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BIO130 Flashcards

Test Review

1
Q

Cell theory

A

Basic organizational unit, all organisms made of calls, cells come from pre existing cells

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2
Q

Prokaryotic

A

No nuclei, single cell, bacteria and archaea

No membrane bound organelles, smaller, less DNA

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3
Q

Eukaryotic

A

Nuclei, single/multicellular, plants, fungi, animal/human

Several membrane bound organelles, larger, chloroplast, cell wall, vacuole (1 storage, 1 like animal lysome)

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4
Q

Origin of mitochondria

A

Originally free living aerobic prokaryotes able to use oxygen to generate ATP

E cubed model

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5
Q

Ectosymbiosis

A

Symbiotic behaviour in which organisms live on body surface of another organism, can be internal

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6
Q

E cubed model

A

Origins of mitochondria

Entangle, engulf, endogenize

Encloses endosymbiosis, endosymbiont escapes into cytosol and form into new compartment

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7
Q

Origins of eukaryotes

A

Prokaryote > bacteria/archaea > mitochondria > single cell eukaryotes

Mitochondria and chloroplast have remnants of genomes, DNA, and membranes that signify derived from engulfed bacterial ancestor

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8
Q

Endosymbiont

A

Cell living in cell with mutual benefit

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9
Q

Model organisms

A

Living thing selected for intensive study as a representative of a large group of species

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10
Q

Attributes of a model organism

A

-Rapid development with short life cycles
-Small size
-Readily available
-Tractability : ease of manipulation
-Understandable genetics

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11
Q

Central dogma

A

Explanation of the flow of genetic information

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12
Q

Genome

A

All DNA/DNA sequences in cell or organism

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13
Q

Transcriptome

A

All RNA/RNA sequences in cell or organism

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14
Q

Proteome

A

All protein/protein sequences in cell or organism

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15
Q

Interactome

A

Protein-protein interactions in cell or organism

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16
Q

Metabolome

A

Small molecule metabolites in cell or organism

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17
Q

Phenome

A

All phenotypes in cell or organism

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18
Q

Nucleic Acid

A

Genetic material in the cell

DNA: deoxyribonucleic acid
RNA: ribonucleic acid

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19
Q

Nucleotide parts

A

1) Pentose sugar
-scaffold for base
2) Nitrogenous base
-varies
3) Phosphate group
-backbone
-1, 2, 3

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20
Q

Base Types

A

Pyrimidine: 1 Ring
Purine: 2 Rings

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21
Q

Pyrimidines

A

-Uracil
-Cytosine
-Thymine

“U C The PYRamids”

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22
Q

Purines

A

-Adenine
-Guanine

“Al Gor stinks PU”

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23
Q

DNA v RNA

A

Off the 2’ carbon RNA has oxygen DNA doesn’t

RNA: GCAU
DNA: GCAT, extra methyl group

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24
Q

Nucleoside

A

Base+Sugar

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25
Q

Nucleotide

A

Base+Sugar+@ least 1 phosphate group

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26
Q

Nucleic acid chains

A

-DNA synthesized from dNTPs (deoxyribonucleoside triphosphate)
-RNA synthesized from NTPs (ribonucleoside triphosphate)
-Nucleotide linked by phosphodiester bonds

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27
Q

Interactions between individual molecules usually mediated by non covalent attractions

A

-Electrostatic attractions
-Hydrogen bonds
-Van Der Waals (Base stack)
-Hydrophobic force (Base ring structures)

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28
Q

Base Pairs

A

G-C bond
-3H bonds
-Stickier

A-T bond
-2H bonds

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29
Q

Complementary

A

Sequence of 2 strands

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30
Q

Denaturation

A

Destroy normal structure

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31
Q

Antiparallel

A

5’ > 3’ and 3’ > 5’
Double helix organized like this

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32
Q

5’

A

Phosphate group
-PO4

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33
Q

3’

A

Hydroxyl group
OH

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34
Q

Protein Structure: Primary

A

Amino acid sequence

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35
Q

Primary Structure: Secondary

A

Lots of examples

A helix

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36
Q

Protein Structure: Tertiary

A

3D structure

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37
Q

Protein Structure: Quaternary

A

More than 1 polypeptide chain

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38
Q

Protein Structure: Multi Protein Complexes

A

Multi protein complexes and molecular machines

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39
Q

Side chain/R group

A

Variable and determines the type of amino acid

Identify amino group, R group, carboxyl group, alpha carbon

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40
Q

Amino acid categories

A

-Acidic
-Basic
-Uncharged polar
-Nonpolar

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41
Q

Peptide bonds

A

-Occurs in the ribosome
-Condensation rxn
-OH off carboxyl: Carbonyl C
-H off another: Amide N
-Doesn’t change R group
-Backbone: everything except for R group

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42
Q

Alpha Helix

A

Could be entire polypeptide chain or just a small part

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43
Q

Alpha helix v DNA double helix

A

-R groups stick out : bases face inward
-R groups don’t support : base groups hold it together
-Single strand : double strand
-N and C end : 5’ and 3’ end

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44
Q

H Bonds: In atoms

A

Between carbonyl oxygen and amide hydrogen (peptide backbone)

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45
Q

H Bonds: Alpha helices

A

4 AA apart within same segment of chain (n-n+4)

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46
Q

H Bonds: Beta sheet

A

Between AA in different segments/strands of the chain

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47
Q

Coiled coil

Super secondary structure

A

-Helices do not have to create a coiled coil
-Amphipathic (define)
-Found in alpha keratin of skin, hair, and myosin motor proteins
-Helices wrap around each other to minimize exposure to hydrophobic AA R group to aqueous environment

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48
Q

Amphipathic

A

2 different biochemical/physical properties on different sides

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49
Q

Tertiary structure: held together by…

A

-Hydrophobic interactions
-Non covalent bonds
-Covalent disulfide bonds
-Other interactions among residue backbones and R groups
-Also between many helices and beta sheets
-How the rest of the polypeptide chain folds

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50
Q

Proteins fold into shape dictated by ________ but _______ help make the process more efficient and reliable in living cells

A

AA sequence

Chaperone proteins

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51
Q

Protein domains

A

-Often specialized for different functions
-Portion of protein that has its own tertiary structure, often semi independent structure
-Eukaryotic proteins often have 2 or more domains connected by intrinsically disordered sequences (Forming a larger overall tertiary structure)
-Important for protein evolution
-Src Protein Kinase

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52
Q

Protein families

A

-Have similar AA sequences and tertiary structure
-Members have evolved to have different functions
-Most proteins belong to families with similar structural domains

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53
Q

Quaternary Structure

A

Hemoglobin
-Formed from separate units/polypeptides 2a and 2B
-Sickle cell anemia, cause by mutation in B sub unit

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54
Q

Multi protein complexes

A

Many identical sub units
-Actin filaments
Mixture of different proteins and DNA/RNA
-Viruses and ribosomes
Very dynamic assemblies of proteins to form molecular machines
-machines for DNA replication initiation or for transcription

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55
Q

Studying proteins: Single or few

A

-Consider protein diversity
-Purify protein of interest (electrophoresis and affinity chromatography)
-Determine amino acid sequence
-Discover precise #D structure (x ray, crystallography, NMR spectroscopy, cryo electron microscopy, and AlphaFold)

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56
Q

Studying proteins: Large scale

A

-Identity/Structure
-Protein protein interaction
-Abundance/turnover
-Location in cell/tissue

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57
Q

Genome

A

All an organisms hereditary information

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58
Q

Base pair

A

Nucleotide pairs

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59
Q

Human genome

A

-3 billion base pairs per genome
-One genome from 1 parent and one from the other
-Standard human cell, 6 billion bp, 2 genomes
-20,000 protein coding genes
-50% repetitive DNA
-Less than 1% encodes protein

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60
Q

Genome size

A

-Does not equate to actual size
-Not always correlated with # of genes or organism complexity

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61
Q

Human genome: Unique sequences

A

-Non repetitive DNA in neither introns nor exons
-Protein coding exons: transcribed and translated
-Introns: transcribed not translated

ex. sequences that help cells determine with RNA to transcribe and how much

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62
Q

Human genome: Repeated sequences

A

-Segment duplication: thousands-hundreds of thousands bp
-simple repeats
-mobile genetic elements: sequences over long period of time cut themselves out, sometimes ate in
-DNA only transposon
-Retrotransposon: made into RNA
-LINEs: long interspersed nuclear element
-SINEs: short interspersed nuclear element (<500bp)

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63
Q

Packing DNA: Non packaged state

A

Small prokaryotic genome occupy considerable portion of cell volume

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64
Q

Packing DNA: Prokaryotes

A

-DNA condensed through folding and twisting
-Forms prokaryotic nucleoid

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65
Q

Packing DNA: Eukaryotes

A

Chromatin
-Tightly packed DNA must remain accessible for transcription, replication, repair

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66
Q

Florescence In Situ Hybridization (FISH)

A

Diagnostic technique for detecting presence of particular sequences

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67
Q

Chromosome

A

Single long linear DNA molecule and associated proteins (Chromatin)

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68
Q

Chromatin

A

-DNA double helix
-Beads on a string
.wrapped around protein
.nucleosome
-30nm fiber
.packed nucleosome
Loops
-Mitotic chromosome
.10,000 fold shorter than fully extended length

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69
Q

Nucleosome

A

-Chromatin isolated from cell in interphase

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70
Q

Core histones

A

-Connected by linker DNA
-DNA wraps 1 2/3 times
-Liner DNA can vary up to 80 nucleotide pairs long
-Middle contains 8 proteins
.rich in lysine and arginine, positive changes neutralizes DNA
-1 linker histone (H1)
.paper clip, clips DNA on

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71
Q

Nucleosome v. Core particle

A

-Core, H1, linker DNA
-no H1

72
Q

Packing chromatin

A

-Specific clamp proteins and cohesins involved in forming chromatin loops
-Cells enter mitosis condensis replace cohesins to form double loops of chromatin to generate compact chromosome
-Packing/Unpacking requires ATP

73
Q

Re-modelling chromatin

A

Chromatin modelling complexes and histone modifying enzymes are examples of proteins that change chromatin structure and alter access to DNA for replication or transcription

74
Q

Heterochromatin

A

-Highly condensed chromatin
-gene expression is suppressed

75
Q

Euchromatin

A

-Relatively non condensed chromatin
-Genes tend to be expressed

76
Q

Transcription factories

A

Regions of the nucleus with lots of substrates and proteins for transcription

77
Q

Conservative DNA replication

A

-Parent cell to daughter cells
-One cell has both parental strands one is entirely new

78
Q

Semi conservative DNA replication

A

-One parent strand per new cell
-Always true in nature

79
Q

Direction of DNA replication

A

-Bidirectional growth from starting point
-DNA is anti parallel
-New DNA 5’ to 3’
-Template read 3’ to 5’
-Replication fork
-Okazaki fragments

80
Q

Replication fork

A

Origin of replication separate parent strands left and right

81
Q

Origins of DNA replication

A

-Easy to open (A-T)
-Recognized by indicator proteins that bind t DNA
-Bacteria: single origin
-Eukaryote: multiple
-Replication fork is asymmetrical
-Leading strand replicated continuous, lagging is discontinuous

82
Q

What do both eukaryotic and prokaryotic cells have

A

Ribosomes

83
Q

What are some methods by which humans can be studied

A

-Cell cultures
-Clinical studies
-Organoids

84
Q

On a molecular level it is possible that 2 prokaryotic species could be as different from each other as either is from eukaryotes

A

True

85
Q

What organelles ancestor was likely engulfed by an early anaerobic eukaryote

A

Mitochondrion

86
Q

Nomenclature for a nucleoside

A

Deoxycytidine

87
Q

How many water molecules are created in the condensation rxn that creates a polypeptide chain from three amino acids

A

2

88
Q

Why are alpha helices and beta sheets common folding patterns in polypeptides

A

Amino acid side chains are not involved in forming the hydrogen bonds, allowing many different sequences to adopt these folding patterns

89
Q

______ bonds covalently link neucleotides together to make DNA or RNA while, ______ bonds covalently link together AA in polypeptides

A

Phosphodiester

Peptide

90
Q

Extracellular proteins are directly exposed to extracellular conditions. To help maintain their specific 3D shape the polypeptide chains are often stabilized with …

A

Disulfide bonds

91
Q

Protein domains are often connected by relatively short lengths of polypeptide called …

A

Intrinsically disordered sequences

92
Q

Areas of the human genome that are not “protein encoding exons” include …

A

DNA sequences that ensure transcription of the proper gene at the proper time, level, and space

93
Q

A laboratory uses single stranded DNA probes with florescent dyes to detect the presence of cells infected with the human papillomavirus. This technique is known as …

A

In Situ Hybridization

94
Q

Chromosome duplication occurs during ____, starting at ____

A

Interphase

Origins of replication

95
Q

Histone proteins pack DNA into a repeating arrat of DNA protein particles called …

A

Nucleosomes

96
Q

Okazaki fragments are found associated with the leading strand template

A

False

97
Q

Primase is known as a …

A

RNA polymerase

98
Q

Enzyme telomerase solves the problem of replication at the ends of linear chromosomes by …

A

Adding numerous short DNA sequences to the 3’ end of the lagging strand template

99
Q

Regarding double stranded DNA breaks, how are they caused, how can they be solved

A

Can be caused by radiation

Can be solved with non homologous end joining or homologous recombination

CANNOT repair by editing function of DNA polymerase

100
Q

Copying errors not caught by the replication machinery can be corrected by …

A

The DNA mismatch repair system

101
Q

How does UV radiation from sunlight typically damage DNA

A

Promotes covalent linkage between 2 adjacent pyrimidine bases

102
Q

How is transcription similar to DNA replication

A

Both processes depend on complementary base pairing of incoming nucleotides to a DNA template

103
Q

mRNA represents the major class of non coding RNA

A

False

104
Q

bacteria and eukaryotes do not require a primer to initiate transcription

A

True

105
Q

While both bacterial and eukaryotic mRNA transcripts will have 3 phosphate groups at or near their 5’ ends, only eukaryotic transcripts will also have a 7 mehtylguanosine attached there

A

True

106
Q

Assembly of general transcription factors to a eukaryotic promoter begins at what sire in a promoter

A

The TATA box

107
Q

What is absent in a properly folded tRNA

A

Thymidine dimers

108
Q

Any given mRNA sequence has _____ possible reading frames, and the correct one is set by a _____

A

3

Initiation codon

109
Q

Within the ribosome the formation of peptide bonds is catalyzed by …

A

An RNA molecule in the large ribosomal subunit

110
Q

Typically different aminoacyl-tRNA synthetases for every AA

A

True

111
Q

Proteases that reside in the central cylinder of a proteasome are used to chop proteins into shorter peptides

A

True

112
Q

What do initiator proteins bind to/do?

A

Bind to origin of replication
-destabilization of AT rich sequence
Helps helicase bind
-needs helicase loading protein
-Requires ATP

113
Q

What can single strand binding proteins bond to?
What does this bonding do?
Where are the proteins?

A

-Stick to themselves after helicase, separates with binding ssDNA
-Stick back together after helicase, separates with binding ssDNA
-Prevents H bonding this way
-Single strand bonding proteins on leading lagging strand templates

114
Q

RNA Primers Made by Primase

A

DNA polymerase requires bound primer
-Short sequence of nucleotides with free 3’ OH
Primase synthesizes an RNA primer
-With free 3’ OH that DNA polymerase can use
Primase 3’-5’ along template strand
-Synthesizes 5’-3’ (Adds to 3’)
-Primase + Helicase = Primosome

115
Q

DNA Polymerase

A

Incoming deoxynucleoside triphosphate pairs with base in template
-DNA polymerase catalyzes covalent linkage of deoxynucleoside triphosphate into new strand
-Read 3’-5’

116
Q

What does a sliding clamp do?

A

Holds the DNA polymerase on the newly synthesized strands

117
Q

How are okazaki fragments on lagging strands linked together?

A

-DNA polymerase adds nucleotides to 3’ end of new RNA primer to synthesize new okazaki fragments
-Previous RNA primer removed by nucleases and replaced with DNA by repair polymerase (Gaps are called Nicks)
-Nick sealed by DNA ligase (covalent bond)

118
Q

Replisome

A

-Type of molecular machine
-All proteins in DNA replication working together

119
Q

Leading strand synthesized continuously from ______

A

Single RNA primers

120
Q

Lagging strand synthesized discontinuously from ______

A

Multiple primers

121
Q

Okazaki fragments are made of

A

RNA primer and DNA

122
Q

What happens as DNA is unwound

A

DNA double helix want to spin
-Unable to spin due to space
-Twists around itself, super coil + torsion
-problem in circular chromosomes and larger linear eukaryotic chromosomes

123
Q

What is the solution to super coils due to DNA spinning?

A

Topoisomerase
-Cuts 1 of 2 strands to unwind then reseals the Nick
-Transient single strand break

124
Q

What happens at the end of eukaryotic linear chromosomes during replication?

A

Lagging strand has issues
-Primase isn’t good at putting a primer at the very end
-Where it does put the primer it needs to be removed
-After removal left with 5’ ends DNA cannot add to
-Incompletely replicated: loss of sequence information

125
Q

How can we fix issues with the lagging strand at the end of eukaryotic linear chromosome replication?

A

Telomerase
-Repetitive sequence added to 3’ end of parent strand
-Has RNA template, bp with DNA
-Adds more DNA on 3’ end then releases and re-binds further up (G rich end)
-Completion of lagging with DNA polymerase

126
Q

Telomerase and Cancer

A

-Telomerase is abundant in stem and germ line cells not somatic
-Loss of telomerase limits number of rounds of cell division
-Most cancer cells produce high levels telomerase

127
Q

Finding and Correcting Mistakes: 3’ to 5’ exonuclease repair

A

-Backspace
-Removes misincorporated nucleotide
-DNA polymerase has editing sit

128
Q

Finding and Correcting Mistakes: Standard directed mismatch repair eukaryotes

A

-If proofreading fails
-Initiated by detection of distortion in geometry of double helix generated by mismatched base pairs
-MutS protein recognizes and locks onto DNA mismatch
-MutL scans DNA (Sliding clamp:strand with nick)
-MutL nuclease activated + initiates strand removal

129
Q

Finding and Correcting Mistakes: Prokaryotes

A

-Typically don’t detect nicks
-Detect methylated adenines
-New strand doesn’t have them

130
Q

After synthesis DNA can still be damaged, how?

A

Pyrimidine dimer
-Covalent bonds between bases, messes up locations
Spontaneous damage
-Water with wrong nrg, wrong place/time, bumps into purine and goes through depurination
Spontaneous damage
-Water, bumps into cytosine turns uracil, deamination

131
Q

How do we fix double stranded breaks?

A

Non homologous end joining
-Break repaired with loss of neucleotides at repair site
Homologous recombination
-Recombination specific nuclease (trim) but use other strand as template

132
Q

Molecular definition of a gene

A

Genes are segments of DNA that are transcribed into RNA

133
Q

What does RNA do? How does it function?

A

-RNA can encode for protein
-RNA functions as RNA and may not need to be translated into protein
-More mRNA means more of that protein

134
Q

Ribonucleotides

A

-Ribonucleotides triphosphates used (ATP, UTP, CTP, GTP)
-RNA is made antiparallel and complementary to DNA
-RNA is made in the 5’ to 3’ direction adding to the 3’ end
-DNA template read 3’ to 5’

135
Q

RNA Transcript

A

-ssDNA template
-Phosphodiester bonds
-Base pairing

136
Q

Transcription Cycle

A

-Sigma factor binds to RNAP ad fins promoter sequence
-Binds to core enzyme to form holoenzyme
-Localized unwinding of DNA, few short RNAs synthesized initially and then RNAP clamps (Abortive transcription: Copy 1st 10) down sigma factor released
-Elongation
-Termination and release of RNA
-NO primer

137
Q

Promoter Sequence

A

-Sigma factor binds to this
-We call the promoter what the factor binds to and the in between
-1st pair +1 on DNA (nucleotide #)
-Higher # downstream
-Promoter consensus sequence shown (-10, -35)

138
Q

Eukaryotic transcription is more complex

A

True

139
Q

Transcription Initiation

A

-mRNA, rRNA, and tRNA
-Eukaryotes have a few more RNAs including temolerase, snRNA (splicing of pre mRNA), and miRNA (block translation causeing degradation)
-Eukaryotic RNA polymerase
.each RNAP is a multi subunit protein
.responsible for transcription of different RNA
.1: rRNA
.2: mRNA (protein coding genes) miRNA
.3: tRNA, 5s rRNA

