Midterm Flashcards
suffer
1
Q
What does a centrosome do
A
Organizes microtubules, and duplicates to make two poles of the mitotic spindle
2
Q
What is a centriole
A
Cylindrical microtubules at the centrosome during interphase, also at cilia and flagella
3
Q
What is chromatin
A
DNA and proteins that make up chromosomes. Single, long DNA molecule with protein that’s tightly packaged but accessible for transcription, replication, repair.
4
Q
What is a nucleolus
A
Part of the nucleus that makes ribosomes from ribosomal RNA, assembling subunits. It doesn’t have membrane.
5
Q
What are intermediate filaments
A
Medium thickness cytoskeleton that strengthen most animal cells
6
Q
What is a mitochondria
A
THE POWERHOUSE OF THE CELL (actually it uses energy from oxidization of sugars to make ATP)
7
Q
What does the Golgi do
A
Packages and modifies ER shit
8
Q
What three cell parts are exclusive to plants and prokaryotes?
A
Cell wall, vacuole, chloroplast
9
Q
What is a peroxisome
A
Small membrane enclosed organelle that has enzymes to degrade lipids and destroy toxins
10
Q
Name cytoskeleton from thinnest to thickest
A
Actin filaments, intermediate filaments, microtubules
11
Q
What do actin filaments do
A
Muscle contraction, they are common in muscle cells
12
Q
What do microtubules do
A
Pull duplicated chromosomes apart and distribute it in daughter cells. Thickest cytoskelly.
13
Q
What is a lysosome
A
Small, irregular organelles where intracellular digestion happens and food, waste is broken down for recycling or secretion
14
Q
What is an ER
A
Interconnected, membrane enclosed spaces for protein synthesis, enlarged in protein secretion cells.
15
Q
What are the thought origins of mitochondria
A
Ectosymbiosis which refers to organisms living on the body surface of another or inside.
16
Q
What type of cells were mitochondria and archaeon cells that engulfed mitochondria?
A
Mitochondria were aerobic, archaeon were anaerobic.
17
Q
What organelles were formed around the time of ingestiong mitochondria
A
The ER was made as the cell membrane folded in, nucleus formed around the same time as mitochondria.
18
Q
What is a model organism and what traits does it need
A
They represent a group of species. You need rapid development, small reproductive size, they need to be readily avaliable, tractable, and with understandable genetics. Regular development and growable indoors are bonuses.
19
Q
What is the endosymbiont hypothesis
A
Mitochondria have own genomes, genetic systems, protein, DNA, similar bacterial membranes
20
Q
What is the central dogma of biology
A
DNA is made into tRNA which transport amino acids to make proteins, mRNA to be translated into proteins, and rRNA, part of the ribosome. Then RNA translated into protein. Centra dogma refers to information flow
21
Q
What is a genome
A
All DNA or DNA sequences in a cell or organism
22
Q
What is a transcriptome
A
All RNA or RNA sequences in a cell or organism
23
Q
What is a proteome
A
All proteins in cell or organism
24
Q
What is an interactome
A
All protein/protein interactions in cell or organism
25
What is a metabolome
Small molecule metabolites in cell organism (such as cholesterol, hormones, nutrients, waste)
26
What is a phenome
All the phenotypes, this depends on the DNA, RNA, Protein, Interactome, and Metabolome
27
How do the -omes of the central dogma interact with each other
Proteome and interactome regulates transcriptome, transcriptome regulates genome. Proteins make up the interactome. Metabolome regulates transcriptome and genome
28
What are the three parts of a nucleotide?
phosphate, sugar, and base.
29
How many carbons are in the sugar ring? How many are there total? For nucleotide sugar
5, but only 4 in the ring. The fifth connects with phosphate.
30
How does the sugar differ between RNA and DNA, in nucleotides
DNA misses the O on the OH attached to 2' carbon.
31
What is a nucleotide
Sugar, base and at least one phosphate. Adenine, thymine, uracil, etc.
32
What is a nucleoside
Base and sugar with no phosphate.
33
What is a nucleoside monophosphate
sugar and base with one phosphate. You basically add a phosphate to a nucleoside. A NUCLEOSIDE MONOPHOSPHATE IS A NUCLEOTIDE
34
What are nucleic acid chains made from
DNA from deoxyribonucleoside triphosphates called dNTPs, or similarly for NTPs. They are nucleosides of the respective sugars with three phosphates chucked on.
