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HTHSCI 1I06 > Proteins > Flashcards

Proteins Flashcards

1
Q

Proteins

A

-are the information
-they tell your body what to do
-only a small amount of genes code for them
-virtually make up everything

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2
Q

Protein examples

A

Receptors, enzymes, antibodies, hormones

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3
Q

Protein composition

A

-amino acids joined together by peptide bonds
Amino acids
-an amine group
-a carboxylic group
-a side chain (R)

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4
Q

Formation of a peptide bond

A

-carboxyl group of one amino acid binds with the amino group of the other AA
-in doing so, H2O is removed (condensation/dehydration reaction)

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5
Q

How to break peptide bonds

A

Hydrolysis (the breaking of water)
-adding water to break bond

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6
Q

Polypeptides

A

Peptide chains of 3 or more AAs that have not undergone processing (once processed, they are known as proteins)

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7
Q

How many amino acids does are body make naturally

A

22

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8
Q

Conditional stop codons

A

UAG and UGA are only stop codons if the conditions are right

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9
Q

Amino Acids (Translation regulation)

A

Location: Cytoplasm
Possibility: Rare

Pyrrolysine (Pyl) is encoded by UAG
-the polypeptide chain never actually stops growing even though UAG is a stop codon

Selenocysteine (Sec) is encoded by UGA
-When selenium is not present, UGA does not work as a STOP codon, so the end result is a non functional-truncated protein
-this occurs in mercury poisoning

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10
Q

Where are proteins made?

A

Usually made on the endoplasmic reticulum (not in nucleus)

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11
Q

Membrane bound ribosomes (Proteins)

A

-most common
-proteins released from membrane bound ribosomes are used in the plasma membrane or are released from the cell via exocytosis

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12
Q

Free ribosomes (proteins)

A

-proteins released from the free ribosomes are released into the cytosol and are used within the cell

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13
Q

Where could things go wrong?

A

Anything made in the nucleus (like DNA), is extremely hard to act on. Since protein synthesis does not happen in the nucleus, it’s easier to manipulate.

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14
Q

How long does it take to make proteins? (eukaryotes)

A

HOURS TO DAYS
Transcription and translation happen everywhere (in and out of nucleus) - takes forever

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15
Q

How long does it take to make proteins? (prokaryotes)

A

MINUTES TO HOURS
Transcription and translation happen at the same time in the cytosol - way faster

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16
Q

Where do we have prokaryotes

A

Bacteria in the gut

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17
Q

Polysomes (translation regulation)

A

Location: Cytoplasm
Possibility: Not rare
Polysomes are a cluster of ribosomes that translate mRNA at the same time. This parallel processing speeds up translation.

multiple ribosomes=multiple proteins

Way more proteins can be formed because they are each forming their own polypeptide.
(works on prokaryotes and eukaryotes)

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18
Q

Ribosomal math

A

60+40=80 and 30+50=70
-these values have the unit of Svedbergs, which relates to their rate of sedimentation (how long it takes for them to settle out from other materials) in a centrifuge.
-rate of sedimentation largely depends on surface area
-total surface area is reduced by combining the two subunits; there is less exposed space where the 2 subunits meet

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19
Q

Tetracycline (translation regulation)

A

Location: Cytoplasm
Possibility: Not super rare, only applicable to bacterial illness, ex; could be used for h pylori bacteria

START
-Tetracycline binds on the small subunit (30S) at the A (Aminoacyl) site to prevent the tRNA from binding there
-Thus, this stops from translation from occurring

END
-If the Tetracycline cant compete enough with A-Site, it will persist and Inhibit release factors R1 and R2 from termination. This way protein synthesis will also be inhibited.

