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Biol 130 > Final Exam > Flashcards

Final Exam Flashcards

1
Q

Who invented the microscope

A

Hans Lippershey / Hans and Zachairas Janssen

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2
Q

Who is credited for the term “cell”

A

Robert Hooke

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3
Q

Who is considered the father of biology

A

Antonie Van Leeuwenhoek

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4
Q

Rank the following in order of size, smallest to largest
1. Organelles
2. Molecules
3. Cells
4. Atoms

A

4, 2, 1, 3

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5
Q

Who discovered the nucleus

A

Robert Brown

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6
Q

Who discovered that all plant tissues are composed of cells

A

Matthias Schleiden

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7
Q

Who discovered that all animal tissues are composed of cells, respectively to Schleiden’s work

A

Theodor Schwann

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8
Q

Who is most responsible for cell theory

A

Theodor Schwann

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9
Q

What are the three components of cell theory

A
  1. all organisms consist of one or more cells
  2. the cell is the basic unit of structure for all living things
  3. cells only come from pre-existing cells
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10
Q

What is the difference between a fact and the scientific method

A

facts are concrete, non negotiable, and do not evolve
the scientific method uses what is believed to be true, but can evolve over time with further observations

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11
Q

What is the scientific method

A
  1. make observations
  2. create a hypothesis
  3. make predictions based on the hypothesis
  4. make further observations to test the hypothesis using controlled experiments
  5. interpret results
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12
Q

What is a theory

A

A critically tested hypothesis under many conditions that becomes widely accepted by science
- the “solid ground” of science

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13
Q

What is more solid than theory

A

Laws (ie. gas laws, gravity, etc.)

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14
Q

What are the three strands of cell biology

A

biochemistry, genetics, and cytology

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15
Q

All of the discoveries previously mentioned by scientists are considered in which branch of cell biology

A

cytology

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16
Q

What is histology

A

the study of cells under microscope

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17
Q

What is SEM vs TEM in electron microscopy

A

S=surface (images of the surface of cells)
T=through (scans through the middle of cells)

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18
Q

What are the basic properties of all cells

A

atoms, molecules, macromolecules, organelles

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19
Q

Where are the components of the cell enclosed

A

in the plasma membrane

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20
Q

What is the central ‘genetic program’ used

A

The central dogma

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21
Q

What is it called when cells acquire/use energy

A

bioenergetics

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22
Q

What is it called when cells carry out chemical reactions

A

cellular metabolism

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23
Q

What are the mechanical activities within cells

A
  • transport of materials in/out
  • assembly/disassembly of structures
  • motility/movement
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24
Q

What are examples of signal responses in cells

A

move away/toward stimuli, respond to hormones, growth signals, etc.

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25
Q

What is the order of the central dogma

A

DNA synthesis (replication), RNA synthesis (transcription), and protein synthesis (translation)

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26
Q

What are the two classes of cells

A

Prokaryotes - no nucleus
Eukaryotes - nucleus

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27
Q

What are the two domains of prokaryotes

A

bacteria and archaebacteria

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28
Q

What is the only bacteria without a cell wall

A

mycoplasma

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29
Q

Are most bacteria capable of carbon fixation

A

Yes, most can conduct photosynthesis

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30
Q

What is the most diverse cell group

A

prokaryotes - their most common shape being rod-shaped (“generic” bacterial cell)

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31
Q

Instead of a nucleus, what do prokaryotic cells have

A

1 long strand of DNA clustered together in the middle of the cell

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32
Q

What do prokaryotes and plants have in addition to the plasma membrane

A

a cell wall

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33
Q

Which type of cell has one large vacuole

A

plant cells

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34
Q

What are the four groups of eukaryotes

A

protists, fungi, plants, and animals

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35
Q

How are protists and fungi different from plants and animals

A

protists and fungi are mainly unicellular, plants and animals are multicellular

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36
Q

Which type of eukaryote are heterotrophs

A

plants

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37
Q

What is the difference between heterotrophs and autotrophs

A

hetero - self feeding
auto - have to digest plants to gain nutrients and organic compounds

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38
Q

What is the difference between the terms cytoplasm and cytosol

A

cytoplasm = everything within the plasma membrane, including organells
cytosol = just the fluid component

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39
Q

What is the endomembrane system

A

internal membranes that are either in direct contact or connected via transfer of vesicles