35
What bonds are nucleotides linked together by
Phosphodiester bonds. The phosphate OH and 3'OH of the sugar react
36
How many hydrogen bonds are in A-T and G-C? What does this imply
A-T bonds have 2 H bonds, G-C has 3, G-C is a lot stickier and harder to break apart
37
What forces keep DNA together
Base pairing is due to hydrogen bonds, hydrophobic interactions keep the base pairs facing in, and the backbone is negatively charged and hydrophilic.
38
Why is DNA built like that
It needs to be in energetically favorable conformation, proteins need to recognize and make contact with the sequence on major and minor grooves.
39
What properties of DNA help it be transcribed and replicated.
Complementary and unzippable structure
40
What is on the 5' and 3' end of DNA
Phosphate and hydroxyl, respectively
41
WHat is denaturation, and what bonds are broken?
Noncovalent bonds, it happens around 100 degrees and renaturation restores the helices. It is a reversible process
42
What does the primary protein structure determine
Behavior and the secondary, tertiary, quaternary structures
43
What is the amino acid anatomy
The r group can vary, it determines the amino acid. The alpha carbon is in the middle, and the carboxyl group is bound to the alpha carbon, and so is the amino group. The alpha carbon has a hydrogen to fill octet
44
What types of r-groups are there
Acidic, basic (these two are both polar and charged), and uncharged, nonpolar.
45
How are amino aicds grouped together in the genetic code
By similar properties, to withstand some mutations.
46
What does cysteine do and what bonds does it form? What purpose do these bonds serve.
It forms disulphide bonds when oxidized, and this happens in the ER lumen. Disulphide bonds are like braces, they hold the protein stable.
47
How are disulphide bonds broken
When reduced in cytosol
48
How to form peptide bonds
The carboxyl O and H on amino hydrogen H bond when spaced. The OH on the carboxyl and H on the amino are yoinked as water, and now the carboxyl carbon and amino nitrogen are connected
49
What is a residue
Monomers of polypeptides (basically amino acids, but peptide bonded)
50
What part of the amino acid is not involved in peptide bond formation?
The R group, alpha carbon. Only carbonyl and amino acid are modified
51
What is the amino acid backbone
Everything aside from R groups
52
Is N-Tyr-Gly-Gly-Phe-Leu-C different from N-Leu-Phe-Gly-Gly-Tyr-C?
Yes, you cannot flip order of nucleotides
53
What is an alpha helix
When part of the polypeptide chain or the whole thing forms H bonds between carbonyl oxygen (double bonded to C) and amide hydrogen.
54
What groups do not participate in the structure of alpha helix
R groups
55
How do you know which residues will form H bonds.
Residue # n and n + 4
56
What are differences between alpha helix and DNA helix
Alpha helix: r groups face out and do not reinforce, it is single sranded, and has a C and N terminus. DNA: bases inward, are used to reinforce structure. It is double stranded and 3'-5'
57
What is a beta sheet and how does it bond
H bonding between C double bonded to O and amide hydrogen (same atoms) of neighboring strand. R groups not involved but project up and down.
58
What are two ways beta sheets can be organized? How many strands do they tend to have
Antiparallel and parallel. They can have 4-5 strands but you can have 10 or more
59
What is a coiled coil and what secondary structure is it formed from
It is formed by alpha helixes, but helices do not have to become a coiled coil. It is a type of supersecondary structure
60
What does it mean to be amphipathic, apply this to coiled coils
To have different biochemical properties on different sides. A coiled coil is an example, the inside of it is hydrophobic and the outside are R groups that are polar
61
Where are coiled coils found
Alpha keratin of skin hair, myosin motor proteins
62
What bonds participate in tertiary structure? What is tertiary structure.
It is the overall structure of protein held together by hydrophobic interactions, noncovalent bonds, covalent disulfide bonds (from cysteine). Basically other interactions from the residue backbones, r-groups, helices, and beta sheets.
63
What determines the tertiary structure
The amino acid sequence, it folds in the most favorable way
64
What proteins help fold tertiary structure
Chaperone proteins, they improve efficiency and reliability. They are more common than not.
65
What are protein domains
Parts of a protein specialized for different functions. They tend to have own tertiary structure, function semi-independently.
