Section 1 (week 1-6) Flashcards
1
Q
Prokaryotic cells are… (3 simple attributes)
A
No nuclei
Single celled
Bacteria and Archaea
2
Q
Eukaryotic cells are… (3 simple attributes)
A
With nuclei
Single celled OR multi celled
Plants, animals, fungi, humans
3
Q
_______ have no membrane bound organelles
Smaller sized than ________
Less Dna than _________
What is this?
A
Prokaryotic cells
Eukarytoes
eukaryotes
4
Q
Eukaryotic plant cell describe
A
nucleus
Several membrane bound oganelles
LArger and more complex
5
Q
Eukaryotic plant cells have …. compared to eukaryotic animal cells
A
vacuoles, chloroplasts, cell wall
6
Q
Describe origins of mitochondria (choloplast behaviour)
hint: aerobic prokaryotes, archaeic cell, ectosymbiosis, bacterial endosymbiont, bacterial symbiosis, endoplastic reticulum
A
Mitochondria were originally free living aerobic prokaryotes able to use oxygen to generate ATP
an archaeic cell couldn’t use oxygen to generate ATP
ectosymbiosis caused the archaiec dna to engulf the mitchondria ancestor, Membrane fused, now the small ATP generator (mitochondria) is a part of the big cell
start to develop as mitochondria, forming nucleus, forming endoplasmic reticulum
7
Q
whats ectosymbiosis
A
a form of symbiotic behaviour in which an organism lives on surface of another organism (big protects small)
8
Q
describe the tree of origins of eukaryotes
hint: anestral prokaryote, archae, bacteria, mitchondria, single celled eukaryote
A
starts as ancestral prokaryotes like bacteria and archae, then combined and formed kinda like mitochondria, then produced early of single celled eukaryotes, lead to chloroplasts to plants and animals
9
Q
Evidence supporting endosymbiont hypothesis (mitochondria + chloroplasts)
hint: resemble
A
they have their own genomes and genetic systems that resemble modern day prokaryotes
they have their own protein DNA synthesis components that resemble prokaryotes
Membranes in mitochondria/chloroplasts resemble ones in prokaryotes and seem to have been derived from engulfed bacterial ancestors
10
Q
model organism
A
living thing selected for intensive study as representative for large group of species
11
Q
Attributes for GOOD model organisms
A
fast growing
short life cycles
small size
easy to obtain
easily modified
understandable genetics
12
Q
Genome
A
all DNA sequences in cell for organism
13
Q
Transciptome
A
All RNA and RNA sequences
14
Q
Proteome
A
Proteins or protein sequences
15
Q
interacdome
A
protein protein interactions (with eachother)
16
Q
metabolome
A
small molecule metabolites eg. lipids, nutrients, steroids, waste
17
Q
Phenome
A
all phenotypes of central dogma
18
Q
RNA sequence is only… direction why
A
5’ to 3’ because it is the opposite of DNA’s template strand that is 3’ to 5’
19
Q
NUCLEOTIDES
A
pentose sugar
Nitrogenous base
Phosphate backbone
20
Q
Nucleotides are the subunits of
A
nucleic acid
21
Q
Difference between DNA and RNA (letters)
A
ribose: G C A U
deoxyribose: G C A T
22
Q
What is phosphate group attached to on the pentose sugar
what is base attached to on the pentose sugar
A
5’ carbon
1’ carbon
23
Q
CUT the PY
A
Cytosine Uracil Thymine are PYRIMIDINES
24
Q
PURE AS GOLD
A
PURINES are adenine and guanine
25
structure of pyrimidine and purines bases
pyrimidine are single rings, purines are double rings
26
Thymine difference to Uracil
extra methyl group
27
Nucleoside is
Sugar + base
28
Nucleotide is
Sugar + base + at least one phosphate
29
Nucleoside monophosphate, diphosphate, triphosphate
1, 2, or 3 phosphate groups on a nucleoside, making it a nucleotide
30
DNA is synthesized from
eg. dATP, dGPT
deoxyribonucleoside triphosphates known as dNTPS
31
RNA is synthesized from
eg. ATP, GPT
ribonucleoside triphosphates or NTPS
32
NUcleotides are linekd by
phosphodiester bonds O--P--O
33
A double stranded DNA is what
anti parallel (3' to 5' against 5' t 3') and complimentary (AT CG)
34
what are bonds holding the DNA double helix together for A-T and G-C
A-T = 2 H bonds
G-C= 3 H bonds
35
what also keeps DNA strands together
Hydrogen bonds
Hydrophobic interactions (bases want to get away from water)
Van der waal attractions (bases stacked, flickering dipoles)
36
what does major and minor grooves affect
certain proteins fit and make contact with specific DNA sequences in the grooves
37
Bases are what form
planar
38
Heat added to and removed from DNA does what
denature (breaks H bonds between nucleotide pairs)
Renature (bonds reform)
39
What is antiparallel
The main DNA had one strand from 5' to 3' other strand is 3' to 5'
40
Protein structure (s) names
Primary (amino acid sequence)
Secondary (Local folding)
Tertiary (long-range folding)
Quatenary (multimetric organization)
Multiprotein complexes
41
what is
Local folding
Tertiary (long-range folding)
Quatenary (multimetric organization)
A helix Beta sheet
3D structures
More than 1 polypeptide chain
42
Amino acid common parts
Alpha carbon ( H--C)
Carboxyl group (OH--C==O)
R group (CH chain)
Amino group (NH2--C) attached to carbon
43
Major categories of amino acids
Acidic, basic, uncharged polar, nonpolar
