20
Q

Fibrous protein: KERATIN
Structural property?
Tissue rich in this protein?
Function of this protein?

A
  • Strong and inelastic
  • Hair
  • Protection
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21
Q

Fibrous protein: Actin and myosin
Structural property?
Tissue rich in this protein?
Function of this protein?

A
  • Contracile
  • Muscle
  • Movement
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22
Q

Name 4 fibrous proteins

A
  • Actin
  • Myosin
  • Keratin
  • Collagen
  • Elastin
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23
Q

Can non-covalent bonds form interactions

between individual polypeptide chains?

A

Yes

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24
Q

What is a binding site of a protein?

A

– where proteins interact with one another

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25
Q

What is asubunit of a protein?

A

each polypeptide chain of large protein

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26
Q

What is a dimer

A

protein made of 2 subunits

-Can be same subunit or different subunits

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27
Q

What is a protein domain?

A

A domain is a basic structural unit of a protein structure – distinct from those that make up the conformations

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28
Q

Can different domains impart different functions to proteins?

A

yes

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29
Q

Can a protein have more than one domain?

A

Yes, depending on its size

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30
Q

What are globular proteins?

For which structure is a vital component?

A

Several polypeptide chains that are folded roughly into a spherical shape like a tangled ball of string

-Also vital component in cell and subcellular membranes

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31
Q

What type of proteins are enzymes?

A

They are globular proteins

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32
Q

Name three categories of proteins that are globular

A

Enzymes, hormones, antibodies

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33
Q

What type of proteins are hormones?

A

They are globular proteins

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34
Q

What are hormones’s function?

A
  • Chemical messengers

- Exert a specific effect on tissues

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35
Q

What type of proteins are antibodies?

A

Globular

36
Q

What is the shape of antibodies?
Where they come from?
Which is their main function?

A

Y-shaped globular proteins
• Made by lymphocytes
• Defend body against antigens

37
Q

What is that makes an antibody able to recognise a specific antigen?

A

The loops of polypeptides on the end of the binding site.

38
Q

How are antibodies able to recognize different antigens?

A

Changes in the sequence of the loops

39
Q

What conjugated proteins are?

A

They are globular proteins associated with a non-protein chemical (e.g. a carbohydrate)

40
Q

Name a class of conjucated proteins and explain what they consist of

A

glycoproteins

41
Q

Name a well-known glycoprotein and the molecules it consists of

A

mucus consists of proteins and carbohydrates

42
Q

What kind of protein is haemoglobin and what its function?

A

Conjugated protein

  • globular protein globin
  • haem (non-protein containing iron)

Oxygen-transporting pigment in blood

43
Q

What haemoglobin consists of? (subunits)

A

2 α globin
subunits
–2 β globin
subunits

44
Q

If a protein has 2 binding sites what kind of formations can it form?

A

– link together as a helix or a ring

45
Q

Where can we found actin fiber ? In what formation does it present there and what consists of?

A

It can be found in muscle and cytoskeleton

It is present as a helica fiber made of actin molecules

46
Q

Where can we found cross linkages in a protein?

A

We can found croos linkages between 2 proteins and between 2 subunits.

47
Q

What special does the cysteine amino acid have?

A

Disulfide bonds (S-S) can be formed between two cysteine amino acids

48
Q

Info: The conformation of a protein gives it a unique function

A

-

49
Q

Can a protein work itself?

A

No, in order to work proteins must interact with other molecles, usually 1 or a few molecules from the thousand proteins available

Some proteins need a prosthetic group too

50
Q

What is a ligand?

A

the molecule that a protein can bind

51
Q

Through which structure can a protein be linked with a ligand

A

Through the binding site

52
Q

How is the binding site be formed?

do the remaining sequences play arole in regulating the protein’s activity?

A

-The binding site forms when amino acids from within
the protein come together in the folding

-The remaining sequences may play a role in regulating
the protein’s activity

53
Q

What is a co-enzyme?Give an example

A

A co-enzyme is an enzyme which in order to work, requires a prosthetic group (usually a metal or a vitamin)

Example:– Hemoglobin requires heme (iron containing compound) to carry the O2

So, heme is a prosthetic group for Hemogoblin

54
Q

How can prosthetic groups be linked to the protein?