66
How many protein domains do eukaryotic proteins tend to have
2 or more
67
What are intrinsically disordered sequences
Sequences of amino acid connecting two domains. It participates in overall tertiary structure
68
What is a protein family
Proteins with similar amino acid sequences and tertiary sequences (if primary and tertiary similar, secondary is too, obviously). They EVOLVED to have different functions
69
How common are protein families, why
Most proteins have families and have similar structural domains
70
What is a quaternary structure? How do you define it
A bunch of tertiary structures that count as one quaternary. It has separate polypeptides, and each polypeptide has a C and N. Arbitrarily defined
71
What is a multiprotein complex and what is it used for
Identical subunits (actin filaments, for example) made of mixtures of DNA, RNA, and protein. They are molecular machines used for things like DNA replication and transcription. Must work together
72
How do you purify amino acid and find amino acid primary sequence
Use electrophoresis and affinity chromatography to purify it. Then mass spectroscopy to determine amino acid sequence
73
How do you determine 3d structure of protein
Cray crystallography, NMR spectroscopy, cryo-electron microscopy, alpha fold.
74
What is proteomics
large scale study of proteins to identify the structures, interactions, location, and turnover(meaning movement in and out, rates of depletion).
75
What is a genome
Entirety of organisms's hereditary information. This is usually DNA but some viruses have RNA genomes
76
How many genomes do yu have in somatic cells, how many base pairs
2 genomes and 6 billion base pairs total. You get one genome from each parent, 3 billion base pairs from each parent in the form of 23 chromosomes
77
How many protein coding genes do you have
20 thousand
78
How many chromosomes do you have in gametes
23 like normal cells, but there are 46 chromatids in somatic and only 23 chromatids in gametes
79
How much of the genome is repetitive, how much encodes protein
50% repeats, 1% encodes protein
80
How do prokaryotes organize genetic information
Nucleoids, they have no membrane but are organized
81
How do eukaryotes organize genetic information
Nucleus, it is a bilayer of inner and outer membrane
82
What is FISH (fluorence in situ hybridization)
Technique for detecting prescence of particular sequences, you label probes with fluorescent dye, denature with heat, and anneal them. DNA will shine with dye. Probe can be single or double stranded, and it is antiparallel. Samples and probes may bind back to itself but there is a ton of probes so some will bind to DNA.
83
What is a karyotype
Ordered array of chromosomes from longest to shortest. They show the chromosomes in somatic cell. One chromosome from each parent to form 23 pairs.
84
Summarize the cell cycle
In interphase, the chromosomes duplicate, genes are expressed, and you have two double helices (two chromatids) with one centromere. The chromatids move to the middle as mitosis begins and they are separated in mitosis
85
What are the chromatin organization structures
Double helix without protein, beads on a string (looping around nucleosome), chromatin fiber of packed nucleosomes, folded chromatin fiber
86
How many times is DNA folded?
10,000
87
What are the widths of beads on a string and packed nucleosomes organizational levels?
Respectively 11nm and 30 nm
88
What is a nucleosome
Basic structural unit in DNa comprised of a nucleosome core particle and linker DNA, and H1
89
What is a nucleosome core particle
Core histones, with 1 and 2/3 times wrapped around with DNA. No H1, No linker DNA
90
What is a histone
Small proteins rich in lysine and arginine, they have a positive charge, cancelling out the negative backbone charge of DNA and making chromosomes generally neutral.
91
What is an octamer core
You have four core histone proteins, TWO of each in the core. H2A, H2B, H3, H4.
92
What is a linker histone
It is not part of the octamer, it is H1, like a 3D printer extruder to fold the DNA in a way to save more space
93
How many nucleotides wrap around one octamer core
147
94
How long can the linker region be
up to 50 nucleotides
95
How is 30nm chromatin further folded
Sequence specific clamp proteins and cohesins form chromatin loops. Cohesins are replaced by condensins to make double loops in mitosis
96
How is DNA wound around octamers. What proteins can change structure of chromatin
ATP dependent chromatin remodelling complex uses ATP to scrunch it. Histone modifying enzymes can also alter chromatin structure.