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20
Q

Use of tetracycline

A

Prevents bacteria in the body from translating new proteins. Thus, they will die. It is administered as an antibiotic used to fight infection caused by bacteria

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21
Q

How to get rid of tetracycline

A

-Efflux proteins (transport proteins) transport antibiotics out of the cell. Thus, they can no longer bind to their ribosome
-Inactivation//Degradation enzymes in the cell can denature or degrade the antibiotic. Thus they no longer work
-The bacteria itself can produce “mimicked” elongation factors which can outcompete tetracycline at the A site

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22
Q

Epigallocatechin- gallate (EGCg)

A

found in green tea, can inhibit the efflux proteins. SO
EGC= more tetracycline= more antibiotic= less bacteria

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23
Q

Primary protein structure

A

Peptide sequence and the identity of the ends

N Terminus (AMIDE):
-“Target Signal”; Tells us where the
protein will go
-Determines how long the peptide can last
before it degrades “N-end rule”

C-Terminus (CARBOXYL)
-“Stored Signal”; Tells us where the
protein is stored
-keeps the protein in the ER and prevents it from leaving
-Adding a lipid anchor allows it to enter the membrane without a transphobic domain

24
Q

C terminus (processing regulation)

A

When you add a lipid anchor to the C terminus, the protein can enter a membrane without having a transmembrane domain (when proteins have the transmembrane domain, this is all they need to be anchored into the membrane)

25
Q

N terminus (processing regulation)

A

N-LINKED GLYCOSYLATION
-The addition of a sugar molecule to N terminus
-Proteins are now soluble and membrane bound
-Called Glycoproteins
-Glycoproteins can now travel to: Golgi
apparatus, lysosomes, plasma membrane, extracellular space
-allows protein to go anywhere

26
Q

What happens if no N-Linked Glycosylation?

A

Some cancer drug, tunicamycin has an
EFFECT of reducing N-linked glycosylation which prevents some proteins from being transported to the golgi apparatus

27
Q

Secondary protein structure

A

FOLDING AND COILING
-Alpha helix
-Pleated sheet

Outside of the protein
-Polar side chains
-They can interact with water (water is
polar)

Insider of the protein
-Non polar side chains are buried on the
inside
-This forms hydrophobic core

Depending on the function of the protein, these features come into play

28
Q

Tertiary protein structure

A

Interactions between the amino acid side chains on the molecule

The side chains on each of the amino acids interact and give the structure its 3D shape. These same side chains add stability

** environment defines the final shape

-More permanent than secondary structure

29
Q

Quaternary protein structure

A

Interaction between multiple polypeptides

-If 2 identical polypeptides bind together, it’s called a dimer

-Once you have an interactions between 21 or more polypeptides you have have a #-mer

30
Q

Structure of proteins…

A

determines FUNCTION

31
Q

Main function of the golgi apparatus

A

Process and Target fully matured proteins to the membrane for secretion
-Proteins packaged into Lysosomes: Used for digesting waste products
-Proteins destined for release: Packed in vesicles that release their contents as
soon as they fuse with the cell membrane OR packed In a vesicle which fuse and release their contents ONLY under the control of a specific signa

32
Q

Prions

A

Prions are misfolded proteins (specifically PrP proteins) with the ability to transmit their misfolded shape onto normal variants of the same protein. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals.

33
Q

Creutzfeldt-Jacob disease (CJD)

A

Caused by prions
A set of diseases—called scrapie in sheep, Creutzfeldt-Jacob disease (CJD) in humans, and bovine spongiform encephalopathy (BSE) in cattle

Creutzfeldt-Jacob Disease (or Mad Cow Disease or bovine spongiform encephalopathy) causes a fatal degeneration in the brain and spinal cord in cows. Humans can’t get this disease, although they can get “variant Creutzfeldt-Jacob Disease”.

34
Q

Stanley B. Prusiner

A

Won the nobel prize in physiology or medicine 1997, for his prion discoveries
AKA MR. PRION

35
Q

Prion comes from…

A

Protein infectION

36
Q

Proteins must be…

A

modified before they are used

37
Q

Protein misfolding (processing) (up regulation)

A

How to fix if there is an accumulation in the cytosol
-the transcription of genes that code for chaperon proteins
-Chaperons helps refold proteins

How to fix if there is an accumulation in ER
-This activates the Unfolded Protein Response
-This is when pre-existing enzymes (OR the transcription of genes that encode for enzyme turns on) will degrade the misfolded proteins

If the situation is beyond control: Apoptosis - programmed cell death

38
Q

Protein misfolding (down regulation)