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40
Q

What are the components of the endomembrane system

A

nuclear envelope/membrane, ER, Golgi, lysosomes, vacuoles

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41
Q

Which organelles have their own genomes

A

mitochondria and chloroplasts

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42
Q

What does the cytoskeleton do

A

regulate cell shape and movement of materials within the cell

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43
Q

Where are the different locations of transcription and translation in the cell

A

transcription - in the nucleus
translation - at the ribosomes in the nucleus

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44
Q

What is the secretory pathway

A

proteins from the ER are transported out to the Golgi, and transported out from the Golgi as vesicles to be secreted from the cell

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45
Q

What is the endocytic pathway

A

molecules brought into the cell via phagocytosis that joins together with vesicles to create lysosomes

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46
Q

Based on the previous question, in what pathway are lysosomes produced

A

endocytic pathway

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47
Q

What is endosymbiont theory

A

eukaryotes are believed to have evolved gradually, and early organelles originated from prokaryotes and were engulfed by the cell (mitochondria and chloroplasts)

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48
Q

Ancient eukaryotic cells were anaerobic, why is that

A

Without the presence of the mitochondria, the cell could not use oxygen, therefore survived anaerobically

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49
Q

Ancient eukaryotes were autotrophs, why is that

A

Without the presence of chloroplasts, the cells could not fix their own carbon atmospheres, and could not complete photosynthesis

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50
Q

What evidence supports this endosymbiont theory

A
  • mitochondria/chloroplasts are similar in size to bacteria
  • have double membranes
  • have their own ribosomes
  • have their own genomes
  • are genetically similar to the proposed “parent” bacteria
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51
Q

Is the organization of eukaryotic cells random

A

NO - this is ensured by the role of the cytoskeleton

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52
Q

Compare and contrast prokaryotes vs eukaryotes

A

prokaryotes: no nucleus, one naked strand of DNA, no membrane-bound organelles, cell wall, very small

eukaryotes: nucleus, membrane-bound organelles, multiple linear strands of DNA packed with histones, cytoskeleton, much larger

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53
Q

What is the model organism for transcription/translation

A

E. coli

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54
Q

What is the model organism for the cell cycle

A

yeast

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55
Q

What is the model organism for mammals

A

mice

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56
Q

What was the first genome to be sequenced

A

C. elegans (the worm)

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57
Q

What is the difference between ribose and deoxyribose sugars

A

ribose has a hydroxyl group on carbon 2, deoxyribose (think de-oxy), have only a hydrogen on carbon 2

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58
Q

What carbon connects to the base

A

carbon 1

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59
Q

What carbon connects to the phosphate group

A

carbon 3

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60
Q

DNA is found in helix and pleated sheet shapes, what are the shapes of RNA strands

A

RNA strands not confined to the continual helix shape, they are found in many winding shapes (still maintain base pairing, just in a less concrete fashion)

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61
Q

How does the shape of RNA matter

A

relates to the proteins and enzymes catalytic activities

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62
Q

Which DNA strand is the resulting mRNA strand identical to (minus T and U swaps)

A

the coding, non-template strand

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63
Q

Which direction is mRNA read vs built

A

read 3’-5’, but only built 5’-3’

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64
Q

What type of bond is found between base pairs

A

hydrogen bond

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65
Q

What kind of bond is found in the sugar backbone

A

phosphodiester bonds

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66
Q

[The following is prokaryotic transcription]

A

this is important because it differs from eukaryotic transcription

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67
Q

At the active site of the transcription, what type of activity is required

A

catalytic activity

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68
Q

Can all types of cells produce various strands of mRNA simultaneously on the same template?

A

Yes - this is possible for prokaryotes and eukaryotes

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69
Q

What is holoenzyme comprised of

A

sigma factor and core enzyme

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70
Q

Where is the active site on holoenzyme

A

at the intersection of the channels running through it

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71
Q

What is core enzyme

A

core RNA polymerase

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72
Q

What happens when RNA poly binds to sigma factor

A

holoenzyme is formed and the DNA strand can be transcribed into mRNA

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73
Q

How does transcription start

A

start of a gene is recognized and bound by RNA poly; this is called the promoter sequence (immediately upstream of the gene)

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74
Q

Which strand is the promoter sequence located on

A

the coding, non-template strand

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75
Q

What are the components of the promoter sequence

A

-35 box and -10 box are base sequences located upstream on the DNA strand that make up the promoter sequence

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76
Q

Where on the strand does transcription begin

A

the +1 site

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77
Q

How long are promoter regions

A

40-50 bps long

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78
Q

Can a strand have more than one complementary sigma protein

A

Yes - for example, many bacteria have multiple sigma proteins for slightly variant sequences on the strand