97
What is euchromatin
Double helix or beads on a string, less condensed, but degree of condensation and activity varies (can be inactive or can be transcribed
98
What is active euchromatin and what is the opposite of that
The opposite is quiescent. If it is active, it is not scrunched and genes are expressed
99
What is heterochromatin where is it common
usually condensed DNA, makes up 40% of interphase chromosome, 80% in mitosis. It is common in meitotic and mitotic chromosomes, at centromeres and telomeres. Gene expression is surpressed
100
What are constitutive and facultative heterochromatin
Respectively almost always condensed, and temporarily condensed
101
How can you switch from one type of chromatin from another
Localized covalent modification of histones, chromatin modelling (unscrunching, mentioned before) and transcription complexes
102
What is the difference between interphase and mitotic chromosomes.
Interphase less schrombled
103
What are transcription factories and how to they help gene expression
Regions of nucleus with lots of substrates and proteins for transcription. Transcription does not need to happen here but it helps. Expressed gene is reorientated within chromatin to make chromatin less compact around it
104
What is the difference between conservative and semiconservative
Conservative is when one daughter cell has completely old DNA, other has new. Semiconservative is when complementary strands are on daughter cells.
105
How do dNTPs form nucleic acid chains
Deoxyribonucleoside triphosphates have 3 phosphates and ends up with one as it is hydrolyzed. It is linked by phosphodiester bonds
106
What does DNA polymerase do
cuts off two phosphates from the deoxyribonucleoside triphosphates and adds on 3' end.
107
What is the direction of DNA replication and why
Bidirectional from one starting point, because the DNA is complementary. You get a mash of leading and lagging strands
108
What are initiator proteins
proteins that help open helix. They bind to origins of replication, needs ATP. They help helicase bind (think about purple worms in slide 6 of week 4)
109
What is characteristic of start sites of replication
A-T rich sequence. Only a part of it needs to be AT rich. This is because AT has 2 H bonds and easier to break apart. There can be many sites but replication always starts at these specific sites
110
What is different between eukaryotic and bacterial DNA replication start sites?
Eukaryotes have many (normal and emergency ones) , bacteria only have one. They still have leading and lagging but you only have one replication start site for circular genomes
111
What direction does DNA synthesis occur
5' to 3', template read 3' to 5'
112
Is the replication fork symmetrical? Why
No, because you have leading strand on both left and righ hand side.
113
Does lagging strand get longer
No, it just gets more fragments
114
How to tell which strand is lagging
The strand close to template 3' lags
115
What is the general procedure for DNA synthesis
separate strands, synthesize, proofread
116
What needed for DNA synthesis
origins of replication, primers (makes RNA), dNTP, ATP, DNA polymerase, accessory proteins
117
How does helicase unwind DNA
The predominant one moves 5' to 4' along lagging strand (the none predominant one is in charge of DNA repair). It uses ATP and is on the separated strand, not the main strand
118
What do single stranded proteins do and what is the shorthand name. Where are they present
SS protein, they prevent rejoining of strands into hairpin shapes, in other words, prevents single strands from H bonding. They are present in every single stranded DNA region
119
What is a primosome
DNA primase stuck to helicase, before the synthesis begins
120
What are loading proteins and why do you need them
loading proteins enable helicase to bind to the DNA by binding to helicase. Initator proteins bind to DNA to help binding of helicase-loading protein complex
121
What are some other names for primase and why
DNA primase (makes primer for DNA synthesis) and RNA primase (makes RNA)
122
Why don't you just synthesize the entire DNA strand with primase
Because it is slow and inaccurate even though it starts from scratch.
123
What direction does primase move and why do you need it
It moves 3'-5' along the TEMPLATE. On the synthesized DNA, it adds on 3'. It provides a free 3'-OH for DNA polymerase to add onto
124
Summarize bacterial DNA replication steps
intiator proteins bind to origin of replication, helicase unwinds forks, single strand binding protein binds to prevent joining back together, primers made by primase
125
What is the purpose of a sliding clamp
To keep polymerase from detaching from the DNA
126
What happens after DNA polymerase is done synthesizing DNA?
RNA primer removed by nucleases and replaced with DNA by repair polymerases. Leaves a nick (small gap between part filled in with repair polymerase and the next DNA. Basically, each fragments miss a bit from the 3' end.
127
What fills the nicks in replication
Ligase
128
What is a clamp loader
It has two long arms and holds the DNA polymrease of the lagging strand in place as DNA forms a loop which enables replisome activity.
