Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

PHGY 170 > Module 2 > Flashcards

Module 2 Flashcards

1
Q

what is the function of the nucleus?

A
  1. allow DNA to be replicated and transcribed into mRNA when needed
  2. regulates which molecules can access DNA and separates DNA from other cell compartments
  3. keeps DNA organized and prevents it from being damaged
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what are the 6 components of the nucleus?

A
  1. nuclear envelope
  2. nuclear pores
  3. nucleoplasm
  4. nucleolus
  5. nuclear matrix
  6. chromosomes and chromatin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

what is the function of the nuclear envelope?

A

it is a double layer membrane that controls what molecules have access to the nucleus. the outer membrane is connected to the ER

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

what is the function of the nuclear pores?

A

they regulate molecular traffic in and out of the cell, nuclear pore complexes (NPCs) regulate the large molecules (mRNA and proteins) and small molecules such as water and oxygen can pass freely

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

what is the function of the nucleoplasm?

A

it serves as a suspension substance for the nucleus contents, it is made up of water and contains dissolved molecules and ions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what is the function of the nucleolus?

A

it stores the DNA that encodes for rRNA and creates rRNA and assembles them into ribosomal subunits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what is the function of the nuclear matrix?

A

it provides the scaffold to maintain the shape and structure of the nucleus and it is a network of filaments within the nucleoplasm that helps organize chromosomes into compartments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

what is the function of chromosomes and chromatin in the nucleus?

A

DNA is organized and stored in chromatin which make up chromosomes and they are located in different defined areas of the nucleus and some areas will be actively transcribed into mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what are the five levels of DNA packaging?

A
  1. DNA double helix
  2. nucleosomes
  3. chromatin fibre
  4. chromatin looped domains
  5. heterochromatin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what is the DNA double helix in terms of DNA packaging?

A

it is the lowest level of DNA packaging and it is made up of complementary base pairing of hydrogen bonding, a phosphate backbone and a 5 carbon sugar (pentose). it is two strands that run antiparallel

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

what is a nucleosome in terms of DNA packaging?

A

it is the second lowest level of DNA packaging. DNA is wrapped around histones twice to form a nucleosome. 8 core histones form a nucleosome and it is called an octamer. there are three components of a nucleosome:
1. histone H1 - protein that pins DNA to the histone octamer
2. linker DNA - sequence that connects nucleosomes together
3. core DNA - about 200 base pairs wrapped around the octamer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what is a chromatin fibre in terms of DNA packaging?

A

it is the third level of DNA packaging and it is a string of nucleosomes that are coiled into a spiralling fibre which forms a helical structure. it shortens the DNA by 42 folds and has a diameter of 30-40nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

what are chromatin looped domains in terms of DNA packaging?

A

it is the fourth level of DNA packaging and it is when chromatin fibres form into loops with an average length of 300nm. it shorts the DNA by 750 folds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

what is a heterochromatin in terms of DNA packaging?

A

it is the fifth level of DNA packaging and it is chromatin looped domains folded into lengths of approximately 700nm. it is hyper condensed DNA present in inactive regions of chromosomes during interphase. during cell division (mitosis/meiosis), they condense into entire chromosomes (1400nm)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what does euchromatin refer to?

A

it refers to levels 1-4 of DNA packaging which is active and easily accessed by proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what is the endomembrane system?

A

system processes and transports cargo throughout the cell. cargo refers to protein, lipids and other macromolecules.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what is exocytosis and endocytosis?

A

exocytosis:
process of moving cargo out of the cell and it uses the exocytic pathway (directs contents of secretory vesicles to the plasma membrane)
endocytosis:
process of moving cargo into the cell and uses the endocytic pathway (absorbs molecules by engulfing them

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what are the five organelles that make up the endomembrane system?

A
  1. nucleus
  2. golgi apparatus
  3. transport vesicles
  4. rough ER
  5. smooth ER
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what does the nucleus do in terms of the endomembrane system?

A

it is connected to the ER cisternae by the outer layer of the membrane and nuclear pores connect the envelope with the ER so some molecules can freely pass

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

what does the golgi apparatus do?

A

it is involved in protein modification and transport. it labels proteins and other molecules with different signals which directs them to different locations in the cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what do transport vesicles do?

A

they are used to deliver cargo between organelles in the cell and they move proteins from the ER to the golgi apparatus

22
Q

what does the rough ER do?

A

it has ribosomes and is the site of protein translation and some modifications. it produces proteins that must go to another organelle (note free ribosomes in the cystol produce proteins that must stay there)

23
Q

what does the smooth ER do?