44
why are similar properties (amino acids) in similar areas
in case of error, its still similar enough since they are in the same area
45
what is amino acid group CH2SH
Cystein
46
why is Cysteine important to know and what is its chemical formula
(think hair curl)
In oxidation, cysteine forms disulfide bonds (COVALENT bonds) and hold the protein shape together (eg. hair gets a shape caused by bonds, then reducted and then re oxidized to get new bonds to form curls)
CH2SH
47
Oxidation form of cysteine is found where
Reduction form of cysteine is found where
Endoplasmic reticulum (ER) and outside of cell
cytosol
48
2 or more amino acids together is a
polypeptide chain
49
Process of peptide bonding
what does it produce? whats the name?
Ribosomes use the OH connected to a CARBOXYL GROUP and the H off of an AMINO GROUP from the next amino acid and form a covalent bond from the remaining carbon and amino group.
H2O, condensation reaction
50
whats a residue
amino acids after they have been combined by the ribosomes
51
Whats a backbone
all proteins atoms except the side chains
52
N terminus and C terminus
NH2 end and carboxyl end in the polypeptide bond
53
Unless specified, what is the terminus order
N (NH2) to C (carboxyl end)
54
Residue bond formula and what forms the hydrogen bonds on an ALPHA HELIX
n ------ n + 4
carbonyl oxygen (red) bonds with amide hydrogen (white) to stabilize
55
Alpha helix vs Double helix
R groups face outwards
vs
Base pairs face inward
R groups don't hold together
vs
Base pairing to hold together
Single strand
vs
Double strand
N end and C end
vs
5' and 3', antiparallel
56
How to stabilize BETA SHEET
Carbonyl oxygen (C==O)and amide hydrogen (N--H)
57
how does the beta sheet work
in ONE polypeptide chain, they can start to fold and make neighbouring strands that are connected by stability bonds and usually a beta sheet is 4-5 strands
58
Beta sheet configuration describe and differentiate
Anti-parallel (N and C terminals alternate
parallel (N and C terminals repeat)
59
Whats a coiled coil (green and red)
what is the reason that a coiled coil forms
Hydrophobic and hydrophilic R groups sticking out on opposite sides of alpha helix.
Amphipathic reaction makes the hydrophobic R groups go together and the hydrophilic R groups go outwards, reacting to H2O in body
60
Tertiary structure combination possibilites
Backbone to backbone
backbone to side chain
Side chain to side chain
61
Proteins generally fold into the conformation that is the most ______________
energenetically favourable
62
What is a protein domain
special regions in protein that are specialized that have their own tertiary structures within the overall tertiary structure
63
whats a intrinsically disordered sequence when talking about protein domains
the seperate protein domains on a single chain that serve different purposes (SEMI INDEPENDANT) but are still connected since they are on the same polypeptide chian
64
whats a quaternary structure
more than 1 polypeptide chain (protein) together to form something (eg. hemoglobin)
65
Whats a multiprotein complex
what does it form (describe)
many identical subunits, mixtures of different proteins and DNA/RNAs
forms a molecular machine (eg. for DNA replication, initiation or transcription)
66
Genomes can come in many different sizes based on their
nucleotide pairs
67
Human genome size (how many base pairs per genome)
3billion
68
how many base pairs does one standard cell have and why
6 billion base pairs since your cell is mom genome plus dad genome
69
How many protein encoding genes are spread across 23 chromosome pairs
20,000
70
genome is not relative to...... (2 things)
organism size and complexity
71
72
50% of genome is and 50% is
repetitve DNA, non repetitive
73
less than _% of genome does what
encode protein
74
What are non repetitive sequences that aren't introns or exons f mor
decide which RNAs get transcribed in which cells and how much
75
Introns get
transcribed then sliced out
76
In repeated seauences , there is
segment duplications - thousands of base pairs are duplicated
simple repeats - CAGCAGCAGCAGCAGCAG
77
Mobile genentic elements
SOMETIMES cut themselves out, sometimes make a copy, sometimes paste themselves back
78
DNA-only transposons
DNA only
79
Retrotransposons
get made into RNA
80
LINEs
Long Intersperced nuclear elements
81
SINEs
short intersperced nuclear elements
82
What does Line and Sine diffent
line = grater than 500 base pairs
sine = shorter than 500 base pairs
83
1% exons are
protein coders
84
In a non-packaged state, small prokaryotic genomes still
occupy considerable portion of cell volume
85
In prokaryotes, the DNA is condensed through
folding and twisting about 1000 fold, complexed with proteins
86
Whats FISH
diagnostic technique to detect a presences of a specific sequence
87
Describe the process of FISH
Dying a probe DNA with a flourescent Dye, combine this dyed sample with a desired sample and denature everything , cool it down, if it binds to the DNA, it will shine. If no flourescense, then no DNA.
