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BIOL 2202 CMB Midterm 1 > Midterm 1 > Flashcards

Midterm 1 Flashcards

Ch. 1,5,7,8

1
Q

what is cell theory and by who?

A

by matthias schleiden & theodor schwann 1839

-all organisms are composed of one or more cells
-the cell is the smallest unit that has the properties of life
-cells arise only from the growth and division of pre-existing cells

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2
Q

for most multicellular organisms all cells contain ______ DNA

A

identical DNA

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3
Q

genome vs proteome

A

genome = full collection of DNA sequence
proteome = full collection of proteins that can be expressed by a cell, tissue or organism

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4
Q

central dogma of biology

A

DNA -> RNA -> Protein

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5
Q

prokaryotes examples

A

bacteria and archaea

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6
Q

eukaryote examples

A

protists
fungi
animals
plants

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7
Q

prokaryotic vs eukaryotic cells

A

prokaryotic
- smaller, less complex
- less genetic info
- lack membrane bound organelles
- no endomembrane system
- cell wall

eukaryotic
- membrane bound organelles
-compartmentalization
- endomembrane system

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8
Q

describe the nucleus

A
  • holds genetic material
    (nucleolus = region of intensive ribosomal RNA synthesis)
  • surface bound by TWO phospholipid bilayer membranes
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9
Q

nuclear pore complex

A
  • small molecules can pass thru nuclear membrane, large molecules (proteins/RNA) cannot move freely so use nuclear pore complex to enter/exit
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10
Q

ribosomes

A
  • site of protein synthesis
  • complex composed of two subunits that attach to messenger RNA
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11
Q

free ribosomes

A
  • suspended in the cytosol
  • build proteins to be used in the cytoplasm
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12
Q

bound ribosomes

A
  • attach to membranes, mainly RER
  • build proteins to be inserted in membranes or exported from the cell
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13
Q

endoplasmic reticulum

A
  • compartmentalizes cell
  • transport of proteins
  • tubules and internal spaces
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14
Q

RER

A
  • abundant in cells that secrete proteins
  • secreted proteins are packaged in transport vesicles
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15
Q

SER

A
  • synthesize lipids
  • permits glucose to exit the cell
  • detoxifies chemicals
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16
Q

golgi apparatus

A
  • collect, modify (glycosylation), tag and package proteins from ER into vesicles to be distributed and used at other locations
  • enter thru CIS leave via TRANS face
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17
Q

vesicles

A
  • used for transport
  • pinch off from RER and SER
  • bud off from golgi
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18
Q

lysosomes

A
  • membrane bounded sac that digests macromolecules
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19
Q

what’s special about the mitochondria and chloroplasts

A
  • both have small quantities of DNA that is prokaryotic in nature
  • both grow and reproduce like bacteria
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20
Q

mitochondria and the two membranes

A

cellular respiration

OUTER smooth membrane
- holds protons (low pH)
- fluid filled space between membranes

INNER highly folded membrane
- cristae (folds) increase SA for proteins that are involved in electron transport and ATP synthesis

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21
Q

mitochondrial matrix

A
  • citric acid cycles occurs here
  • fluid filled space inside inner membrane
  • contains DNA and ribosomes
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22
Q

chloroplasts

A

perform photosynthesis
- solar -> chemical energy
- found in plants/ protists
- inner and outer membrane

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23
Q

thylakoids & thylakoid space

A
  • in the stroma
  • contains chlorophyll (absorbs light)

thylakoid space = lumen inside thylakoids

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24
Q

eukaryotic cells are large and so need extra support, this is carried out by the _____ and describe

A

cytoskeleton
- spatially organize the cell
- positions and transports organelles
- aids cell movement

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25
Q

3 types of cytoskeleton structures and describe

A
  1. microtubules (alpha and beta tublin)
    - structural support
    - form cilia and flagella
    - centrioles/ spindle fibers
  2. intermediate filaments
    - cell structure ( keratins)