A

These groups may be covalently or non-covalently

linked to the protein

55
Q

What the regulation of enzymatic pathways do?

A

Regulation of enzymatic pathways prevent the deletion of substrate

56
Q

What is feedback inhibition?

A

Feedback inhibition is when the end product regulates the enzyme early in the pathway

57
Q

What is negative feedback?

A

Whena pathway is inhibited by accumulation of final product

58
Q

What happens in positive feedback?

A

a regulatory molecule stimulates the activity of the enzyme, usually between 2 pathways

59
Q

Name an example of positive feedback

A

Increasing ADP levels cause the activation of the glycolysis pathway to make more ATP

60
Q

What an allosteric protein consists of (binding sites)

A

active site recognizes substrate

2nd site recognizes the regulatory molecule

61
Q

INFO:In case of ADP:Enzyme is only partially active with sugar only but much more active with sugar and ADP present

A

-

62
Q

What kinases do?

A

-kinases can put the PO4 to amino acids that have -OH groups (Serine , Threonine, Tyrosine)

63
Q

What phospahates do?

A

Phosphatases remove the PO4

64
Q 
INFO:Some proteins are regulated by the
addition of a PO4
group that allows for the
attraction of + charged side chains causing
a conformation change
A

-

65
Q

What happens when a PO4 group is attached to a protein?

A

The protein might be activated or deactivated

66
Q

What are motor proteins

A

Proteins that can move in the cell, say up and down a DNA strand

67
Q

Can an addition ligand regulate the process of a motor protein If not what regulates it?

A

Adding ligands to change the
conformation is not enough to
regulate this process

The hydrolysis of ATP can direct the
the movement as well as make it
unidirectional

68
Q

What motor proteins usually do?

A

The motor proteins that move things along filaments or myosin

69
Q

How does the cytoskeleton structurally supports the cell?

A

– Maintains shape
• Fibers act like a geodesic dome to stabilize and
balance opposing forces
• Provides anchorage for organelles
• Dynamic (Dismantles in one spot and reassembles in
another to change cell shape)

70
Q

INFO: The cytoskeleton also plays a major role in cell
motility.

– This involves both changes in cell location and limited movements of parts of the cell.

• The cytoskeleton interacts with motor proteins.

– In cilia and flagella motor proteins pull components of the cytoskeleton past each other.

– This is also true in muscle cells.

• Motor molecules also carry vesicles or
organelles to various destinations along
“monorails’ provided by the cytoskeleton.

• Interactions of motor proteins and the cytoskeleton circulates materials within a cell via streaming.

• Recently, evidence is accumulating that the
cytoskeleton may transmit mechanical signals that rearrange the nucleoli and other structures.

A

-

71
Q

How many and which are the types of fibers in the cytoskeleton?

A

They are three(3):
microtubules,
microfilaments,
intermediate filaments. (see their structure slide 52)

72
Q 
MICROTUBULES:
What are their characteristics?
What are they made of?
What is their function?
From where they grow out?
A

-Microtubules, the thickest fibers, are hollow rodsabout 25 microns in diameter.

– Microtubule fibers are constructed of the globular
protein, tubulin, and they grow or shrink as more
tubulin molecules are added or removed.

-They move chromosomes during cell division.
- Another function is as tracks that guide motor proteins carrying organelles to their destination.
– These microtubules resist compression to the cell
-Microtubules are the central structural supports in cilia and flagella.

In many cells, microtubules grow out from a centrosome near the nucleus.

73
Q

Where can centrioles can be found and how many are there?
What centrioles consist of?
What is their function?

A

In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring.

  • During cell division the centrioles replicate.
74
Q

What do cilia and flagella consist of?

What are their functions? (Give an example)

A

• Microtubules are the central structural
supports in cilia and flagella.
– Both can move unicellular and small multicellular
organisms by propelling water past the organism.
– If these structures are anchored in a large
structure, they move fluid over a surface.

For example, cilia sweep mucus carrying trapped debris from the lungs.