88
whats a probe DNA
anti parallel and complimentary to desired sequence
89
whats chromatin
tightly packaged single long linear DNA molecule
DNA + Protein = chromatin
90
levels of chromatin organization
DNa by itself, then it wraps around protein called beads on a string form chromatine, then these beads all get packaged into 30mn fiber wide each ting is called a nucleosomes, then nucleosomes get packaged into loops
91
Histones
small proteins rich in lysine and arginine
92
Four core histone proteins are called, what are they called together
Dimers, octomers
93
Outside linker histone is waht, does what
H1, paper clip to stick the beads together
94
nucleosome vs nucleosome core particel
nucleosome core particle excludes the linker dna, H1
95
Ine the 30nm fiber of packed nucleosomes, what is happening so that they can loop (coral shape)
sequence specigic clamp proteins and cohesins involved to form it
96
When cells enter mitosis, cohesions are replaced by _____ for what purpose
condensins to form double loops so that they can form more looops. and compact
97
dna chromatin packing/unpacking requires what to operate
ATP
98
Changing chromatin structure to a usable state requires
ATP
99
Heterochromatin (all)
Highly condensed chromatin
meotic and mitotic chromosomes
centromeres and telomeres
time spent highly condensed varies (constitutive - most time, facultative, some times)
100
Euchromatin
Non-condensed chromatin
Degree of condensation varies
Level of activity varies
101
Heterochromatic regions of interphase chromosomes are areas where gene expression is
surpressed
102
Active euchromatic regions of interphase chromosomes are areas where genes tend to be
expressed
103
How can chromosome regions switch and reserse between euchromatic and heterochromatic
things like localized covalent modification of histones, presence of chromatin remodeling complexes, RNa polymerase
104
how are interphase chromosomes seperated in the nucelus
they are in discrete specific regions
105
A colourful painting of a nucelus full of chromosomes is hwat
a chromosome painting hybridization
106
Homologuus chromosmes are detected by hybridzations via what indicator
the colour
107
if a gene is on, it is
being transcribed, becomes less condensed
108
Conservative replication
daughter's cells are separated. One entirey blue, one entirely red
109
Semiconservative replication
daughter cells are all mixed. One is blue red, other is blue red
110
NUcleotides are linked bye
phosphodiester bonds
111
read template dna from
3' to 5'
112
new strand of DNA is formed from what
adding onto the 3' end
113
3 main models occur in dna replication directionally
DNa is antiparallel
DNA is formed from 5' to 3'
template DNA is read 3' to 5'
114
what are replication forks
they go to left and right when seperating the double helix
115
how is bacteria replication unique
single replication origin
circular
116
How are eukaryotic replication unique
Multiple origins, much bigger
117
Initiator proteins steps for replication in bacteria
Initiator proteins bind to replication origin
helicase loading protein binds to helicase
helicase loading protein binds helicase onto DNA
then it leaves
118
Helicase function
unzips the helix
119
what are the 2 types of helicase
5' to 3' along lagging strand tempalte
120
To prevent DNA from sticking to itself and creating a hairpin after helicase has unzipped it,
Single stranded binding proteins
121
what are names for primase
DNA primase, RNA primase
122
RNA primers made by PRIMASE steps:
DNA polymerase adds to 3' ends, then primase kicks in since there is nothing so it makes a primer. The RNA primer is made from 5' to 3'
123
Primeosome is what
helicase + primase
124
what prevents DNA polymerase from sliding away
sliding clamp holds it in place
125
Whats the process of okazaki fragmentation and connections
The fragments containing RNA has polymerase make DNA approaching the 3' end and the DNa polymerase makes it until they are close together. Nucleases cut out the RNA fragment then there is a nick left over. A DNA LIGASE connects this nick, and links the two DNA segments
126
okazaki fragments on the lagging strand are connecteed through
APT then AMP is released.