3.microfilaments (actin)
- cell movement
- divide cytoplasm

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26
Q

Robert Hooke

A

first to give the name “cells”

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27
Q

who was first microbiologist and discovered what

A

antonie van Leeuwenhoek
-unicellular organisms

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28
Q

light microscope key features (5)

A
  • up to 1000x magnification
  • resolution 0.2 um
  • must be thin specimens / can add dye to see better
  • can look at live specimens
  • widely accessible, low cost
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29
Q

light microscope limitations

A
  • only 0.2 um resolution
  • specimen preparation is required
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30
Q

fluorescence microscope features

A
  • 20 nm resolution
  • up to 1000x magnification
  • can be live or dead CELLS
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31
Q

how does a fluorescence microscope work (3)

A
  • light hits a specimen that is labelled with fluorescent dyes (fluorophores)
  • the light is absorbed by the specimen and emitted
  • light then goes thru a filter that only allows the wavelength emitted when the dye fluoresces (what you see)
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32
Q

what is fluorescence

A

molecules that absorb light at one wavelength and emit it at another (emitted light is always of lower energy)

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33
Q

how do fluorescence label a specimen (2) and describe

A
  1. label with a fluorophore directly or indirectly (thru antibodies/ much more common)
  2. fluorescent protein is expressed with protein
    - there’s colocalization and gene fusion of the protein and fluorescent
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34
Q

what is immunofluorescence? and it is ____ specific?

A

fluorophores attached to antibodies which bind to target - more specific

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35
Q

what is GFP

A

green fluorescent protein
-absorbs blue light and gives off green

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36
Q

what are transgenic organisms

A

fluorescence is inserted into all genes so you get light up organisms

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37
Q

what are fluorescent confocal microscopes

A
  • uses fluorescent dye labelling
  • live or dead cells
  • 3D image that’s more clear
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38
Q

fluorescence microscopy limitations

A
  • resolution
  • can only see structures you label
  • higher cost then light microscopes but less than EMs
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39
Q

electron microscope key features (2)

A
  • highest magnification
  • highest resolving power ~0.2nm
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40
Q

transmission electron microscope

A

(transecting)
-black and white image of details/organelles

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41
Q

scanning electron microscope

A

SCANS the specimen producing a 3D image b&w image

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42
Q

electron microscopy limitations

A
  • high cost
  • no live samples
  • TEM needs extensive prep
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43
Q

which electron microscope has higher mag and resolution and needs _____ prep

A

transmission electron microscope and needs MORE prep

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44
Q

what are purines

A

large bases - A&G

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45
Q

what are pyrimidines

A

small bases - C&T / U in RNA

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46
Q

how are nucleotides bonded vs bases

A

nucleotide = phosphodiester bonds
bases = hydrogen bonds

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47
Q

DNA has _______ replication

A

semi-conservative

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48
Q

pro vs euk cells

A

pro
-circular, shorter DNA
euk
-longer, linear DNA
-23 pairs = 46 chromosomes

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49
Q

what is a gene

A

segment of DNA that contains instructions for making a particular protein or RNA molecule

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50
Q

multicellular eukaryote chromosomes vs bacteria and unicellular

A

multi- much more non coding DNA
uni etc - very condensed

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51
Q

what is chromatin

A

DNA + associated proteins

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52
Q

what is a nucleosome made up of with what charges

A

histones (+) and DNA (-)

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53
Q

1st level of chromatin structure

A
  • DNA is wrapped around histone to form the nucleosome
    -8 histone proteins in core (2 of each H2A, H2B, H3 and H4)
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54
Q

