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Bio 1A03 > Theme 1- Module 3 (Proteins) > Flashcards

Theme 1- Module 3 (Proteins) Flashcards

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1
Q

What are some functions of proteins in our bodies?

A

Transport and signalling

Movement and structure

Enzymes

Defense (i.e. antibodies)

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2
Q

How is the TATA box able to interact with DNA molecules?

A

A groove in the protein allows for this interaction

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3
Q

Porin proteins have a structurally hydrophilic pore. How does this relate to their function?

A

They transport water across the cell membrane; their pore should be hydrophilic (compared to the hydrophobic inner membrane) in order for this to occur.

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4
Q

Heamoglobin is globular and has a hydrophobic interior and a hydrophilic exterior. What does this structure allow it to do?

A

It allows the haemoglobin to be soluble in the aqueous environment of the cytosol

*most soluble cellular proteins have a similar shape

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5
Q

Name two ways protein structures are represented

A

Space-filling diagram

Ribbon diagram

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6
Q

What are some key features of a space-filling diagram?

A

Shows actual size and location of each atom

Atoms rep with diff colours

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7
Q

What are some key features of a ribbon diagram?

A

Lines rep backbone of the polymer

Thicker line = organized reiterated alpha helix
Thinner line = less ordered loop

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8
Q

The genetic info for each protein is encoded in the _____ for each cel

A

DNA

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9
Q

What are the main steps of making proteins?

A

1) Transcribe genetic info from DNA into RNA
2a) Prokaryotes —> RNA goes straight to step 3
2b) Eukaryotes —> RNA to mRNA
3) Transported in cytoplasm
4) Ribosomes translates the thing

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10
Q

It is within the _____ that the ribosomal RNA molecules that are an important component of the ribosomes are transcribed

A

Nucleolus (middle of the nucleus)

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11
Q

Where does transcription occur?

A

Nucleus

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12
Q

What do nuclear pore complexes used for? Describe using the example of ribsomal RNA

A

Allows materials to flow in and out of the nucleus

Ex. Ribosomal RNA manufactured in nucleolus; bind to proteins to make the ribosome subunits; exit via nuclear pores

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13
Q

Where is the ribosomal RNA manufactured?

A

Nucleolus

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14
Q

What can enter the nucleus via the nuclear pores? What can exit?

A

Enter: building blocks of DNA and RNA, enzymes

Exit: ribosomal subunits + RNA

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15
Q

What do the subunits of the ribosome contain?

A

RNA and proteins

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16
Q

What’s the difference between free ribosomes and bound ribosomes?

A

Free ribosomes = remain soluble in the cytoplasm

Bound = attach to the endoplasmic reticulum

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17
Q

What do bound ribosomes produce and what happens to the product?

A

Polypeptide strands into the lumen or membrane of the ER which will be destined for other parts of the cell or secretion

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18
Q

What do free ribosomes produce and what happens to the product?

A

Polypeptide strands that will remain in the cytoplasm of the cell or be transported to other organelles

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19
Q

Amino acids linked together are called…?

A

Polypeptides

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20
Q

What process links amino acids together? What breaks them apart?

A 
Link = condensation (forms water) 
Break = hydrolysis
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21
Q

What does the transfer RNA (tRNA) do?

A

Matches the sequence of nucleotides on the mRNA and carries the appropriate amino acid to the next position in the growing polypeptide chain

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22
Q

What is a peptide bond?

A

The C-N bond that results thru a condensation rxn between a carboxyl group of one amino acid and the amino group of the other

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23
Q

When the amino acids are linked together via peptide bonds, the amino acids are referred to as ______ and the formed polymer is referred to as a polypeptide

A

Residues

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24
Q

What determines the properties of an amino acid?

A

It’s R group

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25
Q

If the proteins were synthesized by free ribosomes (located in cytosol), where do they go?

A

Remain in cytosol or go to various organelles

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26
Q

Examples of proteins that remain in the cytosol?

A

Enzymes involved in glycolysis

Structural proteins of the cell (actin and tubulin)

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27
Q

How do some proteins know that they are targetted towards specific organelles?

A

There are special sequences on the protein

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28
Q

True or false: some proteins are flat and linear

A

False

All proteins take on a three-dimensional, folded shape

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29
Q

In order to function, all proteins require what?

A

Proper folding

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30
Q

Free proteins become folded and functional in the cytosol. Where do bound proteins become folded and functional?

A

The ER

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31
Q

What determines function of a protein?

A

It’s tertiary structure / how it’s folded

32
Q

Why is an alpha helix a spiral?

A

Hydrogen bonds between the carbonyl of the carboxyl group of one amino acid residue and the amide of the amino group of another amino acid residue four positions away

33
Q

The alpha helix is coiled, why is this important in terms of the protein’s properties?

A

Since it’s coiled, the R-groups stick out

This det how it folds (its tertiary structure) and thus det the properties of the protein

34
Q

What is the structure of beta-pleated sheets?

A

Parallel protein strands with hydrogen bonds formed between the carboxyl and amino groups of adjacent strands

35
Q

Where are the R-groups in the beta-pleated sheets?

A

Extend above and below

36
Q

What are the two secondary structures of proteins?

A

Alpha helix

Beta helix

37
Q

Why determines whether or not a protein folds into an alpha helix or a beta-pleated sheet?

A

The interactions between the components of a protein’s backbone

38
Q

When does protein folding occur?

A

Spontaneously as the polypeptide leaves the ribosome

39
Q

What are some cellular mechanisms that assist in protein folding?

A

Molecular chaperones

Chaperonins

40
Q

How do molecular chaperones work?