127
Whats a replisome
molecular machine
128
what direction does primase read the template stran
3' to 5'
129
regarding dna polymerase:
Leading strand is synthesized .......
Lagging strand is synthesized ......
Okazaki fragments consist of ........
Dna ssynthesis is which direction
Primosome
continuously with 1 primer
discontinuously with multiple primers
DNa and rna primer
5' to 3'
Helicase + primaseq
130
predominant helicase is on which strand
lagging
131
Topoisomerase does what
cuts a small cut in the tangled spinning DNA so that it doesnt coil and released the tension
132
PRimase is not good at what, how is this resolved
putting a primer right at the end of the lagging strand.
Telomerase binds to the extra part of the template strand
133
What does telomerase do (whats telomere replication)
It makes the RNA template and keeps extending the 3' template end. it becomes long enough that primase will come in and keep adding the end.
134
How are issues in DNA replication addressed.
3'-5' exonuclease "backspaces" - a part of dNa polymerase
Strand directed mismatchj repair in eukaryotes
135
whata re the 2 cites of dna polymerase
the polymerizing side (making stuff)
the editing side (exonuclease)
136
Whats strand-directed mismath repair in eukarytoes and prokaryotes
an error in the strand, the nick hasnt been sealed yet, which is where the new strand is. So MUtL and MUts proteins remove the strand with error before the nick so that a new one can be repaired.
137
wahts BER and NER
base exersion repaire (one pair error fixed a time)
Nucleotide exision repair (group of multiple nucleotides fixed and replaced at a time)
138
whats nhej and hr
nonhomologus end joining - double strand break is combined with a special dna ligase (quick)
homologous end joining - use info on unbroken strand to use as a template (more accurate and slower)
139
Molecular definition of a gene
genes are segments of DNA that are TRANSCRIBED into RNA
140
more mRNA typically means
more protein
141
If the template DNA strand is read 3' to 5', then RNA is made
5' to 3' since it is antiparallel and complimentary
142
Sense vs antisense strand
Sense is the non template strand in DNA,
antisense is the template strand in DNA
143
What strand is the RNA sequence the same as in the DNA strand
the sense strand (non template) and T is replaced by U
144
RNa nucleotides are linked by
phosphodiester bonds
145
Read dna from _____ make rna from
3' to 5'
5' to 3'
146
RNA polymerase does not require a
primer
147
Incoming ribonucleoside triphosphates are
the particles that go intot he ribonucleoside triphosphate uptake channel that gets made in to the RNA transcript strand (same as sense strand)
148
Sigma factor + Rna polymerase core enzyme
RNAP holoenzyme
149
Sigma factors does what
detects where promoter is so that dna unwind can start, then the sigma factor lets go and the rna poolymerase elongates
150
in a protein sequence, 1 is , -10 is
1 is the start site for TRANSCRIPTION
-10 is where the promoter consensus sequence is and where sigma factor attaches.
151
The promoter is usually behind in orientation compared to
the direction that DNA template is read
152
WHEN NEW rna transcript leaves the RNAP, it begins to
bp with itself creating hairpins
153
Whats a terminator sequence
theres a penis that grows and and its G and C sticking together (hairpin)
154
In prokaryotes transcription and translation are
coupled - before translation is finished, transcript can begine
155
IN eukaryotes, transcription and translation cannot be
coupled
156
A final properly processed eukaryotic MRna looks like
all introns are cut out
exons are non coding and coding
poly a tail and 5' cap
157
RNAP1
most RNA gen
158
RNAPII
All protein encoding genes, special carboxyl terminal
159
RNAPIII
tRNA genes, 5s rNA genes
160
Eukaryoti RNa polymerases require proteins to help position at the promoter called
TRANSCRIPTION FACTORS
161
EUKARYOTIC RNA POLYMERASE DEALS WITH ___ ADN NOT _____
CHROMOSOMAL STRUCTURE
Sigma factors
162
TFIID means
its a TRANSCRIPTION facotr in eukaryotes
163
TATA box is waht
A sequence near 30bp that helps position RNAPII
164
TBP is what
tata box binding protein - mobilize TFIIB complex adjacent to TATA box
165
TBP is a subunit of TFIID and binds to the ----
attracts other transcription factors to help orient -------
TATA box promoter in the minor groove
RNAPii
166
How is RNA polymerase II activated
phosphorylation
167
whats phosphorylated
adding phosphate groups on SER located on the CTD
168
what does TFIIH do
seperate the starands in the initation of transcription
169
in transcription, AUG is where
a bit later on in
170
MRNA PROCESSING REVIEW: WHAT ARE MAIN STEPS
addition of 5' cap
removing introns
processing the poly A tail
171
waht does 5' cap do
protect RNA from 5' exonucleases (backspace)
172
the 5' cap is attached before
the MRna transcription is completed
173
How are introns removed in pre-mRNA
BRANCH POINT A adenine makes the intron into a lasso that binds to itself to fuckoff and then a spliceosome attached the exons
174
Pre-mrnas cannot
spliceosomes contain SnRNAS bound to protein (snRNPS) plus
spliceosomes assemble on mRNA to waht
When splciing complete, exon ...