2nd level of chromatin structure and higher level chromatin structure

A

histone 1 (H1) binds to the linker DNA and facilitates condensation to 30nm fiber
-bring nucleosomes in contact

higher level: 700nm

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55
Q

chromatin structure is ___ static

A

NOT static as cells alter the structure

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56
Q

what is epigenetics and epigenetic modifications are ____

A

changes to chromatin that influences gene expression (phenotype) but does NOT change the DNA sequence

are heritable

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57
Q

what is heterochromatin and has high histone ____

A

CONDENSED / transcription “genes off” / inactive
-high histone methylation

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58
Q

what is euchromatin and has high histone ____

A

UNCONDENSED / transcription “genes on” / active
-high histone acetylation

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59
Q

what are the possible epigenetic modifications (4)

A

=histone modifications
-acetylation and methylation
=DNA methylation
=gene imprinting
=X chromosome inactivation

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60
Q

histone acetylation

A

= gene ON (increases transcription)
-HAT (histone acetyltransferase) add acetyl group to lysine residues

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61
Q

what do acetylated residues do

A

generate binding sites for other protein complexes

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62
Q

what is chromatin remodeling and its complexes

A

rearrange chromatin from condensed to accessible state for TF’s and other binding proteins

complexes = reposition nucleosomes

63
Q

histone methylation

A

= gene silencing (no expression/transcription)
HMT (histone methyltransferase) adds methyl groups to lysine and arginine residues

64
Q

DNA methylation

A

DNMT (DNA methyltransferase) transfers methyl groups to DNA

65
Q

what are CpG islands (3)

A

-found in many promoter regions
-cytosines can be “on” (usually) or “off”
-recruits activator or repressor proteins

66
Q

unmethylated vs methylated CpG islands

A

unmethyl
- bind activators (prevent methylation)
- genes “on” transcription

methyl
- repressors (MeCPs) recruited to methylated sites and close chromatin
- genes “off” no transcription

67
Q

paternally vs maternally imprinted

A

paternally - gene from father silenced so maternal allele is expressed

maternally - gene from mother is silenced so paternal allele is expressed

68
Q

can DNA methylation be inherited

A

yes to daughter cells

69
Q

histone modification inheritance

A

when the cell replicates histones are evenly spread 50/50 between the new cells

so new chromosomes will have 50% old histones and recruit new ones

70
Q

which has a greater variety of functions DNA or RNA?

A

RNA
as DNA only has one main function - to hold instructions

71
Q

transcription overview

A

RNA polymerase unwinds part of helix just ahead of the active site and reads template strand 3’-5’ to build an RNA molecule out of complimentary base pairing - growing the chain 5’-3’

72
Q

what are rRNA

A

(ribosomal RNA) = form the core of the ribosome’s structure and catalyze protein synthesis

73
Q

what are tRNA

A

(transfer RNA) = serve as adaptors between mRNA and amino acids during protein synthesis

74
Q

what are miRNA

A

(microRNA’s) = regulate gene expression

75
Q

what are mRNA

A

(messenger RNA) = code for proteins

76
Q

what are snRNA

A

along with proteins, form the spliceosome complex (snRNP) for splicing of primary mRNA transcripts

77
Q

describe prokaryotic transcription: initiation

A

RNA Pol requires a sigma factor
-this sigma factor allows RNA Pol to recognize and bind to the promoter

bacterial promoter = 2 consensus sequences: -35 sequence and -10 sequence
-located UPSTREAM of the transcription start site

78
Q

prokaryotic transcription: elongation

A

-once ~10 bases have been incorporated into the newly synthesized RNA molecule, the sigma factor is released

-tether attaching RNA polymerase to promoter is broken so elongation can occur
-elongation occurs until is reaches a terminator sequence

79
Q

prokaryotic transcription: termination

A

RNA Pol dissociates from DNA and rebinds with sigma factor
-termination sequence gets transcribed
-promoter sequence does NOT

80
Q

direction of transcription is determined by the _____ as it has _____

A

determined by the promoter as it has polarity

81
Q

which transcription is more complex?