129
What is a replisome
A molecular machine comprised of helicase, polymerase, clamp loader
130
Why do you need a clamp loader, why do you need to make a loop on the lagging strand
To bring the 3' end of the completed Okazaki fragment closer to the start site of the next one
131
What is an Okazaki fragment made of
DNA and RNA primer. There are lots of primers
132
What is supercoiling caused by and how is it solved
Caused by torsional stress from helicase, and it is solved by topoisomerase which makes single stranded breaks. It is targeted for cancers
133
What happens at the end of linear chromosomes when done synthesizing (not circular)?
Chop off primases. Lagging strand has primer at 3' of the template strand, creating loss of info
134
What does Telomerase do
carries its own RNA template and adds repetition to 3' end, in a way resembling reverse transcriptase (RNA to DNA instead of vice versa). It makes a shit ton of G's on the ends, using a shit ton of C's on the RNA template. It works like a hair crimper
135
What direction does telomerase go and why does it need to elongate the 3' template strand
It also goe 5' to 3', it enables a new primer to be on the end and for ligase to seal the nick
136
What is a fixed mutation
when a mutation changes a nucleotide, forming an unusual base pair, then the replicated DNA has a completely different base pairing that you can't tell it's a mistake
137
How big is the human genome and how many nucleotides are changed per division
3* 10^9 base pairs, and 3 nucleotides changed per division
138
What are the two proofreading and repair mechanisms for replication
3'-5' exonuclease and strand directed mismatch repair
139
How does 3'-5' exonuclease work, where does this proofreading occur
Removes misincorporated nucleotides 3'-5'. It happens on the DNA polymerase
140
How does strand directed mismatch repair work
If the 3-5 exonuclease and proofreading fails, muts protein locks onto mismatch from detecting distortion of geometry from mismatched base pairs. MutS gets MutL, then it slides to the sliding clamp and MutL does the cutting. Then polymerase resynthesizes
141
How do prokaryotes repair and proofread replication
They use similar mechanism to detect methylated adenines
142
What is DNA damage caused by and what are some examples
Oxidization, radiation, heat chemicals. It causes cancers and makes pyrimidine dimers
143
Which nucleotides are pyrimidines and which are purines. What are the differences
Pyrimidines are cytosine, uracil, thymine. Purines are adenine and guanine. Purines have two rings.
144
What are examples of spontaneous DNA damage
Depurination, when water hits a purine and it's now gone. Deamination when cytosine turns to uracil. Then the complementary G becomes A. Depurination skips a nucleotide in one of the offpspring DNA, Deamination causes one fixed mutation and one ok offspring
145
What are the two types of DNA repair, when are they used each
Base excision and nucleotide excision. Respectively used with deamination or single nucleotide errors and multiple nnucleotide errors like pyrimidine dimers
146
How does base excision work
Glycosylase removes the nucleotide, endonuclease and phosphodiesterase removes backbone. Polymerase uses bottom template to remake and ligase seals
147
How does nucleotide excision work
cuts a shit ton off with excision nuclease, helicase yoinks it off the template, polymerase and ligase rebuild
148
What is homologous end joining
A repair mechanism for double stranded breaks, it is speedy and inaccurate and smacks shit together at random break point.
149
What is homologous end joining
A repair mechanism for double stranded breaks. It is accurate and slower, recombination nuclease trims the edges of the break point, then it uses the undamaged DNA as template
150
What is a gene
entire nucleic acid sequence needed for synthesis of protein and variants or entire nucleic acid sequence needed for RNA. Basically segments of DNA translated into RNA to do stuff. Because regardless of what stuff you do, you need the DNA to first become RNA
151
What are some stuff DNA can do with genes (basically what do you do with transcribed RNA)
Use to encode protein, if the RNA is mRNA, let the RNA just exist (as tRNA, telomerase RNA, or to stop protein synthesis)
152
What does the rate of transcription tell us about the amount of protein
Usually less mRNA means less protein but this isn't always true
153
What is the directionality of RNA synthesis in transcription
RNA is made 5'-3' like literally every fucking mechanism aren't living organisms funny (add onto 3' and DNA read 3'-5'). It is antiparallel and complementary
154
What nucleosides are used for transcription
This is so easy how am i even making a flashcard for this. Ribonucleoside triphosphates (ATP, UTP, CTP, GTP). DNA uses deoxy-
155
How do you find the 3' end of the DNA strand that the RNA is being synthesized off of
FInd 5' end of RNA, this should be the side where ribonucleoside triphosphates are not flowing in. Find the single DNA strand it is interacting with. The end of that DNA strand on the side of the 5' RNA strand is the 3' of the DNA
156
What is the transcription cycle
Sigma factor binds to RNA polymerase (RNAPII for people), finds the promoter of DNA, locally unwinds the DNA. A few short RNAs synthesized, then the sigma factor is yeeted and the polymerase clamps down on DNA. Then elongation happens (bulk of RNA is synthesized), and finally it is terminated and released
157
What is abortive transcription
Repeatedly making RNAs of 10 nucleotides
158
What is the RNA polmerase core enzyme
RNA polymerase without core enzyme (without sigma factor)
159
Why is Ghost on your kin list
He is fed up with everyone's bullshit, doesn't like talking with people, covers his face, not good at social situations and probably has repressed emotions. Very out of touch with his human desires
160
What is the RNA polymerase hollow enzyme
RNA polymerase with sigma factor or core enzyme
161
What is a promotor consensus sequence
THe most common sequence for promotors where sigma factor binds. It includes the spots ths sigma factor binds and everything in between. Common spots are -35 and -10, with 15-19 nucleotides inbetween.