A

Small, monomeric proteins

Bind to hydrophobic regions of the nascent polypeptide and prevent incorrect folding just long enough for the correct structure to form

41
Q

How do chaperonins work?

A

These are large complex polymers

Form isolation chambers where a single protein (in the middle of forming) is sequestered away so it can fold without interference

42
Q

What are quaternary structures?

A

The association of diff polypeptide subunits to form the final, functional structure

43
Q

What is included in the endomembrane system?

A

Nuclear envelope

ER

Golgi apparatus

Lysosomes

44
Q

What is the importance of the endomembrane system?

A

Allows for the cell to compartmentalize diff areas to serve diff functions

45
Q

Once bound ribosomes produce proteins, where do those proteins go?

A

Goes through the lumen of the ER for further processing (including protein folding)

46
Q

How do certain proteins know that they are supposed to go through the ER and not just into the cytosol?

A

mRNAs that encode proteins destined for the endomembrane system include a special sequence at the beginning

47
Q

Describe the process in which bound ribosomes synthesize proteins in the ER

A

Special signal sequence synthesized by the ribosome

SRP binds to the signal sequence of the growing polypeptide and halts translation

SRP binds to SRPR (SRP receptor) on the ER membrane

SRP brings ribosome to transmembrane channel on ER

SRP dissociates

Protein synthesis resumes, polypeptide chain is threaded thru the ER (via the channel)

Inside lumen, signal sequence is removed and it can now be folded

48
Q

What are vesicles?

A

Small membrane-bound compartments that bud off of the ER

Contain proteins that have been translated by bound ribosomes

49
Q

What is glycosylation?

A

Addition of one or more carb chains to a protein

50
Q

Where does glycosylation take place?

A

The lumen of the ER

Golgi apparatus

51
Q

What kinds of proteins take part in glycosylation?

A

Most secreted and membrane-bound proteins

52
Q

What is an advantage of glycosylation?

A

Helps contribute to protein stablity, folding, and even cell-to-cell recognition

53
Q

How does the cell proteins from the ER to the golgi apparatus?

A

Vesicles that pinch off of the ER fuse with the Golgi and deposit their contents into the lumen of the Golgi apparatus

54
Q

What does the golgi apparatus do?

A

It modifies and ships ER products in new vesicles

55
Q

True or false: all proteins from the golgi apparatus will be secreted from the cell

A

False

Some will stay in the golgi apparatus/ER. Others will go to the cell membrane, or to other organelles

56
Q

What kinds of proteins are secreted from the cell?

A

Antibodies

Hormones

Enzymes

57
Q

What kinds of proteins will be shipped to the cell membrane?

A

Porins

Receptors

58
Q

What is the leading hypothesis as to how these proteins are sorted as they leave the Golgi?

A

Proteins are tagged with specific markers that target them to diff regions of the cell

These tags, when added to proteins, bind to receptors on the internal membrane of the Golgi and form transport vesicles

59
Q

What happens once the tagged vesicles reach their destination?

A

Once at the destination, the vesicle fuses with the membrane/organelle. This allows for the release of soluble proteins or the embedding of transmembrane proteins

60
Q

How is the vesicle able to bind with the membrane?

A

It also has a phospholipid bilayer

61
Q

How are vesicles able to travel to their destinations?

A

Motor proteins attach to transport vesicles and walk from negative to positive along polar microtubules

62
Q

Microtubules are part of a larger network. What is this network called and what is its purpose?

A

Cytoskeleton

Dense network of fibers that help maintain and change cell shape

63
Q

What are microtubules?

A

Polymerized tubulin proteins that form long fibers which stretch thru the cell and act as roadways

64
Q

Give two examples of motor proteins

A

Kinesin

Dynein

65
Q

True or false: the transport of vesicles to their various destinations does not require energy

A

False

66
Q

Where are soluble proteins synthesized and folded?

A

In cytosol in free ribosomes

Some stay there others are transported afterwards

67
Q

Proteins destined for membrane bound organelles required for fatty-acid metabolism (i.e. mitochondria, chloroplasts, and peroxisomes) are synthesized where?

A

Free ribosomes

68
Q

Are proteins synthesized in free ribosomes folded before transport to the organelles or after transport?

A

Both

69
Q

Describe the aquaporin structure

A

4 protein subunits (monomers) that together form the tetrameric aquaporin channel

Each subunit contains membrane-spanning alpha-helixes that form a central pore; each monomer contains an independent water pore; a central pore in the middle

70
Q

Is the tetrameric aquaporin channel its tertiary or quaternary structure?

A

Quaternary

71
Q

Why is the aquaporin’s structure important for its function?

A

The independent water pores (in each monomer) allow water to move through in either direction

Centralized pore allows several water molecules to move simultaneously thru

72
Q

True or false: like the sodium-potassium pumps, aquaporins also undergo changes in shape in order to transport water

A

False

Each water molec forms specific hydrogen-bonds with hydrophilic amino acid side groups that line the core of the monomer.

This displaces nearby water molecules that pass ahead thru the channel

73
Q

Describe the structure of prok membrane pores compared to euk pores

A

Beta sheets form a barrel with hydrophobic exterior and hydrophilic interior

74
Q

True or false: those beta-sheet barrels are only found in prok membranes

A

False

Also found in mitochondria and chloroplast membranes

*Further evidence of prokaryotic ancestry

75
Q

What causes cystic fibrosis?

A

Genetic mutation that leads to the malfunction (misfolding) of a cystic fibrosis transmembrane conductance regulator (CFTR) ion channel protein. Causes accumulation of thick mucus in the lungs

Bio 1A03 (18 decks)

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