A

it is responsible for synthesizing lipids (phospholipids and steroids), it is the location for carbohydrate metabolism (converts glucose 6 phosphate into glucose) and it regulates calcium ion concentration in muscle cells

24
Q

what is vesicle mediated transport?

A

it is when small vesicles bud off from lipid membranes of organelles or the cell as a whole with the purpose of transporting cargo. once the vesicle reaches its final destination it fuses with the other lipid membrane to deposit cargo

25
Q

what are the three different golgi networks?

A
  1. cis
  2. medial
  3. trans
26
Q

what does the cis golgi network do?

A

it receives proteins from the ER

27
Q

what does the medial golgi network do?

A

its where oligosaccharides are added to proteins, where existing oligosaccharides are modified and is where sugar groups can be added to lipid (one sugar modification is the addition of mannose 6 phosphate (M6P))

28
Q

what does the trans golgi network do?

A

it performs the final packaging to send materials to different organelles and it sorts cargo cargo to go to specific destinations. some proteins from the ER have an ER retention signal so proteins are packed up with COPI coating proteins and recycled back to the ER. additionally M6P receptors in the network recognize proteins with M6P tags and send them to the lysosome to be degraded

29
Q

what do endosomes do?

A

they hold content coming into the cell and they sort and send cargo to the correct final locations

30
Q

what do lysosomes do?

A

they are a waste disposal and they break down proteins, lipids and sugars into their molecular building blocks

31
Q

what do peroxisomes do?

A

they break down molecules that generate hydrogen peroxide as a byproduct. they neutralize the hydrogen peroxide to prevent cell damage

32
Q

what are signal sequences?

A

they are used to target a protein for different areas of the cell. organelle target proteins have a target signal or are tagged in the endomembrane system. proteins targeted for the cells cytosol lack signal peptides as free ribosomes translated them already in the cystol so a sequence is not needed. proteins that are secreted out have a signal sequence specific for cargo in the vesicles

33
Q

explain translocation for proteins that are being translated into the ER

A
  1. during translation a signal sequence is translated as part of the protein
  2. after the signal sequence emerges from the ribosome while it is translating SRP binds pausing translation (GTP also binds as energy is need)
  3. during the pause is translation the ribosome docks onto the ER membrane by SRP interacting with an SRP receptor and a complex called the translocon (facilitates the translocation into the ER)
  4. once in the ER translation restarts and the signal peptide sequence is cleaved off by translocase
  5. once translation is finished the protein is folded in the ER lumen and is destined to be soluble
34
Q

explain translocation for proteins that are being embedded into the membrane

A
  1. signal sequence called the transmembrane signal anchor sequence is translated
  2. the transmembrane signal sequence becomes embedded into the lipid bilayer and will be the transmembrane domain of the protein once it is functional and mature
35
Q

once a protein is in the lumen in the ER what modifications occur?

A
  1. addition of proteins, sugars, lipids and functional groups which can change the final target location, structure or function
  2. cutting of the peptide bonds in proteins
  3. the ER signal sequence which is typically on the N terminus is removed
36
Q

what are the two enzymes involved in protein folding?

A
  1. protein disulphide isomerase (PDI)
  2. chaperonins
37
Q

what does protein disulphide isomerase (PDI) do?

A

it is an enzyme involved in protein folding and it helps forms bonds disulfide bonds between the thiol groups and the side chains of cysteine which stabilizes and helps the protein fold properly

38
Q

what does chaperonins do?

A

they are enzymes involved in protein folding and they help fold polypeptides by binding hydrophobic patches. one example is BiP which helps fold to form a hydrophobic interior of mature proteins (once folded BiP can no longer access the patches)

39
Q

what is a peptide bond and how is it formed?

A

it is the bonding of a carboxylic acid group and amino group through a dehydration reaction (water released). a polypeptide has an N terminus and C terminus and the amino acids can rotate around bonds formed as the bond is a rigid plane

40
Q

explain the levels of protein structure

A
  1. primary - linear amino acid sequence
  2. secondary - alpha helix or beta sheets
  3. tertiary - 3D structure (chaperones needed and disulfide bonds formed)
  4. quaternary - multiple proteins assembled into a complex (proteins called subunits if they cannot exist outside the complex)
41
Q

what is the difference between alpha helix and beta sheets?

A
  1. alpha helix - tight coil that forms H bonds between the backbone of every 4th amino acid
  2. beta sheets - planes formed between rows of amino acids with H bonds between backbones (parallel N to C and N to C for rows, antiparallel direction switches)
42
Q

what is a domain?