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79
Q

What is the role of sigma factor once it has bound to the promoter

A

unwind helix and begin transcription - this process is called initiation

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80
Q

What happens in the elongation period of transcription

A

sigma factor releases and transcription continues

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81
Q

What happens in the termination period of transcription

A

RNA poly reaches a termination signal in the DNA template strand

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82
Q

What does the termination sequence do to the mRNA strand

A

codes for RNA that folds back on itself and forms a hairpin structure, disrupting the transcription progress

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83
Q

How is RNA released from the DNA strand and accompanying enzymes

A

RNA poly releases it

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84
Q

Once transcription is done and the mRNA strand has released, what happens to the accompanying enzymes

A

they also release, sigma factor rebinds to RNA poly to reform holoenzyme, and it moves to repeat the process with a new strand

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85
Q

How is the template strand determined

A

Promoters are asymmetrical and bind to polymerase in only one direction, it depends on the gene

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86
Q

Which strands promoter does the enzyme bind to

A

the promoter will end up being on the non-template strand - it depends on the gene for which strand that will be, but the promoter is always the non-template

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87
Q

[The following is eukaryotic transcription]

A

this is important because it differs from the previous prokaryotic transcription

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88
Q

What is different about DNA in eukaryotes

A

deal with DNA packaging (not just 1 long strand)

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89
Q

What are the types of RNA poly in eukaryotes

A

RNA poly I, II and III

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90
Q

What is different about eukaryotic promoters

A

they are more diverse and complex: many include a sequence called a TATA box (recognized by RNA poly II), while RNA poly I & III interact with completely different sets of promoters

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91
Q

What is required by eukaryotic RNA polys

A

accessory proteins - eg. general transcription factors that assemble at the promoter alongside RNA poly

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92
Q

What must happen to mRNA AFTER transcription in eukaryotes, that doesn’t happen in prokaryotes

A

mRNA must undergo processing before leaving the nucleus

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93
Q

What are the three processing things that need to occur

A

addition of 5’ cap
addition of poly-A tail
removal of introns

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94
Q

How are eukaryotic genes “spread out” in comparison to prokaryotic genes

A

include introns and exons, making them much longer than just one solid sequence of coding DNA - the introns in eukaryotic mRNA has to be removed for it to be efficient

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95
Q

How are introns removed

A

via “splicing” at the expense of spliceosomes

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96
Q

What is the final outcome of DNA protein packing

A

chromatin

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97
Q

What are the proteins involved in DNA packaging

A

histones

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98
Q

Why is DNA wrapped around histones, what is the purpose?

A

allows for compact packaging and more strict regulation of gene expression

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99
Q

How is transcription initiated in eukaryotic cells

A

TATA box is recognized by a TATA-binding protein (TBP)

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100
Q

What is TBP

A

TATA-binding protein, which is a subunit of TFIID (transcription factor II D)

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101
Q

How are transcription factors classified

A

Here, we are only seeing transcription factor II’s, and they are classified by letter (in reality they are classified by both number and letter and perform a variety of tasks, were just only focused on one here)

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102
Q

What does the binding of TFIID allow for

A

distorts the helix (since it is part of initiation), and allows for more transcription factors (A, B, C, etc.) to be added on

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103
Q

When the transcription factors come together on the strand, what is formed

A

The transcription factor complex - this allows transcription to occur

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104
Q

What is the only constant TFII to be concerned about in this case

A

TFIID - recognizes the promoter region (TATA box)
- the rest of the TFII’s vary by promoter

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105
Q

What does the TBP do to the helix itself

A

creates bends in the structure to partially unwind the helix and begin transcription

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106
Q

Once the complex is formed and transcription can be initiated, what happens

A

The enzymes break off, a phosphorylated tail is added, and TFIID stays on the strand - mRNA is transcribed

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107
Q

When is the processing factors completed on mRNA

A

during transcription

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108
Q

What enzymes carry out the processing

A

enzymes that ride on RNA poly II

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109
Q

What are the processes?