A

eukaryotic

82
Q

describe the RNA polymerases

A

RNA pol I - transcribes rRNA
RNA pol II - transcription of most eukaryotic genes
RNA pol III - transcribes tRNA, 5S rRNA and other small RNA’s

83
Q

eukaryotic transcription: initiation

A
  • consensus sequence in eukaryotic promoter = TATA box
  • need general transcription factors at promoter to help recruit RNA polymerases
  • TFIID binding to TATA box causes distortion in DNA and this flags the promoter to recruit other TF’s and RNA Poll II
    -once all the general TF’s and RNA Pol II has assembled at the promoter (forming the transcription initiation complex) elongation can begin
84
Q

once the DNA distorts (due to TFIID binding to TATA) the promoter is flagged and recruits what (5)

A

TFIIB
TFIIE and TFIIH
TFIIF
RNA Pol II
other accessory proteins

85
Q

eukaryotic transcription: elongation

A

-TFIIH pries apart the double helix at start site which exposes the template strand of gene
-TFIIH PHOSPHORYLATES the C-terminal tail of RNA Pol II, releasing the polymerase from the initiation complex
-once elongation begins the transcription factors dissociate from the promoter region
-ends at the terminator where RNA Pol II will dissociate and is de-phosphorylated

86
Q

transcription factors general notes (3)

A
  • eukaryotes require GTF’s
  • GTF must assemble at the promoter before transcription can begin
  • GTFs help position RNA Poll II at the promoter , help pull apart 2 strands of DNA and release RNA Pol II from promoter to allow elongation
87
Q

what are the 3 eukaryotic modifications and where are the enzymes for them located

A
  1. 5’ end cap (guanine is added to help protect mRNA)
  2. 3’ poly A tail (help direct export of mRNA)
  3. splicing (introns removed, exons spliced together)

located = C-terminal tail of RNA Pol II

88
Q

mRNA splicing occurs at nucleotide ______ _______ located at intron-exon junctions

A

consensus sequences

89
Q

what are the 3 important sites for splicing

A
  • 5’ splice site (5’ end of intron)
  • branch-point site (A)
  • 3’ splice site (3’ end of intron)
90
Q

how does splicing work (4)

A
  1. branch point A nucleotide attacks 5’ splice site and cuts the sugar-phosphate backbone
  2. 5’ end of intron covalently linked to A
  3. the free 3’-OH of the exon then reacts with the start of the next exon sequence, joins the exons
  4. lariat released and degraded in nucleus
91
Q

what are the 5 types of snRNP’s involved in RNA splicing

A

U1, U2, U4, U5, U6

92
Q

what is the spliceosome

A

RNA protein complex that catalyzes the removal of introns from pre-mRNA

93
Q

when does RNA splicing occur and why use it

A

when = DURING the elongation phase of transcription

why = to produce different proteins from the same gene

94
Q

how many amino acids are in eukaryotes and how many are essential

A

20 total and 9 are essential

95
Q

the genetic code is ____ and ______

A

redundant and universal

96
Q

what is a codon

A

grouping of 3 nucleotides that codes for an amino acid

97
Q

how many codons are there and how many are sense codons?

A

64 and 61 are sense

98
Q

why is there only one reading frame

A

because there’s the start codon AUG that dictates the beginning of translation

99
Q

eukaryotic translation: transfer RNA (5)

A

each tRNA binds to both amino acid and mRNA (linking AA to its codon / bridge)

  • amino acid at 3’ loop
  • anticodon: 3 nucleotides long and pairs with the complementary codon in mRNA molecule
  • T-loop: attachment to the ribosome
  • D-loop: binds to enzyme to make sure anticodon is paired to correct amino acid
100
Q

whats the wobble hypothesis

A

3rd nucleotide can allow tRNA to bind to more than one codon

101
Q

amino-acyl tRNA sythetases

A

catalyzes the aminoacylation reaction

aminoacylation: makes sure the correct amino acid is paired with its anti-codon

synthetases: recognize tRNAs with anticodons and covalently link to these tRNAs

102
Q

which way is codon strand read vs anticodon strand

A

codon is 5’-3’
anticodon 3’-5’