162
What is the start site of transcription, and is it in the promotor sequence
It is denoted by +1. It is not in the promotor sequence and NOT AUG
163
What is up and downstream
Left of the transcription start site is up, right is down
164
How do sigma factors change RNA product
Different sigma factor factors bind to different, specific sequences.
165
How do you know which strand is transcribbed
It could be any as long as it's 3'-5'. On the template, there must be a promotor region on the end of the gene that is closer to 3'
166
What happens to the RNA after it leaves and is done being synthesized
It base pairs with itself forming hairpins
167
What are two parts of RNA synthesis, which one is more efficient
Initial steps, present in abortive, are less efficient, and elongation is more efficient
168
How is transcription terminated
Hairpin structures are formed by stronger G-C sequences that triple H bond with itself and pries the RNA polymerase off. It messes up the H bonding between transcript DNA polymerase, freeing the RNA. This G-C rich sequence is followed by a ton of A-T on the DNA sequence because they are weak and can be broken easily
169
How does prokaryotic gene expression differ from eukaryotic
Prokaryotic gene expression has circular DNA without nucleus and translation and transcription is coupled. You can make proteins before you are even done making RNA. Not for eukaryotic
170
What is pre-mRNA made of
Introns and exons
171
What happens in the nucleus of eukaryotes for gene expression
transcription, 5' capping, RNA splicing (removing introns), 3' polyadenylation. makes mature mRNA
172
What happens in cytosol of eukaryotes in for gene expression
translation and degradation of RNA to be reused as ribonucleoside triphosphates
173
What is a mature mRNA made of
a 5' cap made of a methylated guanine and 3 phosphates, exons (has a noncoding 5' untranslated region/UTR and noncoding 3'UTR) and a poly a tail
174
How long are poly A tails
150-200 nucleotides
175
What do untranslated regions (UTR) do in mature mRNA
It controls how much translation and RNA stability
176
What three types of RNA are present in both prokaryotes and eukaryotes
mRNA, rRNA, tRNA
177
WHat are the eukaryote specific RNAs and what do they do
Telomerase RNA: template for telomerase enzyme to extend chromosomes (it's the hair crimper RNA). snRNA: small nuclear RNA, it slices pre-mRNA in the nucleus.
178
What are the three eukaryotic RNA polymerases and what do they transcribe
RNAPI: most rRNA genes, RNAPII: mRNAs (protein coding genes and noncoding mRNAS), RNAPIII: tRNA. THey are all multi-subunit proteins
179
What is unique about RNAPII
It has a carboxyl terminal domain and no other RNA polymerase does
180
How many subunits are in RNAP II and how many are in RNAP for prokaryotes
Respectively 12 and 5
181
What positions eukaryotic RNA polymerases, where is it positioned. What eukaryote-specific problem does it have to deal with
Transcription factos (complicated sigma factors, basically). It is positioned at promoters and need to deal with chromosomal structures
182
What is different about eukaryotic promoters
THey have more variation, have specific sequences called elements at specific locations. Elements are recognized by specific or general transcription factors that position polymerase
183
What is a TATA box
An element about 30 bp upstream of the start site, it positions RNAP II and general transcription factors
184
How is transcription initiated
TBP subunit of transcription factor II D (TF2D) binds to the Tata box, TF2B binds adjacent. Other transcription factors bind, to help orient the RNAP II, and the polymerase and transcription factors can bind at the transcription start site.
185
What does the transcription factor II helicase do
Adds phosphate to C-terminal domain (onto Serine), activating it so transcription can begin. It uses ATP to pry the DNA strands apart
186
What does the mediator do in transcription
Activates factors (looks like its hugging factors)
187
What does the activator protein do in transcription
Activates mediator, FINALLY BEGINS TRANSCRIPTION SLOW ASS MECHANISM
188
What is characteristic of the C-terminal domain in RNAP II
Repeats 7 amino acids in tandem. 26x for people and 52x for people. Essential for viability
189
What things make up mRNA processing
Adding 5' cap, processing and poly adenylation (adding A's repeatedly) onto 3' tail. Splicing of introns.
190
How do mRNA processing occur
Capping proteins and splicing proteins go to 5'mRNA from phosphorylation of C-terminal tail
191
What is 5' pre-mRNA capping and why do you need it
It prevents 5'-3' exonuclease from eating it by chopping phosphodiester bonds. It forms a 5'-5' triphosphate bridge by adding a methylguanosine to the 5' end. Done before mRNA is fully transcribed
192
How is intron removed
You have a 2'HO (exclusive to RNA), which forms a 2'-5' phosphodiester bond with the 5' side of the intron. It makes a lariat. The 2'OH is connected to branch point A. Then the OH of the 3' attacks the 5' of the end which the lariat is attached, freeing the lariat. Lariat is now gone
193
What enzyme do you need for removing intron, what is this enzyme made of
Spliceosome: it contains snRNAs + proteins. snRNAs + proteins are called snRNPs. snRNPs are thus a part of spliceosome
194
Why can't DNA be spliced
Because 2'OH is needed but DNA does not have that on deoxyribose
195
What is added after slicing is done, why
Exon junction, to show the thing has been spliced
196
Can intron removal happen wherever you want
No you idiot you need specific sequences that are recognized by snRNAs used by spliceosomes
197
What does alternative splicing do
Creates different gene products such as different cell types
198
What can single nucleotide changes to do splicing
Destroy splice sites and the exon is removed with intron, activate cryptic splice site extending the exon, creating a new splice site, adding exon in the middle of an intron
199
What does the phosphorylation of CTD determine
It determines what proteins can be on it
200
What happens to the consensus sequences (G-U rich)? Are they in the genome, are they transcribed
They are in the genome and transcribed, but they are discarded by 3' end processing proteins that trash them in the nucleus. Poly A sequence is not in the genome. It is added after G-U rich stuff is trashed. BTW the GU-rich is on the 3' end because it is at the end of the RNA, and that's the thing that made the hairpin to terminate transcription
201
How does the cleavage of G-U rich sequences happen
Cleavage factors go from CTD to RNA, cleaves the ends.
202
How are poly As added, what proteins does mature mRNA have on tail
Poly-A polymerase adds onto the end and RNA synthesizing Gu/U ends stop. 3' end processing proteins go from CTD to RNA. PAP and Poly A binding protein extends it. Then the 3' end proteins leave, leaving only poly A binding proteins on and you have mature mRNA
203
What is the purpose of the poly A
To protect from 3' exonuclease
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Where does translation happen
In the cytoplasm
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What is the genetic code
It tells you what codons are correlated to what mRNA triplets
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What is redundancy
There are multiple codons for most amino acids
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How does translation start
5'most AUG is the start of translation but not transcription. There will be more nucleotides on the RNA before the AUG
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What are the two types of mutations, how do you see the effect?