A

capping, splicing, and polyadenylation

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110
Q

What is polyadenylation in simpler terms

A

addition of poly-A tail to the sequence

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111
Q

Why is the 5’ cap important

A

it is the recognition signal for translational machinery - the mRNA won’t be converted into protein without it

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112
Q

Why is the poly-A tail important

A

it protects the protein from degradation once translation begins

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113
Q

Why is splicing important

A

removes non-coding portions of the mRNA sequence, making the sequence entirely coding for a specific gene

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114
Q

What is the primary transcript of mRNA

A

the mRNA BEFORE the introns are removed

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115
Q

When does splicing occur

A

AFTER capping, but still during transcription

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116
Q

How are introns cued to be removed

A

each intron has a short sequence at the beginning and end of its sequence that code for removal

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117
Q

What happens when introns are removed

A

it folds up into a structure similar to a hairpin, and branch point A attacks the splice site on the opposing end of the intron, cutting the splice site and creating a loop. the hydroxyl group on the end of the exon that has just been cut is now exposed, coming together with the splice site on the other side of the intron, removing the intron entirely and fusing the two exons together.

118
Q

What happens to the lariat-shaped introns that have been removed

A

they degrade

119
Q

What are spliceosomes made of

A

5 snRNPS (small nuclear ribonucleic particles) + RNA + 100 proteins

120
Q

Where does the catalytic activity in snRNPs come from

A

the RNA

121
Q

Are spliceosomes ribozymes?

A

Yes - they are made up of both ribosomal and protein components, making them ribozymes

122
Q

What happens if introns are not removed

A

splice mutations occur and genetic malfunctions happen

123
Q

What is the advantage of RNA splicing

A

can create different proteins from the same gene/strand with the removal of different pieces

124
Q

What are the disadvantages of RNA splicing

A

more steps = more work
more steps = more opportunity for error (this creates greater opportunity for mutations or mistakes to occur)

125
Q

Only _______ mRNA is exported from the nucleus

A

mature

126
Q

What happens directly before mRNA can be exported

A

cap and poly-A tail are marked by proteins, a group of proteins called exon junction complex (EJC) binds to the mRNAs, and the mRNAs are finally able to be exported from nuclear pores into the cytosol

127
Q

What is the genetic code

A

considers all 64 possible codons and matches them with their according amino acids (only 20 amino acids)

128
Q

What is the most variable base in a codon

A

the third base

129
Q

What is the exception of stop codons in the mitochondria

A

mitochondria in animal cells use the UGA stop codon to encode tryptophan, therefore it is not used as a stop codon in animal cells

130
Q

Is the exception of mitochondria also applicable to plants

A

NO

131
Q

What are examples of frame shift mutations

A

insertions & deletions

132
Q

Who discovered tRNA molecules

A

Francis Crick (from the double helix invention of Waston and Crick)

133
Q

The ____ end of the tRNA is the binding site for amino acids, while the loop opposite is the location of the ___________

A

3’ end, anticodon

134
Q

What is the wobble hypothesis

A

the third base in the sequence may not match the anticodon, but are still connectable based on variability

135
Q

What is the purpose of the active site on tRNA synthetase

A

binds the ATP to the amino acid - this makes the amino acid now “active”

136
Q

Once active, what happens with the tRNA synthetase

A

complementary tRNA is bound to the enzyme

137
Q

Once the tRNA is bound to the enzyme containing its amino acid, what occurs

A

the amino acid and the tRNA bind together and are released from the enzyme as a now effective aminoacyl tRNA molecule

138
Q

What are the components of a ribosome and where are they found in the cell

A

a large subunit and small subunit make up the ribosome, and these subunits are found dissociated from one another in the cytosol prior to activation

139
Q

What is the function of the large subunit

A

catalyzes formation of peptide bonds

140
Q

What is the function of the small subunit

A

matches tRNAs to the codons

141
Q

Where does mRNA lie when the subunits are connected to form a ribosome

A

on the connective plane between the two subunits

142
Q

When does translation begin

A

When the anticodon of a charged tRNA binds to a codon in mRNA

143
Q

When does translation end

A

when that amino acid forms a peptide bond with growing chain

144
Q

What are the three sites on the ribosome

A

A site - acceptor site for the aminoacyl tRNA
P site - peptide bond forms between adjacent amino acids
E site - the exit site of empty tRNA molecules

145
Q

What initiates translation in eukaryotic cells

A

the AUG codon on the strand reached the MET amino acid with the help of a translational initiation factor and the small ribosomal subunit

146
Q

What terminates translation in eukaryotic cells

A

presence of a stop codon, which is read and does not have a complementary tRNA molecule, instead it binds to a release factor molecule, which releases the amino acid chain (and the subunits then detach from the mRNA transcript and go back to their original state)

147
Q

Is the ribosome and enzyme or a ribozyme

A

it is a ribozyme; it is an RNA molecule with a well-defined tertiary structure that enables catalytic activity (actions of both an enzyme and a ribosome)

148
Q

In relation to the ribozyme classification, what is the large subunit completely made up of