103
Q

how many rRNA in ribosomes do eukaryotes have and what are the subunits

A

4

subunits: 80s (60 large/ 40 small)

104
Q

what does the small ribosomal subunit do vs large subunit

A

small = matches tRNA to mRNA
large = catalyzes peptide bond formation

105
Q

how many binding sites are on a ribosome

A

3
-A site (aminoacyl)
-P site (peptidyl)
-E site (exit)

106
Q

eukaryotic translation: initiation

A
  • initiator tRNA carries amino acid methionine (Met) and initiation factors help with the association with mRNA
  • small ribosomal subunit and tRNA-Met will scan the mRNA until it reaches AUG (start codon)
  • large ribosomal subunit is recruited and initiation factors are released
  • all newly made proteins have Met at N-terminus (5’) for now
107
Q

what is the function of peptidyl transferase and which subunit is it located ?

A
  • catalyzes the peptide bond between amino acids / growing the chain

located in large subunit

108
Q

eukaryotic translation: elongation

A
  • tRNA enters the A site and large subunit translocate, moving the tRNA’s into the E and P sites
  • small subunit translocates 3 nucleotides along the mRNA molecule to line back up with the large subunit and this ejects tRNA from E site (ready for new tRNA)
109
Q

eukaryotic translation: termination

A
  • stop codon enters A site and a release factor binds
  • this binding alters the activity of the peptidyl transferase (has nothing to bind with) and so releases H20
  • ribosome dissociates
110
Q

whats the proteasome and which one do we specifically look at

A

proteasome = degrades short lived and misfolded proteins

ubiquitin = if a protein is tagged with ubiquitin its sent to proteasome to get degraded

111
Q

different cell types within the same organism contain the same ____ but differ in both _____ and ______

A

contain the same DNA but differ in both structure and function

112
Q

most human cells express about ___% of their genes

A

50%

113
Q

a cell can change the expression of its genes by ….. (2)

A
  • permanently (cell identity) or in response to its environment
114
Q

what techniques are used to investigate gene expression

A

for proteins - 2D gel
RNA - PCR or microarrays

115
Q

what is the most important type of regulation and why

A

transcriptional control because its the most energy efficient and ensures nothing is unnecessarily produced

116
Q

what are transcriptional switches

A

ensures the organism can respond to its environment

-transcriptional regulators bind to regulatory DNA sequences

117
Q

what are regulatory DNA sequences

A

almost all genes have these and are used to switch the gene on/off upon the binding of transcriptional regulators

118
Q

whats negative vs positive regulation

A

negative - bound repressor protein prevents transcription

positive - bound activator protein promotes transcription

119
Q

what makes up the operon

A

promoter, operator and genes

120
Q

what is trpR

A

gene that codes for the trp repressor (not part of operon)

121
Q

genes in an operon are all transcribed _____ and this allows for ______ regulation

A

transcribed together and allows for coordinated regulation

122
Q

what is the trp operon

A

genes that code for tryptophan synthesis enzymes

123
Q

inactive trp repressor vs active trp repressor

A

inactive trp repressor (default) = low trp in cell, so need to make it
-RNA polymerase binds to promoter and gene is transcribed

active trp repressor = binds to operator so RNA polymerase cant bind to promoter and gene is NOT transcribed

124
Q

describe activators

A

bind to regulatory site on DNA and with RNA pol help initiate transcription

125
Q

what is the lac operon

A

has enzymes (LacZ) that are involved in lactose breakdown

126
Q

for the lac operon where does the repressor bind vs the activator

A

repressor binds to operator
activator binds to CAP binding site

127
Q

when is the lac operon ON vs OFF

A

ON = when repressor is not bound ( high lactose) and activator is bound ( low glucose)

OFF = when repressor is bound ( low lactose) and activator is not bound ( high glucose)