A

Protein Misfolded → Change of Shape → This change in shape leads to loss of…
-Loss of important function
-Gain of an unwanted function
-Aggregation with other proteins which may cause both loss of function and the gain of unwanted function (protein aggregates cause disease such as neurodegeneration)

Protein that is misfolded that is retained in the ER has a big effect, even though perhaps it would function perfectly normal if it reached the plasma membrane

-Chaperons could be using too much of the cells energy, which could lead to down regulation

39
Q

What monitors the amount of misfolded proteins

A

The body’s cells

40
Q

Edman degradation (sequencing)

A
  1. Digest proteins into progressively small
    fragments
  2. Phenyl isothiocyanate is added to the
    N-terminal of the protein
  3. The N terminal AA is cleaved (we take this
    AA and view it)
  4. The AA is then identified by
    chromatography
  5. This process is repeated for each amino
    acid
41
Q

Mass spectrometry (sequencing)

A
  1. Two different enzymes, which cut diff AA, digest, vaporize and ionize the sample and peaks are detected.
  2. Overlapping sequence are recognized by the computer and the sequence is inferred
42
Q

Immunochemistry (identification)

A

Slice of a tissue, adhere it to a glass slide, then view the colour using light microscopy

  1. A primary antibody is used that specifically detects your target. The antibody sticks to the target protein
  2. Amplify the signal by adding a labelled antibody (something you can see called a reporter) that finds anything from the same species in which your antibody was generated. Typically, many antibodies stick to one primary antibody (amplifying it)
  3. Add an enzyme that activates or changes the color of the secondary antibody.
  4. Look under the microscope and see your protein target highlighted

SHOWS: Same as a western blot but instead you identify a proteins presence and location in tissue samples

43
Q

Western Blot (identification)

A

Process;
1. Purify Protein sample: lyse the cells in a buffer that has a
detergent
2. Gel Electrophoresis: Now you separate the protein sample
based on molecular size
3. Membrane Transfer: gel to paper
4. Blocking: On the paper, you block non specific activity in
your sample that could interact with the next step.
5. Apply a specific antibody that sticks only to the target protein.
After a brief wash, add a secondary antibody that will stick only to the first antibody. This second antibody has a chemical marker attached so you can see it.

Perform Analysis; Use chemiluminescent detection to analyze the bands and see how much of the protein is present.

44
Q

ELISA (identification)

A

Inverse of a western blot
Determining the presence of antibody
Ex; if person does not have the virus, they will not have an antibodies present that bind to the antigen (a toxic substance)

45
Q

Computational Method such as BLAST
(identification)

A

Will identify the sequence for you

46
Q

Organ bath (isolated tissue bath)

A

Test how much does a tissue respond when a drug is added, how much antagonism is observed when a drug and its antagonist are added

47
Q

Cell line assays, ELISA, western blot

A

Test if there is a specific protein in these cells, and how much of the protein is expressed

48
Q

Biosensors and tags

A

Test levels of cAMP or other messengers changing

49
Q

Using molecule with known effects

A

Test does a a compound X behave the same way as a compound with known effect

50
Q

(insert compound) assay

A

Test levels of (insert compound) that are present in the sample

51
Q

Genomic control points

A

Direct DNA interaction, transcriptional control, RNA processing, RNA transport, Translation, RNA degradation, protein activity

52
Q

Protein coding genes

A

makes up 1.5% of total human genome

53
Q

Theodor H.E Svedberg

A

Swedish chemist, came up with ribosome ultracentrifugation (Svedberg)

54
Q

1 svedberg =

A

10^-13 seconds (or femtoseconds)

55
Q

Tetracycline inhibits…

A

the release factors RF-1 and RF-2

56
Q

Christian Anfinsen

A

theorized that the primary structure should fully determine the tertiary structure in his acceptance speech for the 1972 Nobel Prize in Chemistry (thermodynamic hypothesis)

57
Q

Camillo Golgi

A

Proteins that are secreted need to be modified before they can be released. Much of this occurs in the Golgi, the structure named after Camillo Golgi who first observed these using a light microscope in 1897.

Golgi shared a Nobel prize in 1906 with Santiago Ramón y Cajal for their studies on the structure of the nervous system.

HTHSCI 1I06 (5 decks)

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