A

RNA

149
Q

Where are proteins found in ribosomes

A

mostly just on the surface, helping to maintain shape of the RNA core

150
Q

What are polyribosomes

A

Multiple ribosome units come together on a strand to create multiples of the amino acid chain

151
Q

Are polysomes big or small

A

they are significant in size due to the binding of various ribosomes at the same time

152
Q

How is the process of transcription and translation different in prokaryotic cells

A

Everything happens simultaneously, since there is no nucleus, no processing occurs, and the strands do not have to undergo a transition of any sort between transcription and translation

153
Q

Which is faster, prokaryotic or eukaryotic transcription and translation

A

prokaryotic - much less complicated and everything is simultaneous

154
Q

When does protein folding begin

A

during translation

155
Q

Although it requires no energy, what molecules often assist protein folding

A

molecular chaperones

156
Q

What are post-translational modifications

A

chemical modifications of protein structure that generally involves addition of functional groups or small molecules

157
Q

What are some types of post-translational modification (PTMs)

A

many types, including;
- glycosylation *
- addition of lipids
- phosphorylation *
- ubiquitination

158
Q

What is the purpose of PTMs

A

effect shape, charge, and activity of the protein

159
Q

What is the function of the plasma membrane

A

compartmentalization, selective permeability, transport, energy transduction, and respond to external signals

160
Q

What are the 4 types of membrane phospholipid

A

PS, PE, PC, PI

161
Q

Where are the 4 membrane lipids found

A

in the plasma membrane

162
Q

Flashback: what are lipids made up of

A

polar head group, phosphate, glycerol, fatty acid chains

163
Q

All membrane lipids are _______________

A

amphipathic

164
Q

What does amphipathic mean

A

has hydrophilic and hydrophobic parts

165
Q

In what way do lipid bilayers form

A

spontaneously

166
Q

How do lipid bilayers physically form themselves

A

hydrophobic molecules exclude water and cluster together, drawing the hydrophilic components inwards and exposing the hydrophobic heads to the exterior

167
Q

How are the conflicting forces of amphipathic molecules resolved

A

by the formation of a bilayer

168
Q

What are the characteristics of lipid bilayers

A

closed, self-sealing (important for budding and cell fusion)

169
Q

What is the “fluid mosaic model”

A

the organization of the lipid bilayer - with hydrophobic heads outward and hydrophilic tails inward, creating a fluid inner portion

170
Q

How do phospholipids move within the bilayer

A

rotation of individual phospholipids in place and lateral diffusion WITHIN a leaflet

171
Q

What movement does not occur in the lipid bilayer

A

movement BETWEEN leaflets rarely occurs because that would involve the hydrophobic head travelling through the hydrophilic tails

172
Q

What impacts membrane fluidity

A

temperature and lipid composition
- tightly packed tails = less fluid, loosely packed tails = more fluid

173
Q

In what circumstances will lipid fluidity change

A

if temp changes at a constant composition, or if composition changes at constant temp

174
Q

What is Tm

A

transition temp; the temp at which a membrane transitions between the fluid phase and the gel phase

175
Q

What happens above Tm? and what happens below Tm?

A

above = increased fluidity, the membrane “melts” - this is good
below = decreased fluidity, the membrane “gels” - this is bad

176
Q

What is Tm affected by

A

altered length of fatty acid chains: longer tails mean more tightly packed and less fluid, takes more to melt
altered amount of saturated fatty acids: more double bonds means less packing and more fluid, takes less to melt
altered amount of sterol (cholesterol): higher cholesterol at cool temps, membrane more fluid, and higher cholesterol at low temps, membrane less fluid

177
Q

What is the typical lipid composition in the tails of membrane phospholipids

A

Usually, one tail is saturated and done contains one or more double bonds

178
Q

How to organisms adapt to temps and maintain membrane fluidity

A

dealing with low temps: shorter fatty acid chains & increase double bonds

179
Q

What are desaturate enzymes

A

triggered in organisms at low temps, enable the phospholipids to be desaturated

180
Q

How are extremophiles different from other organisms in the sense of lipid composition

A

extremophile archaebacteria have branched isoprene chains in place of the fatty acid chains
- this results in L-glycerol instead of D-glycerol and ether linkages instead of ester

181
Q

What are the classifications of lipid proteins

A

transmembrane, monolayer-associated, lipid-linked, and protein linked

182
Q

Hydrophilic channels are formed from several __ __________

A

a-helices

183
Q

Proteins folded into ________ ________ can create pores

A

pleated sheets

184
Q

What is an example of how cells can constrict movement of membrane proteins

A

tight junctions - prevent apical and basolateral proteins from moving to opposing sides of the cell