self splice
other associated proteoins
remove introns
exon junction complex added
175
Different cells have different rna splicing differently cuz
they have different functions
176
whats a CTD
c terminal domain tail that is key to loading thee proteins
177
what does poly a tail do
protects the mRNA from the 3' exonuclease
178
CLeavage and addition of poly a tail
pac man and all the green beens on tthe A
179
Codons are read as mRNA triplets and they encode for..... how is redundancy good
all 20 amino acids
redundacy exists so that if a small mistake happenbs, its still may be the same and if its in the similar groups, its ok not big deal
180
codons are read
5' to 3'
181
only after the 5' AUG is when
the codons start making amino acids
182
all the mutations on nucleotide pairs
in book
183
all the frameshift mutations
184
what foes TRNA do
tRNAs recognize the codon on mRNA and bring it to the proper codon
Transcribed per usual (5' to 3')
Base pair itself in diff regions
anticodon is hwere it binds to mRNA, antiparallel, compoiemnary
185
How is redundancy managed in genetic code translatation
more than 1 trna for each codon
some trna recognise multiple codonds (wobble)
186
what is wobble
wobble is the 5' on the 3' and it cabn bascially wobble to change to possible anticodon bases
187
what is aminoacyl-tRNA synthetase
recognise amino acid, place on correct tRNA
188
Ribosomal structure
Large subunit and small subunit
these subunits are made up of proteins + rrnas
189
Ribosome cites are...... located on
APE cites
aminoacyl
peptidyl
exit
endoplasmic reticulum, in cytosol
190
how does translation work
the chain is created by the ribosome by it shifting forward when inputting the spaces of the correct tRNA.
191
EFTU and EF1
EF1 is in eukaruotes
EFTU is prokaryotes
(BINDER)
checks the aminoacyl tRNA to see if its right, then EF-tu cuts off phosphate off of GTP into GDP and ef-tu is released.
192
Slight delay before formation of p.p. bond in translation is to
allow one last check for accurate base pariing
193
waht does EF2 and EFG do
they are MOVERS
helps the ribosome move forward so that translation is faster.
194
overall mRNA structure in eukaryotes vs prokaryotes: EUkaryotes
5' cap and 3' poy a tail (protect from the 5' and 3' exonucleases)
In mature, introns get cut out and exons are coding and non coding regions
there are 5' and aslo 3' UTR (untranslated regions)
195
overall mRNA structure in eukaryotes vs prokaryotes: Prokaryotes
polycistronic (1 mrna encodes multiple proteins)
no cap or tail
multiple non coding regions since there are multiple AUG instead of just 1
196
whats polycistronic mrna
multiple proteins encoded by 1 mnra
197
197
the coding region in prokaryotuc mrna extends from
5' AUG --> stop
then next AUG --->. stop
198
waht are ribosome binding cites and what are they called
where the AUG is about to start
shine dalgarno sequences
199
200
Poolyribosomes
a chain of ribosomes that spiral (both pro and euk)
201
Whats the process of protein folding
Many proteins go through phosphorylastio and glycosylation
covalent modifications may be required to make protein active
202
How is protein degradation controlled (proteasomne and proteases)
Some last longer, some last shorter, so proteins that are targeted for degradation have a UBIQUITIN attached to it, and that directs the protein to the proteosome where proteases are made to recycle the protein into new ones
203
what is ubiquuiten
when a short live protein has a little protein attached to it called ubiquiten that leads it to the proteosome so that it can release proteases on to that specific short life protein so it can be recycled
204