128
Q

what is combinatorial regulation

A

multiple transcriptional regulators work together to control activity of a single promoter

129
Q

high levels of glucose and lactose will produce what level of transcription

A

low levels of transcription

130
Q

high vs low levels of cAMP

A

high levels = low glucose, cAMP can bind to CAP so transcription is enhanced

low levels = cAMP cannot bind to CAP site so only low transcription rate

131
Q

does eukaryotic DNA contain operons

A

no each gene can be controlled seperately

132
Q

are general transcription factors in eukaryotes or prokaryotes

A

GTFs in eukaryotes

133
Q

where do activators and repressors bind in eukaryotes

A

activators bind to enhancers
repressors bind to silencers

134
Q

which has more transcription regulators pro or euk

A

eukaryotes

135
Q

transcription initiation complex

A

-activator protein binds to enhancer
-promoter is far away
- DNA flips upside down and loops around (with spacer DNA)
- activator protein binds to mediator and other GTFs

136
Q

what do all the transcription regulators do

A

act as a committee making a decision if should be transcribed or not ( some have strong opinions, weak or neutral)

137
Q

what is the gene control region

A

includes promoter and regulatory sequences to which regulatory proteins bind to control rate of transcription

138
Q

what is the mediator

A

takes in all the info from the regulators on whether should transcribe or not

139
Q

why is chromatin remodeling needed for gene expression

A

HAT loosens up histones and opens up chromatin so transcriptional factors, mediator, RNA can bind and initiate transcription

140
Q

what is coordinated expression

A

at each gene there is combinatory control but they must be multiple genes with the same regulator acting in order to switch them all on at the same time

141
Q

different combinations of transcription regulators lead to ________________

A

different types of specialized cells

142
Q

what is de-programming

A

transcription regulators can push differentiated cells into induced pluripotent stem cells (then can be specialized however you want)

143
Q

once a cell has differentiated into a particular cell type it will ____________ and _______

A

remain differentiated and all its progeny will stay that same cell type

144
Q

epigenetics allows for ___ _____ and what is it

A

cell memory
= cells ability to remember its identity (which genes are turned on/off) and these patterns inherited

145
Q

the 3 ways cell memory is obtained

A

1 - positive feedback loop (master transcriptional regulator activates its own gene expression AND then other genes / is inherited

2 - DNA methylation ( template strand keeps a methyl group and maintenance methyltransferase recognizes it and adds a matching methyl group to new strand/ inherited

3 - histone modifications (daughter cells can inherit parental histone code which determines chromatin structure)

146
Q

2 and 3 of gene regulation

A

2 = RNA processing control - RNA splicing allows for different forms of proteins to be expressed

3 = mRNA transport and localization control - nucleoporins regulate nuclear export of mRNAs

147
Q

4 in gene regulation

A

mRNA degradation control

148
Q

describe miRNAs steps

A
  • mircro RNAs (base pair with mRNAs to target them for destruction)
  • dicer
  • associate with RISC
  • search for a mRNA match to degrade (good or bad match)
  • RISC released
149
Q

describe siRNAs

A

small interfering RNAs = short FOREIGN RNA fragments that base pair with foreign RNAs to target them for degradation important in cell defense
- cleaved by dicer
- associate with RISC
- binds and foreign RNA is degraded
- RISC released

150
Q

5 of gene regulation

A

translation control
-no repressor on ribosome binding site = protein made
-repressor on binding site = no protein made

151
Q

6 and 7 of gene regulation

A

6 - protein degradation control (ubiquitin / tagged proteins are degraded by the proteasome)

7 - protein activity control (post translational modifications / activate or de-active proteins)

152
Q

what does RISC stand for

A

RNA-induced silencing complex

153
Q

where can heterochromatin be found

A

centromeres/ telomeres/ inactivated X chromosomes

BIOL 2202 CMB Midterm 1 (1 decks)

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