75
Q 
INTERMEDIATE FILAMENTS:
What are their characteristics?
What are they made of?
What is their function?
What is special for them in comparison to the other cystoskeleton's fibers?
A
  • Intermediate filaments, intermediate in size at 8 - 12 nanometers,
  • Intermediate filaments are built from a diverse class of subunits from a family of proteins called keratins
  • are specialized for bearing tension.
  • They reinforce cell shape and fix organelle location.

-Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes.

76
Q

MICROFILAMENTS:
What are their characteristics?
What are they made of?
What is their function?

A

the thinnest class of the cytoskeletal fibers, are solid rods of the globular protein actin.

– An actin microfilament consists of a twisted double
chain of actin subunits

  • Microfilaments are designed to resist tension.
  • With other proteins, they form a threedimensional-network just inside the plasma membrane
77
Q

How actin filaments are arranged in muscle cells?

A

Parallel

78
Q

INFO:Thicker filaments, composed of a motor protein,

myosin, interdigitate with the thinner actin fibers.

A

-

79
Q

How myosin contributes to muscle cell contraction?

A

Myosin molecules walk along the actin filament,
pulling stacks of actin fibers together and shortening
the cell. (see slide 58)

80
Q

What muscle fatigue means?

What its cause?

A

Muscle fatigue is a condition in which the muscle is no longer able to generate or sustain the expected power output.

-Its thought to mainly arise from failure in excitation-contraction coupling within the muscle than from presynaptic factors

81
Q

What is central fatigue?

A

Central fatigue include subjective feelings of tiredness and a desire to cease activity. Its thought that central fatigue precedes physiological fatigue in the muscle. Acidosis of lactic acid dumped into the bloodstream may influence the sensation of fatigue perceived in the
brain.

82
Q 
Exolain the followin Muscle Disorders:
Muscle overuse 
Muscle disuse 
Acquired disorder
•Inherited disorders
A
  • Muscle overuse resulting in muscle fatigue. Trauma may also cause tearing of the tissue.
  • Muscle disuse could be just as bad as overuse, resulting in muscle atrophy. E.g. muscle immobilized in a cast for long periods. The blood supply to the muscle diminishes and muscle fibres get smaller. Atrophy longer than an year is permanent.

-Acquired disorders, such as weakness resulting from infectious diseases, such as,
influenza, poisoning by toxins such as that producing botulism (botulinum toxin) and tetanus (tetanus toxin).

-Inherited disorders are the hardest to treat. E.g. muscular dystrophy as well as biochemical defects in glycogen and lipid storage.

83
Q

What is the cause of Duchenne muscular dystrophy ?

What is the estimated living time?

A

Duchenne muscular dystrophy is due to the absence of a cytoskeletal protein known as dystrophin. These
muscle fibres have tiny tears which allow Ca2+ ions to enter them and activate enzymes that break down fibre components.

-Patients usually die before 30.

84
Q

Name some diseases that derived from motor prteins that fail to fulfil their function

A

The importance of motor proteins in cells becomes
evident when they fail to fulfill their function

e.g Dynein deficiencies can lead to chronic
infections of the respiratory tract as cilia fail
to function without dynein.

Defects in muscular myosin predictably cause
myopathies and damaged muscle tissue.

85
Q

What can the accumulation of misfolded proteins cause ?

A

Accumulation of misfolded proteins can cause disease,

and unfortunately some of these diseases, known as amyloid diseases, are very common.

86
Q

Name an amyloid disease?What is the percentage of infections in the popularity?
Which other diseases have similar amyloid origins?

With what kind of accumulation are these diseases associated specifically?

A

-The most prevalent one is Alzheimer’s disease, which affects about 10 percent of the adult population.

-Parkinson’s disease and Huntington’s disease have
similar amyloid origins

-These age onset degenerative diseases are associated with the aggregation of misfolded proteins into insoluble, extracellular aggregates and/or intracellular inclusions including cross-beta sheet amyloid fibrils.

INFO:While it is not completely clear whether the aggregates are the cause or merely a reflection of the loss of protein homeostasis, the balance between synthesis, folding, aggregation and protein turnover.

Molecular Biology (9 decks)

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