185
Q

Where are sugars found on eukaryotic cells

A

on the exterior (in the extracellular space)

186
Q

Why is the bilayer asymmetrical

A

due to the sugars on the extracellular side but not on the cytosolic side

187
Q

What is the most extensive part of the cell

A

the ER

188
Q

Why does the ER synthesize proteins

A

secretion, insertion into membranes, and lysosome formation

189
Q

How does the ER assemble the membrane

A

adds free fatty acids in the cytosol to the cytosolic side of the membrane, and scrambles scramble the phospholipids around to ensure equal amounts on both sides

190
Q

How does the Golgi assemble the membrane

A

via flipases, the PS and PE heads are moved to the cytosolic side (so non-cytosolic side consists only of PI and PC, while the cytosolic side consists of PS and PE along with leftover PI and PC
- this creates membrane asymmetry from this point forward

191
Q

What are the components of the cytosolic side of the bilayer

A

PS & PE (with leftover PC/PI)

192
Q

What are the components on the non-cytosolic side

A

Only PC and PI, with sugar components

193
Q

What remains equal amongst both sides of the bilayer

A

cholesterol

194
Q

What are the model organisms for the plasma membrane

A

RBCs

195
Q

When a solute is added to solution, what happens to achieve no NET flux

A

the solutes spread out evenly throughout the solution to create equal concentration

196
Q

What is another term for solutes in relation to osmosis

A

osmotically active particles

197
Q

When concentrations are equal on both sides of a membrane, the cell is ________

A

isotonic

198
Q

When the concentration is greater on the exterior of the membrane, the cell is ________

A

hypertonic (loses water to exterior)

199
Q

When the concentration is greater on the inside of the membrane, the cell is ________

A

hypotonic (gains water)

200
Q

What is the normal state for an animal cell vs a plant cell

A

animal = isotonic
plant = hypotonic (turgid)

201
Q

What are the three terms for plant cell state based on osmosis

A

turgid (ideal), flaccid, and plasmolyzed

202
Q

What is turgor pressure

A

pressure of the cell contents against the cell wall in plant/bacterial cells

203
Q

What are osmoconformers

A

ex. marine animals; adjust internal salt concentrations to match seawater

204
Q

What are osmoregulators

A

single-celled eukaryotes have contractile vacuoles that pump out water (they don’t have a cell wall)

205
Q

List in order, the permeability of the following from most permeable to least permeable…
1. ions
2. small nonpolar molecules
3. small uncharged polar molecules
4. large uncharged polar molecules

A

2, 3, 4, 1

206
Q

How are carriers and channels different

A

Carriers: specific to substrates, remain in a “closed” position until bound to the proper molecule
Channels: open, free flow

207
Q

How are carriers and channels similar

A

Both passageways for particular classes of molecule, and most are multi-pass, move things down their concentration gradient

208
Q

What makes channels selective

A

focuses on charge and size of the molecules

209
Q

What is chemical vs concentration gradient

A

chemical: how much of a specific solute resides on either side of the membrane
electrical: whether it is being attracted by its opposite charge, or repelled by like charges

210
Q

Who gained a Nobel prize for the selectivity of the potassium channels

A

Roderick MacKinnon

211
Q

What are the 4 types of channels talked about

A

voltage-gated, ligand-gated (inner vs outer), and mechanically-gated

212
Q

Carriers mediate which type of transport

A

passive, facilitates diffusion

213
Q

What is an example of a solute moved by carrier proteins

A

GLUT1

214
Q

Transporting against a gradient is which type of transport

A

active transport - uses energy to move solutes “up hill”

215
Q

What was the first pump to be discovered

A

sodium potassium pump

216
Q

How does the sodium potassium pump work

A

moves Na+ in and K+ out in a 3:2 ratio respectively

217
Q

Why is sodium potassium pump electrogenic

A

creates a charge due to the imbalanced transfer ratio

218
Q

What is the enzyme that regulates the sodium-potassium pump, and what is its significance

A

Na/K ATPase: both a membrane protein and an enzyme, its present in ALL animal cells (contributes to basal metabolic rate), maintains Na+ gradient and uses it to transport other molecules

219
Q

How does activation of pumps occur

A

phosphorylation of the membrane protein to activate the function

220
Q

How are pumps and carriers different

A

Carriers are passive, pumps are active
Carriers move down a gradient, pumps move against a gradient