A

a domain is the basic building blocks of a protein structure. some domains have clearly defined functions associated with them and they are discrete structural units that is assumed to fold independently

42
Q

what are factors affecting protein conformation?

A
  1. temperature
  2. pH
  3. presence of ions like calcium or magnesium (can alter folding)
  4. protein modification or binding to other proteins
  5. chemicals
43
Q

what are the two types of chemical protein modifications?

A
  1. covalent (long lasting) - disulfide bonds, addition of lipids or sugar structures. adding phosphate groups, methyl groups or acetyl groups can inactive or activate proteins or change how they interact with other proteins
  2. non covalent (short) - proteins interacting with each other in binding sites or small molecules like oxygen, calcium or magnesium binding transiently
44
Q

what are the three types of coating proteins?

A
  1. COPII - ER uses to shuttle to the protein
  2. COPI - proteins that are returned to the ER
  3. clathrin - used by golgi to form vesicles for exocytosis, endocytosis and transport to the endosome
45
Q

explain the process of vesicle mediated transport

A
  1. cargo selection - signal sequences and receptors on the membrane gather the required cargo to the area of the membrane that will turn into a vesicle
  2. coat proteins - coat proteins present in the cytosol bind to the area on the membrane that will become the outside of the vesicle and they cause receptor and other proteins with signal sequences to cluster on the surface of the membrane
  3. budding - coat proteins interact with cytosolic adaptor proteins so a mesh like network is formed to pull the membrane into a bulging shape that will become the vesicle
  4. scission - dynamin pinches off the formed vesicle from the membrane to release it into the cytoplasm
  5. uncoating - coat and adapter proteins disassemble uncoating the vesicle (allows cell to reuse)
  6. transport - vesicles attach to motor proteins in the cytosol allowing for movement throughout the cell along the microtubules of the cyoskeleton
  7. tethering - once at the destination tether proteins are used to attach to a receptor on the acceptor membrane which allows the vesicle to be close enough to try to find the correct acceptor target protein
  8. docking - if the target protein is found the vesicle docks on the surface
  9. fusion - the lipid membrane and acceptor membrane become continuous and pairs of v-SNARES and t-SNARES interact allowing the cargo to be discharged
  10. disassembly - the remaining tether and fusion proteins and other receptors disassemble and the cargo is released into the accepting organelle
46
Q

what are the stages of exocytosis?

A
  1. proteins are translated in the ER
  2. post translational modification and folding occurs in the ER
  3. vesicle mediated transport between the ER and golgi (other macromolecules may be produced in their respective location and sent to the golgi)
  4. further modification and packaging by the golgi occurs
  5. cargo constitutively secreted or undergo regulated secretion
47
Q

what are the two ways exocytosis is regulated?

A

it is cargo and cell dependent
1. constitutive secretion - uncontrolled and always happening (collagen)
2. regulated secretion - requires a signal to stimulate the cell and cells often have specialized storage granules that are released in response to specific signals (neurotransmitters)

48
Q

explain how the formation of the early endosome

A
  1. endocytic vesicles containing cargo and cargo receptors form from the plasma membrane (clathrin initiations the invagination of the plasma membrane)
  2. clathrin disassembled by cytosolic proteins (auxilin and Hsc70) causes the vesicles to transport and fuse with the early endosome
  3. vesicles with M6P receptors and cargo (proton pumps, lysosomal integral membrane proteins (LIMPs), hydrolases with M6P modifications) fuse with the endocytic vesicle forming the early endosome
  4. proton pumps begin acidifying the endosome lumen
  5. the acidicty of the early endosome (pH 6.4-.6.8) causes cargo receptors and M6P receptors to change shape releasing their cargo
49
Q

what is the early endosome made up of?

A

it is made of vesicles from the plasma membrane and vesicles from the trans golgi network

50
Q

how is the late endosome formed?

A
  1. the early endosome matures
  2. proton pumps on vesicles from the trans golgi network lowers the pH (5.0-6.0)
  3. continued recycling of receptors and cargo is performed
  4. cargo is degraded as the pH drops which provides the building blocks for repurposing
51
Q

how is the lysosome formed?

A
  1. the pH is below 5 leading to enzymes included proteases to activate leading to the conversion to the lysosome
  2. a protective glycocalyx layer of LIMPs and glycosylated proteins from to prevent the lysosome from degrading itself (protects from digestion by most proteases)

PHGY 170 (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions