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Bio130 bitchhhh > Midterm > Flashcards

Midterm Flashcards

suffer

1
Q

What does a centrosome do

A

Organizes microtubules, and duplicates to make two poles of the mitotic spindle

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2
Q

What is a centriole

A

Cylindrical microtubules at the centrosome during interphase, also at cilia and flagella

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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.

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4
Q

What is a nucleolus

A

Part of the nucleus that makes ribosomes from ribosomal RNA, assembling subunits. It doesn’t have membrane.

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5
Q

What are intermediate filaments

A

Medium thickness cytoskeleton that strengthen most animal cells

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6
Q

What is a mitochondria

A

THE POWERHOUSE OF THE CELL (actually it uses energy from oxidization of sugars to make ATP)

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7
Q

What does the Golgi do

A

Packages and modifies ER shit

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8
Q

What three cell parts are exclusive to plants and prokaryotes?

A

Cell wall, vacuole, chloroplast

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9
Q

What is a peroxisome

A

Small membrane enclosed organelle that has enzymes to degrade lipids and destroy toxins

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10
Q

Name cytoskeleton from thinnest to thickest

A

Actin filaments, intermediate filaments, microtubules

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11
Q

What do actin filaments do

A

Muscle contraction, they are common in muscle cells

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12
Q

What do microtubules do

A

Pull duplicated chromosomes apart and distribute it in daughter cells. Thickest cytoskelly.

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13
Q

What is a lysosome

A

Small, irregular organelles where intracellular digestion happens and food, waste is broken down for recycling or secretion

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14
Q

What is an ER

A

Interconnected, membrane enclosed spaces for protein synthesis, enlarged in protein secretion cells.

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15
Q

What are the thought origins of mitochondria

A

Ectosymbiosis which refers to organisms living on the body surface of another or inside.

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16
Q

What type of cells were mitochondria and archaeon cells that engulfed mitochondria?

A

Mitochondria were aerobic, archaeon were anaerobic.

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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.

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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.

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19
Q

What is the endosymbiont hypothesis

A

Mitochondria have own genomes, genetic systems, protein, DNA, similar bacterial membranes

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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

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21
Q

What is a genome

A

All DNA or DNA sequences in a cell or organism

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22
Q

What is a transcriptome

A

All RNA or RNA sequences in a cell or organism

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23
Q

What is a proteome

A

All proteins in cell or organism

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24
Q

What is an interactome

A

All protein/protein interactions in cell or organism

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25
Q

What is a metabolome

A

Small molecule metabolites in cell organism (such as cholesterol, hormones, nutrients, waste)

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26
Q

What is a phenome

A

All the phenotypes, this depends on the DNA, RNA, Protein, Interactome, and Metabolome

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27
Q

How do the -omes of the central dogma interact with each other

A

Proteome and interactome regulates transcriptome, transcriptome regulates genome. Proteins make up the interactome. Metabolome regulates transcriptome and genome

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28
Q

What are the three parts of a nucleotide?

A

phosphate, sugar, and base.

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29
Q

How many carbons are in the sugar ring? How many are there total? For nucleotide sugar

A

5, but only 4 in the ring. The fifth connects with phosphate.

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30
Q

How does the sugar differ between RNA and DNA, in nucleotides

A

DNA misses the O on the OH attached to 2’ carbon.

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31
Q

What is a nucleotide

A

Sugar, base and at least one phosphate. Adenine, thymine, uracil, etc.

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32
Q

What is a nucleoside

A

Base and sugar with no phosphate.

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33
Q

What is a nucleoside monophosphate

A

sugar and base with one phosphate. You basically add a phosphate to a nucleoside. A NUCLEOSIDE MONOPHOSPHATE IS A NUCLEOTIDE

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34
Q

What are nucleic acid chains made from

A

DNA from deoxyribonucleoside triphosphates called dNTPs, or similarly for NTPs. They are nucleosides of the respective sugars with three phosphates chucked on.

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35
Q

What bonds are nucleotides linked together by

A

Phosphodiester bonds. The phosphate OH and 3’OH of the sugar react

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36
Q

How many hydrogen bonds are in A-T and G-C? What does this imply

A

A-T bonds have 2 H bonds, G-C has 3, G-C is a lot stickier and harder to break apart

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37
Q

What forces keep DNA together

A

Base pairing is due to hydrogen bonds, hydrophobic interactions keep the base pairs facing in, and the backbone is negatively charged and hydrophilic.

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38
Q

Why is DNA built like that

A

It needs to be in energetically favorable conformation, proteins need to recognize and make contact with the sequence on major and minor grooves.

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39
Q

What properties of DNA help it be transcribed and replicated.

A

Complementary and unzippable structure

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40
Q

What is on the 5’ and 3’ end of DNA

A

Phosphate and hydroxyl, respectively

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41
Q

WHat is denaturation, and what bonds are broken?

A

Noncovalent bonds, it happens around 100 degrees and renaturation restores the helices. It is a reversible process

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42
Q

What does the primary protein structure determine

A

Behavior and the secondary, tertiary, quaternary structures

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43
Q

What is the amino acid anatomy

A

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

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44
Q

What types of r-groups are there

A

Acidic, basic (these two are both polar and charged), and uncharged, nonpolar.

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45
Q

How are amino aicds grouped together in the genetic code

A

By similar properties, to withstand some mutations.

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46
Q

What does cysteine do and what bonds does it form? What purpose do these bonds serve.

A

It forms disulphide bonds when oxidized, and this happens in the ER lumen. Disulphide bonds are like braces, they hold the protein stable.

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47
Q

How are disulphide bonds broken

A

When reduced in cytosol

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48
Q

How to form peptide bonds

A

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

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49
Q

What is a residue

A

Monomers of polypeptides (basically amino acids, but peptide bonded)

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50
Q

What part of the amino acid is not involved in peptide bond formation?

A

The R group, alpha carbon. Only carbonyl and amino acid are modified

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51
Q

What is the amino acid backbone

A

Everything aside from R groups

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52
Q

Is N-Tyr-Gly-Gly-Phe-Leu-C different from N-Leu-Phe-Gly-Gly-Tyr-C?

A

Yes, you cannot flip order of nucleotides

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53
Q

What is an alpha helix

A

When part of the polypeptide chain or the whole thing forms H bonds between carbonyl oxygen (double bonded to C) and amide hydrogen.

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54
Q

What groups do not participate in the structure of alpha helix

A

R groups

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55
Q

How do you know which residues will form H bonds.

A

Residue # n and n + 4

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56
Q

What are differences between alpha helix and DNA helix

A

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’

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57
Q

What is a beta sheet and how does it bond

A

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.

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58
Q

What are two ways beta sheets can be organized? How many strands do they tend to have

A

Antiparallel and parallel. They can have 4-5 strands but you can have 10 or more

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59
Q

What is a coiled coil and what secondary structure is it formed from

A

It is formed by alpha helixes, but helices do not have to become a coiled coil. It is a type of supersecondary structure

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60
Q

What does it mean to be amphipathic, apply this to coiled coils

A

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

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61
Q

Where are coiled coils found

A

Alpha keratin of skin hair, myosin motor proteins

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62
Q

What bonds participate in tertiary structure? What is tertiary structure.

A

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.

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63
Q

What determines the tertiary structure

A

The amino acid sequence, it folds in the most favorable way

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64
Q

What proteins help fold tertiary structure

A

Chaperone proteins, they improve efficiency and reliability. They are more common than not.

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65
Q

What are protein domains

A

Parts of a protein specialized for different functions. They tend to have own tertiary structure, function semi-independently.

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66
Q

How many protein domains do eukaryotic proteins tend to have

A

2 or more

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67
Q

What are intrinsically disordered sequences

A

Sequences of amino acid connecting two domains. It participates in overall tertiary structure

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68
Q

What is a protein family

A

Proteins with similar amino acid sequences and tertiary sequences (if primary and tertiary similar, secondary is too, obviously). They EVOLVED to have different functions

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69
Q

How common are protein families, why

A

Most proteins have families and have similar structural domains

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70
Q

What is a quaternary structure? How do you define it

A

A bunch of tertiary structures that count as one quaternary. It has separate polypeptides, and each polypeptide has a C and N. Arbitrarily defined

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71
Q

What is a multiprotein complex and what is it used for

A

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

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72
Q

How do you purify amino acid and find amino acid primary sequence

A

Use electrophoresis and affinity chromatography to purify it. Then mass spectroscopy to determine amino acid sequence

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73
Q

How do you determine 3d structure of protein

A

Cray crystallography, NMR spectroscopy, cryo-electron microscopy, alpha fold.

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74
Q

What is proteomics

A

large scale study of proteins to identify the structures, interactions, location, and turnover(meaning movement in and out, rates of depletion).

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75
Q

What is a genome

A

Entirety of organisms’s hereditary information. This is usually DNA but some viruses have RNA genomes

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76
Q

How many genomes do yu have in somatic cells, how many base pairs

A

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

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77
Q

How many protein coding genes do you have

A

20 thousand

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78
Q

How many chromosomes do you have in gametes

A

23 like normal cells, but there are 46 chromatids in somatic and only 23 chromatids in gametes

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79
Q

How much of the genome is repetitive, how much encodes protein

A

50% repeats, 1% encodes protein

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80
Q

How do prokaryotes organize genetic information

A

Nucleoids, they have no membrane but are organized

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81
Q

How do eukaryotes organize genetic information

A

Nucleus, it is a bilayer of inner and outer membrane

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82
Q

What is FISH (fluorence in situ hybridization)

A

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.

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83
Q

What is a karyotype

A

Ordered array of chromosomes from longest to shortest. They show the chromosomes in somatic cell. One chromosome from each parent to form 23 pairs.

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84
Q

Summarize the cell cycle

A

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

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85
Q

What are the chromatin organization structures

A

Double helix without protein, beads on a string (looping around nucleosome), chromatin fiber of packed nucleosomes, folded chromatin fiber

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86
Q

How many times is DNA folded?

A

10,000

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87
Q

What are the widths of beads on a string and packed nucleosomes organizational levels?

A

Respectively 11nm and 30 nm

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88
Q

What is a nucleosome

A

Basic structural unit in DNa comprised of a nucleosome core particle and linker DNA, and H1

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89
Q

What is a nucleosome core particle

A

Core histones, with 1 and 2/3 times wrapped around with DNA. No H1, No linker DNA

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90
Q

What is a histone

A

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.

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91
Q

What is an octamer core

A

You have four core histone proteins, TWO of each in the core. H2A, H2B, H3, H4.

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92
Q

What is a linker histone

A

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

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93
Q

How many nucleotides wrap around one octamer core

A

147

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94
Q

How long can the linker region be

A

up to 50 nucleotides

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95
Q

How is 30nm chromatin further folded

A

Sequence specific clamp proteins and cohesins form chromatin loops. Cohesins are replaced by condensins to make double loops in mitosis

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96
Q

How is DNA wound around octamers. What proteins can change structure of chromatin

A

ATP dependent chromatin remodelling complex uses ATP to scrunch it. Histone modifying enzymes can also alter chromatin structure.

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97
Q

What is euchromatin

A

Double helix or beads on a string, less condensed, but degree of condensation and activity varies (can be inactive or can be transcribed

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98
Q

What is active euchromatin and what is the opposite of that

A

The opposite is quiescent. If it is active, it is not scrunched and genes are expressed

99
Q

What is heterochromatin where is it common

A

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
Q

What are constitutive and facultative heterochromatin

A

Respectively almost always condensed, and temporarily condensed

101
Q

How can you switch from one type of chromatin from another

A

Localized covalent modification of histones, chromatin modelling (unscrunching, mentioned before) and transcription complexes

102
Q

What is the difference between interphase and mitotic chromosomes.

A

Interphase less schrombled

103
Q

What are transcription factories and how to they help gene expression

A

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
Q

What is the difference between conservative and semiconservative

A

Conservative is when one daughter cell has completely old DNA, other has new. Semiconservative is when complementary strands are on daughter cells.

105
Q

How do dNTPs form nucleic acid chains

A

Deoxyribonucleoside triphosphates have 3 phosphates and ends up with one as it is hydrolyzed. It is linked by phosphodiester bonds

106
Q

What does DNA polymerase do

A

cuts off two phosphates from the deoxyribonucleoside triphosphates and adds on 3’ end.

107
Q

What is the direction of DNA replication and why

A

Bidirectional from one starting point, because the DNA is complementary. You get a mash of leading and lagging strands

108
Q

What are initiator proteins

A

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
Q

What is characteristic of start sites of replication

A

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
Q

What is different between eukaryotic and bacterial DNA replication start sites?

A

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
Q

What direction does DNA synthesis occur

A

5’ to 3’, template read 3’ to 5’

112
Q

Is the replication fork symmetrical? Why

A

No, because you have leading strand on both left and righ hand side.

113
Q

Does lagging strand get longer

A

No, it just gets more fragments

114
Q

How to tell which strand is lagging

A

The strand close to template 3’ lags

115
Q

What is the general procedure for DNA synthesis

A

separate strands, synthesize, proofread

116
Q

What needed for DNA synthesis

A

origins of replication, primers (makes RNA), dNTP, ATP, DNA polymerase, accessory proteins

117
Q

How does helicase unwind DNA

A

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
Q

What do single stranded proteins do and what is the shorthand name. Where are they present

A

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
Q

What is a primosome

A

DNA primase stuck to helicase, before the synthesis begins

120
Q

What are loading proteins and why do you need them

A

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
Q

What are some other names for primase and why

A

DNA primase (makes primer for DNA synthesis) and RNA primase (makes RNA)

122
Q

Why don’t you just synthesize the entire DNA strand with primase

A

Because it is slow and inaccurate even though it starts from scratch.

123
Q

What direction does primase move and why do you need it

A

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
Q

Summarize bacterial DNA replication steps

A

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
Q

What is the purpose of a sliding clamp

A

To keep polymerase from detaching from the DNA

126
Q

What happens after DNA polymerase is done synthesizing DNA?

A

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
Q

What fills the nicks in replication

A

Ligase

128
Q

What is a clamp loader

A

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
Q

What is a replisome

A

A molecular machine comprised of helicase, polymerase, clamp loader

130
Q

Why do you need a clamp loader, why do you need to make a loop on the lagging strand

A

To bring the 3’ end of the completed Okazaki fragment closer to the start site of the next one

131
Q

What is an Okazaki fragment made of

A

DNA and RNA primer. There are lots of primers

132
Q

What is supercoiling caused by and how is it solved

A

Caused by torsional stress from helicase, and it is solved by topoisomerase which makes single stranded breaks. It is targeted for cancers

133
Q

What happens at the end of linear chromosomes when done synthesizing (not circular)?

A

Chop off primases. Lagging strand has primer at 3’ of the template strand, creating loss of info

134
Q

What does Telomerase do

A

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
Q

What direction does telomerase go and why does it need to elongate the 3’ template strand

A

It also goe 5’ to 3’, it enables a new primer to be on the end and for ligase to seal the nick

136
Q

What is a fixed mutation

A

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
Q

How big is the human genome and how many nucleotides are changed per division

A

3* 10^9 base pairs, and 3 nucleotides changed per division

138
Q

What are the two proofreading and repair mechanisms for replication

A

3’-5’ exonuclease and strand directed mismatch repair

139
Q

How does 3’-5’ exonuclease work, where does this proofreading occur

A

Removes misincorporated nucleotides 3’-5’. It happens on the DNA polymerase

140
Q

How does strand directed mismatch repair work

A

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
Q

How do prokaryotes repair and proofread replication

A

They use similar mechanism to detect methylated adenines

142
Q

What is DNA damage caused by and what are some examples

A

Oxidization, radiation, heat chemicals. It causes cancers and makes pyrimidine dimers

143
Q

Which nucleotides are pyrimidines and which are purines. What are the differences

A

Pyrimidines are cytosine, uracil, thymine. Purines are adenine and guanine. Purines have two rings.

144
Q

What are examples of spontaneous DNA damage

A

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
Q

What are the two types of DNA repair, when are they used each

A

Base excision and nucleotide excision. Respectively used with deamination or single nucleotide errors and multiple nnucleotide errors like pyrimidine dimers

146
Q

How does base excision work

A

Glycosylase removes the nucleotide, endonuclease and phosphodiesterase removes backbone. Polymerase uses bottom template to remake and ligase seals

147
Q

How does nucleotide excision work

A

cuts a shit ton off with excision nuclease, helicase yoinks it off the template, polymerase and ligase rebuild

148
Q

What is homologous end joining

A

A repair mechanism for double stranded breaks, it is speedy and inaccurate and smacks shit together at random break point.

149
Q

What is homologous end joining

A

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
Q

What is a gene

A

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
Q

What are some stuff DNA can do with genes (basically what do you do with transcribed RNA)

A

Use to encode protein, if the RNA is mRNA, let the RNA just exist (as tRNA, telomerase RNA, or to stop protein synthesis)

152
Q

What does the rate of transcription tell us about the amount of protein

A

Usually less mRNA means less protein but this isn’t always true

153
Q

What is the directionality of RNA synthesis in transcription

A

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
Q

What nucleosides are used for transcription

A

This is so easy how am i even making a flashcard for this. Ribonucleoside triphosphates (ATP, UTP, CTP, GTP). DNA uses deoxy-

155
Q

How do you find the 3’ end of the DNA strand that the RNA is being synthesized off of

A

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
Q

What is the transcription cycle

A

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
Q

What is abortive transcription

A

Repeatedly making RNAs of 10 nucleotides

158
Q

What is the RNA polmerase core enzyme

A

RNA polymerase without core enzyme (without sigma factor)

159
Q

Why is Ghost on your kin list

A

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
Q

What is the RNA polymerase hollow enzyme

A

RNA polymerase with sigma factor or core enzyme

161
Q

What is a promotor consensus sequence

A

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
Q

What is the start site of transcription, and is it in the promotor sequence

A

It is denoted by +1. It is not in the promotor sequence and NOT AUG

163
Q

What is up and downstream

A

Left of the transcription start site is up, right is down

164
Q

How do sigma factors change RNA product

A

Different sigma factor factors bind to different, specific sequences.

165
Q

How do you know which strand is transcribbed

A

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
Q

What happens to the RNA after it leaves and is done being synthesized

A

It base pairs with itself forming hairpins

167
Q

What are two parts of RNA synthesis, which one is more efficient

A

Initial steps, present in abortive, are less efficient, and elongation is more efficient

168
Q

How is transcription terminated

A

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
Q

How does prokaryotic gene expression differ from eukaryotic

A

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
Q

What is pre-mRNA made of

A

Introns and exons

171
Q

What happens in the nucleus of eukaryotes for gene expression

A

transcription, 5’ capping, RNA splicing (removing introns), 3’ polyadenylation. makes mature mRNA

172
Q

What happens in cytosol of eukaryotes in for gene expression

A

translation and degradation of RNA to be reused as ribonucleoside triphosphates

173
Q

What is a mature mRNA made of

A

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
Q

How long are poly A tails

A

150-200 nucleotides

175
Q

What do untranslated regions (UTR) do in mature mRNA

A

It controls how much translation and RNA stability

176
Q

What three types of RNA are present in both prokaryotes and eukaryotes

A

mRNA, rRNA, tRNA

177
Q

WHat are the eukaryote specific RNAs and what do they do

A

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
Q

What are the three eukaryotic RNA polymerases and what do they transcribe

A

RNAPI: most rRNA genes, RNAPII: mRNAs (protein coding genes and noncoding mRNAS), RNAPIII: tRNA. THey are all multi-subunit proteins

179
Q

What is unique about RNAPII

A

It has a carboxyl terminal domain and no other RNA polymerase does

180
Q

How many subunits are in RNAP II and how many are in RNAP for prokaryotes

A

Respectively 12 and 5

181
Q

What positions eukaryotic RNA polymerases, where is it positioned. What eukaryote-specific problem does it have to deal with

A

Transcription factos (complicated sigma factors, basically). It is positioned at promoters and need to deal with chromosomal structures

182
Q

What is different about eukaryotic promoters

A

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
Q

What is a TATA box

A

An element about 30 bp upstream of the start site, it positions RNAP II and general transcription factors

184
Q

How is transcription initiated

A

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
Q

What does the transcription factor II helicase do

A

Adds phosphate to C-terminal domain (onto Serine), activating it so transcription can begin. It uses ATP to pry the DNA strands apart

186
Q

What does the mediator do in transcription

A

Activates factors (looks like its hugging factors)

187
Q

What does the activator protein do in transcription

A

Activates mediator, FINALLY BEGINS TRANSCRIPTION SLOW ASS MECHANISM

188
Q

What is characteristic of the C-terminal domain in RNAP II

A

Repeats 7 amino acids in tandem. 26x for people and 52x for people. Essential for viability

189
Q

What things make up mRNA processing

A

Adding 5’ cap, processing and poly adenylation (adding A’s repeatedly) onto 3’ tail. Splicing of introns.

190
Q

How do mRNA processing occur

A

Capping proteins and splicing proteins go to 5’mRNA from phosphorylation of C-terminal tail

191
Q

What is 5’ pre-mRNA capping and why do you need it

A

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
Q

How is intron removed

A

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
Q

What enzyme do you need for removing intron, what is this enzyme made of

A

Spliceosome: it contains snRNAs + proteins. snRNAs + proteins are called snRNPs. snRNPs are thus a part of spliceosome

194
Q

Why can’t DNA be spliced

A

Because 2’OH is needed but DNA does not have that on deoxyribose

195
Q

What is added after slicing is done, why

A

Exon junction, to show the thing has been spliced

196
Q

Can intron removal happen wherever you want

A

No you idiot you need specific sequences that are recognized by snRNAs used by spliceosomes

197
Q

What does alternative splicing do

A

Creates different gene products such as different cell types

198
Q

What can single nucleotide changes to do splicing

A

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
Q

What does the phosphorylation of CTD determine

A

It determines what proteins can be on it

200
Q

What happens to the consensus sequences (G-U rich)? Are they in the genome, are they transcribed

A

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
Q

How does the cleavage of G-U rich sequences happen

A

Cleavage factors go from CTD to RNA, cleaves the ends.

202
Q

How are poly As added, what proteins does mature mRNA have on tail

A

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
Q

What is the purpose of the poly A

A

To protect from 3’ exonuclease

204
Q

Where does translation happen

A

In the cytoplasm

205
Q

What is the genetic code

A

It tells you what codons are correlated to what mRNA triplets

206
Q

What is redundancy

A

There are multiple codons for most amino acids

207
Q

How does translation start

A

5’most AUG is the start of translation but not transcription. There will be more nucleotides on the RNA before the AUG

208
Q

What are the two types of mutations, how do you see the effect?

A

Subsitution and deletion. To see the effect you need to see the genetic code

209
Q

What are the types of effects of mutations

A

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)

210
Q

How does tRNA bind to amino acid and how does it bind to mRNA

A

Anticodon is antiparallel to mRNA and complementary, and the 3’ end of tRNA attaches to the amino acid. It recognizes the codons

211
Q

How do you find the amino acid bound to tRNA

A

Read 5’-3’ on the mRNA complementary to anticodon because GENETIC CODE TABLE IS 5’-3’

212
Q

How long are tRNAs

A

80 nucleotides

213
Q

How are the 5’ and 3’ ends transcribed for tRNA

A

As normal RNA

214
Q

Why does tRNA have double helical regions

A

Base pairs with itself (hydrogen bonding)

215
Q

How is redundancy dealt with

A

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

216
Q

How are errors prevented in translation

A

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

217
Q

How many amino-acyl tRNA synthetases are there, are there more or less tRNAs than amino-acyl tRNA synthetases

A

20, one for each amino acid. There are tRNAs because you can have more than one for an amino acid

218
Q

How does the synthetase recognize tRNA

A

Identifies the anticodon nucleotides and the 3’ end which will then bind to an amino acid. Also checks elsewhere

219
Q

Where are ribosomal subunits in the cell

A

ER and cytosol

220
Q

What is the big and small subunits of ribosomes made of respectively

A

Many proteins and many rRNAs. Small has many proteins ONE rRNA.

221
Q

Where are rRNAs common in ribosome subunits

A

At the three sites

222
Q

What are the three ribosome sites

A

E for exit, p for peptidal (holding in Place) and A for aminoacyl (entrAnce)

223
Q

Why is peptide synthesis energetically favorable

A

Energy stored in covalent bond between amino acid and tRNA in P site makes it favorable. It is high energy.

224
Q

What is formation of peptide bond in ribosomes catalyzed by

A

The peptidyl transferase in the large ribosomal subunit

225
Q

What is a ribozyme

A

RNA molecules that have catalytic activity. RNA part of ribosome catalyzes peptide bond formation, for example

226
Q

Is there more RNA or protein in ribosomes

A

RNA, it’s at the 3 sites

227
Q

What does EF-Tu do? What is the eukaryotic version

A

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

228
Q

Aside from elongation factors, what further helps quality control

A

Slight delay before formation of polypeptide bond before last check for base pairing

229
Q

What does EF-G do, what is the eukaryotic version

A

Moves the mRNA forward one codon and helps speed up the elongation. EF2 in eularyotes. It is hydrolyzed as well. Big subunit moves first

230
Q

Can you translate without elongation factors

A

Yes but its slower.

231
Q

What is the difference between noncoding sequences and UTR

A

noncoding sites include the part before AUG, ribosome binding sites in prokaryotes. they also include the UTRs.

232
Q

What is a polycystronic mRNA and where is it present

A

It is in prokaryotes, meaning multiple proteins in one mRNA

233
Q

What is a shine dalgarno sequence and what is the normal name

A

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).

234
Q

How does prokaryotic translation begin after small subunits are positioned on AUG

A

fMethionine is bound to AUG, large subunit binds

235
Q

How is eukaryotic translation began

A

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.

236
Q

What does it mean for a tRNA to be charged

A

When it has an amino acid. Done by aminoacyl tRNA synthetase

237
Q

How to terminate translation

A

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

238
Q

What type of macromolecule is the human translation release factor

A

Protein, not tRNA

239
Q

What is a polysome, why and in what organisms.

A

When before translation finishes, another begins in another spot. Because protein synthesis is kinda slow. In bacteria and eukaryotes

240
Q

How far apart are ribosomes for polysomes

A

80 nucleotides

241
Q

What are post translational modification examples

A

Phosphorylation, glycosylation, non-covalent binding to other proteins. Covalent modifications make the protein active and get it to recruit correct membrane or organelle

242
Q

How long do proteins last

A

Some short, others months or years

243
Q

What is ubiquitin and where does it bring proteins

A

Small protein covalently attached, directs to proteasome, where it is eaten by proteases. Recycled into new.

244
Q

What happens if you inhibit translation and transcription.

A

Kills cells. Poison is if its eukaryotes, bacteria is antibiotics

Bio130 bitchhhh (2 decks)

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