221
Q

What is coupled transport

A

when more than one molecule is being transported across the membrane at once (opposite of uniport)

222
Q

What is symport vs anti port

A

symport: moving 2 molecules in the same direction
antiport: moving 1 molecule one direction and 1 the other

223
Q

Coupled-mediated transport is also known as ________ _____________ ____________

A

indirect/secondary active transport (eg. glucose into the bloodstream via the action of the Na/K pump)

224
Q

What type of pump is common in plant cells

A

proton pumps

225
Q

What determines the transporters located on a specific membrane

A

the genes present in the protein

226
Q

What would happen if a mutation occurred in a transmembrane protein

A

channelopathies (ion channel diseases) where things either cannot be transported as they should or things are being transported that should not be passed through

227
Q

How is the evolution of the nucleus and ER similar to that of the mitochondria

A

thought to have been absorbed by a bigger cell, and implemented in the make up of a cell at some point in time

228
Q

What are the three ways to transport proteins into organelles

A

nuclear transport, transport across membranes, and transport by vesicles

229
Q

What would happen as a result of the deletion of a signal sequence

A

the protein would reside in the cytosol, because it no longer contains its “address”

230
Q

Describe the nuclear pore complex

A

highly selective gates, nuclear pores contain a nuclear basket that only allows for the passing of specific solutes

231
Q

How are proteins imported into the nucleus

A

contain a nuclear localization signal, that binds to a nuclear import receptor, and passes through the pore accordingly

232
Q

All except proteins are small enough to be _______ transported into the nucleus through the pores

A

uniport

233
Q

do proteins fold as they pass through nuclear pores while bound to the receptor signal?

A

NO

234
Q

What are examples of things moving OUT of the nucleus

A

mRNA and rRNA

235
Q

What are examples of things moving INTO the nucleus

A

histones (DNA packing), proteins required for transcription, dNTPs and rNTPS

236
Q

What is important to remember about the mitochondria membrane

A

it is double layered - there are two membranes

237
Q

What part of the protein initiates the transfer into the mitochondria

A

the signal sequence

238
Q

What does the signal sequence on the protein bind to on the ER outer membrane

A

an import receptor protein

239
Q

Once attached to the import receptor protein, what happens next

A

a protein translator on the inner membrane matches the import receptor on the outer membrane and binds to form a transmembrane path for the protein

240
Q

Once inside the mitochondria, what is the last step of the protein transport

A

the signal sequence is cleaved off, to reveal the functional protein

241
Q

What terminus is the signal sequence located at on the protein

A

the N terminus

242
Q

What is important to consider about protein shape in relation to transport

A

the protein must unfold to be transported across the mitochondrial membrane

243
Q

Transport within an organelle happens how?

A

a new signal sequence is revealed when the original one is cleaved off, allowing for the same process to be repeated within the organelles

244
Q

What is the most extensive membrane system

A

the ER

245
Q

How is the ER vital for transport

A

serves as an entry point for itself and the rest of the endomembrane system,, including Golgi, lysosomes, endosomes, etc.

246
Q

Once in the ER, can proteins go back into the cytosol?

A

NO

247
Q

What are the two types of ribosome cycles

A

free in cytosol, and membrane-bound to ER

248
Q

When does mRNA translate into the ER

A

When the strand presents a signal sequence targeting the ER and binds to protein translocators

249
Q

Explain the process of ribosomal function on the ER membrane

A

The peptide strand displays a signal sequence that binds to a signal recognition particle (SRP). The SRP binds to an SRP receptor on the surface of the ER membrane, which connects with a translocation channel. Once all connected, the peptide chain can pass down into the ER lumen

250
Q

What are the two types of proteins transferred into the ER

A

water-soluble proteins destined for the lumen, and transmembrane proteins only partially tranlocated across, destined for plasma membrane, ER membrane, or membrane of another organelle

251
Q

What is a single pass protein

A

a protein that partially passes the membrane only once, so one side is in the organelle, and the other is out in the cytosol

252
Q

What is a multi pass protein

A

a protein that partially passes the membrane various times, so parts of the protein are inside the organelle, and some parts are not (ie. GPCR)

253
Q

Are vesicles permanent or temporary

A

temporary

254
Q

Describe the pathway of a vesicle moving OUT of the cell

A

ER, Golgi, (other organelles), plasma membrane

255
Q

Describe the pathway of a vesicle moving INTO the cell

A

plasma membrane, endosomes, lysosomes

256
Q

What is the most common protein coat discussed

A

clathrin

257
Q

How are coat proteins applied to a vesicle

A

cargo molecules match with cargo receptors within the extracellular space and bind to adaptin and a protein coat on the cytosolic side. the protein coats pull the receptors, which eventually bud off as vesicles, entirely surrounded by the protein coats

258
Q

What cuts the vesicle away from the plasma membrane

A

dynamin

259
Q

Once the coated vesicle has been cut from the membrane, what happens?