Subsitution and deletion. To see the effect you need to see the genetic code
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What are the types of effects of mutations
Silent causes nothing, missense causes wrong amino acid, nonsense causes early stop codon. It does not necessarily cause frame shift (if three nucleotides are deleted, you will just miss an amino acid, the following amino acids will stay the same)
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How does tRNA bind to amino acid and how does it bind to mRNA
Anticodon is antiparallel to mRNA and complementary, and the 3' end of tRNA attaches to the amino acid. It recognizes the codons
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How do you find the amino acid bound to tRNA
Read 5'-3' on the mRNA complementary to anticodon because GENETIC CODE TABLE IS 5'-3'
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How long are tRNAs
80 nucleotides
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How are the 5' and 3' ends transcribed for tRNA
As normal RNA
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Why does tRNA have double helical regions
Base pairs with itself (hydrogen bonding)
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How is redundancy dealt with
More than 1 tRNA for many amino acids. Some tRNAs recognize and base pair with more than one codon, known as wobble base pairing. it's at the 5' end of the anticodon or the 3' ed of the codon that allows many bases including modified ones
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How are errors prevented in translation
Amino acyl tRNA synthetases recognize tRNA, put correct amino acid on. Then it base pairs with correct nucleotides. Amino acyl tRNA synthetase corrects errors with hydrolytic editing
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How many amino-acyl tRNA synthetases are there, are there more or less tRNAs than amino-acyl tRNA synthetases
20, one for each amino acid. There are tRNAs because you can have more than one for an amino acid
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How does the synthetase recognize tRNA
Identifies the anticodon nucleotides and the 3' end which will then bind to an amino acid. Also checks elsewhere
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Where are ribosomal subunits in the cell
ER and cytosol
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What is the big and small subunits of ribosomes made of respectively
Many proteins and many rRNAs. Small has many proteins ONE rRNA.
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Where are rRNAs common in ribosome subunits
At the three sites
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What are the three ribosome sites
E for exit, p for peptidal (holding in Place) and A for aminoacyl (entrAnce)
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Why is peptide synthesis energetically favorable
Energy stored in covalent bond between amino acid and tRNA in P site makes it favorable. It is high energy.
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What is formation of peptide bond in ribosomes catalyzed by
The peptidyl transferase in the large ribosomal subunit
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What is a ribozyme
RNA molecules that have catalytic activity. RNA part of ribosome catalyzes peptide bond formation, for example
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Is there more RNA or protein in ribosomes
RNA, it's at the 3 sites
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What does EF-Tu do? What is the eukaryotic version
EF1, it is quality control and an elongation factor. If base pairing is wrong, EF-Tu or EF1 will not go away and peptide bond will not form. If correct, GTP hydrolyzed and released. Releases energy
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Aside from elongation factors, what further helps quality control
Slight delay before formation of polypeptide bond before last check for base pairing
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What does EF-G do, what is the eukaryotic version
Moves the mRNA forward one codon and helps speed up the elongation. EF2 in eularyotes. It is hydrolyzed as well. Big subunit moves first
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Can you translate without elongation factors
Yes but its slower.
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What is the difference between noncoding sequences and UTR
noncoding sites include the part before AUG, ribosome binding sites in prokaryotes. they also include the UTRs.
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What is a polycystronic mRNA and where is it present
It is in prokaryotes, meaning multiple proteins in one mRNA
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What is a shine dalgarno sequence and what is the normal name
also called ribosome binding sites, they are prokaryotic and bind with rRNA on the small ribosomal subunits to move the units to AUG. Requries initiation factors (not elongation).
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How does prokaryotic translation begin after small subunits are positioned on AUG
fMethionine is bound to AUG, large subunit binds
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How is eukaryotic translation began
initiator tRNA with Met (amino acid) on small subunit with translation initiation factors binds to mRNAs, looks for 5'most AUG. Translation initiaton factors leave, large subunit binds. tRNA with amino acid binds to A site, first peptide bond forms.
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What does it mean for a tRNA to be charged
When it has an amino acid. Done by aminoacyl tRNA synthetase
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How to terminate translation
Protein release factor binds to A site, large subunit moves forth. Now the release factor is in P site, and the tRNA for the previous amino acid is n E. The chain is released, and ribosome yeets itself. For all organisms
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What type of macromolecule is the human translation release factor
Protein, not tRNA
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What is a polysome, why and in what organisms.
When before translation finishes, another begins in another spot. Because protein synthesis is kinda slow. In bacteria and eukaryotes
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How far apart are ribosomes for polysomes
80 nucleotides
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What are post translational modification examples
Phosphorylation, glycosylation, non-covalent binding to other proteins. Covalent modifications make the protein active and get it to recruit correct membrane or organelle
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How long do proteins last
Some short, others months or years
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What is ubiquitin and where does it bring proteins
Small protein covalently attached, directs to proteasome, where it is eaten by proteases. Recycled into new.
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What happens if you inhibit translation and transcription.
Kills cells. Poison is if its eukaryotes, bacteria is antibiotics