A

the protein coats release from the vesicle, and the naked vesicle can now be transported effectively

260
Q

What does vesicle docking depend on

A

tethers and snares

261
Q

What are Rab proteins

A

monomeric GTPases displayed on the vesicle surface

262
Q

What are tethering proteins

A

proteins that extend from the outer surface of the membrane, and bind to the Rab protein on the vesicle

263
Q

What are snares

A

v-snare = v for vesicle, snare located on the outer surface of the vesicle
t-snare = snare located on the membrane
- snares intertwine together and pull the vesicle towards the membrane to fuse

264
Q

Upon fusion, where is the cargo protein

A

successfully implanted in the membrane

265
Q

How are proteins covalently modified in the ER

A
  • disulphide bonds are added in between proteins and within protein folding
  • glycosylation (addition of sugar groups) to protect protein degradation, direct to proper organelle, and allow for cell-cell recognition
266
Q

Explain N-linked glycosylation in the ER

A

as the protein enters the ER membrane via the transmembrane pathway, N-acetylglucosamine in a lipid-linked oligosaccharide breaks away from the phosphate group and attaches itself to the asparagine (Asn) amino acid

267
Q

Only properly __________ proteins are allowed to leave the ER

A

folded

268
Q

What assists in refolding misfolded proteins

A

chaperone proteins

269
Q

How does the ER detect misfolded proteins

A

hydrophobic residues that should be tucked away are recognized by the ER

270
Q

What is the UPR

A

unfolded protein response: various proteins on the outer surface of the ER membrane set off a series of events in the cytosol that activate chaperone genes

271
Q

What happens if there are too many misfolded proteins that cannot be fixed

A

accumulate together and kill the cell

272
Q

Cis and trans ends of the Golgi network

A

Cis end = close to ER
Trans end = close to plasma membrane

273
Q

What is the name for the series of flattened sacs that make up the Golgi

A

cisternae

274
Q

What are the functions if the Golgi

A
  • modify proteins arriving from the ER: peptide chains shortened by proteases, amino acids modified, CHO groups added in ER modified or removed, glycosylation
  • most complex polysaccharides synthesized in the Golgi
275
Q

What is O-linked glycosylation

A

Different CHO groups added to different AAs (set, thr)

276
Q

What is the difference between constitutive vs regulated secretion

A

constitutive: unregulated, involves plasma membrane proteins, happens at all times
regulated: regulated, involves signal transduction, happens upon signalling

277
Q

What is the endocytic pathway

A

taking substances into the cell by surrounding them with a membrane

278
Q

What are the 2 main types of endocytic pathway

A

pinocytosis = cell drinking
phagocytosis = cell eating

279
Q

What is the difference between pinocytosis and phagocytosis

A

pino = ‘drinking’ because it involves much smaller vesicles formed called endosomes
phago = ‘eating’ because it involves much larger vesicles formed called phagosomes

280
Q

What is the third type of endocytosis in animal cells

A

receptor-mediated endocytosis

281
Q

How does receptor-mediated endocytosis work

A

particular molecules called ligands match receptors on the membrane called coated pits, and bind/fuse

282
Q

What are the sites of cellular digestion

A

lysosomes

283
Q

What are the three digestive processes in lysosomes

A

endocytosis, phagocytosis, autotrophy

284
Q

What are the three components that come together to form a lysosome

A

phagosome, autophagosome, and late endoscope

285
Q

What are the two types of short-range communication

A

paracrine and contact-dependant

286
Q

What are the two types of long-range communication

A

endocrine and neuronal

287
Q

What’s another term for signalling molecule

A

ligand

288
Q

Explain the steps of a signalling pathway

A

ligand synthesized and released by signalling cell
signal molecule travels to the target cell
signal binds to a receptor protein
change in protein activity results in a change in gene expression
change in cell shape, movement, metabolism, secretion, etc.

289
Q

What is the basis of signal receptors

A

ligand binds and alters a function

290
Q

What are the two types of signal receptors

A

cell-surface and intracellular

291
Q

What is an example of small hydrophobic signal molecules that can cross the membrane into the cell

A

steroids

Biol 130 (5 decks)

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