140
Q

Eukaryotic II v. Bacterial RNAP

A

Bacterial
-5 sub units
-Sigma subunit: similar function transcription factor
Eukaryotic II
-12 sub units
-Special carboxyl terminal domain (CTD)
-Require proteins to help position @ promoter (Transcription factor)
-Need to deal with chromosomal structure

141
Q

Eukaryotic Promoters

A

-More variable than bacterial
-1 or more specific sequences called elements
-Elements @ specific locations
-Elements recognized by specific general transcription factors which help position RNAP

142
Q

TATA Box

A

-30 base pairs upstream from start site of transcription
-Helps position RNAPII and general transcription factors
-Binding of TATA binding protein sub unit of transcription factor II in minor groove
-Mobilizes binding of TFIIB complex adjacent TATA box
-Other transcription factors bind
-RNAP II with other TFs will bind in correct orientation and transcription start site
-Helicase activity and phosphorylation of CTD of RNAP II
-Enhancer sequences with activation proteins, activates mediator, activates protein

143
Q

Phosphorilate

A

Add phosphate group to S (Ser) located by the CTD

144
Q

C Terminal Domain

A

-Tandem repeats of 7AA

145
Q

mRNA Processing

A

-Coupled with transcription
-Phosphorylation of C terminal tail resulting in binding of RNA processing proteins and additional phosphorylation of CTD, including Ser 2

146
Q

mRNA Processing: Capping

A

-Helps protect RNA from exonucleus
-Completed before mRNA fully transcribed
-Cap has triphosphate bridge (2 5’ ends) exonuclease cannot cut it, too weird
-7 methylguanosine

147
Q

mRNA Processing: Splicing

A

-Splicesome
-Branch point A attack 5’ splice site
-Adenine from phosphodiester bond between 2’ and 5’ of intron
-3’ of one exon reacts with 5’ of next exon to release intron
-Pre mRNA cant self splice
-Splicesomes have snRN bound to protein
-Splicing complete: exon junction complex added

148
Q

mRNA Processing: Abnormal Splicing

A

-Exon skipping
-Activated cryptic site
-New exon

149
Q

mRNA Processing: Consensus Sequence + 3’ End Modifying Proteins

A

-After transcribed 3’ end processing proteins recognize and are recruited to mRNA
-Poly A sequence is not encoded in the genome
-Consenses sequence direct cleavage and polydenylation to 3’
-3’ processing proteins move from CTD to mRNA
-Result: mature mRNA

150
Q

mRNA Export

A

Move mRNA to cytosol (Protein synthesis)
-Cap binding proteins
-Poly A binding proteins
-Exon junction complexes: Semi optional, some mRNA don’t get spliced

151
Q

Reading Frames: Translation

A

Define amino acid sequence
-5’ most AUG, read 3 nucleotides at a time

152
Q

Nucleotide Pair Substitution

A

Silent
-Same amino acid created
Missense
-Different amino acid created
Nonsense
-Stop codon

153
Q

tRNA: Translation

A

-Recognizes the codon on mRNA and brings the proper amino acid
-About 80 nucleotides long
-5’ and 3’ ends, transcribed as per usual
-Base pairs with itself in regions, making double helicase regions
-3’ end is where the AA gets attached
-Anticodon binds to mRNA codon, antiparallel and complementary
-Modified bases

154
Q

Genetic Code

A

-Reads as mRNA triplets
-Encoding all 20 amino acids
-Redundancy: Multiple codons for the same amino acid

155
Q

How do we manage redundancy in the genetic code?

A

-More than 1 tRNA for many amino acids
-Some tRNA can recognize and base pair with more than 1 codon (Wobble)

156
Q

Explain the Wobble Position

A

-Manages redundancy
-3’ of codon and 5’ of anticodon
-Many anticodon bases for the wobble codon base (Variety)
-There’s rules
-Bacteria is more flexible than eukaryotes
-I: Inosine

157
Q

How do we ensure fidelity?

A

-Aminoacyl-tRNA synthase recognizes tRNA and put the proper AA
.identify tRNA anticodon nucleotides, recognizes nucleotide sequences of 3’ end, reading nucleotide sequences at additional positions
-Base pairing

158
Q

Where are ribosomes found and how are they built?

A

-On endoplasmic reticulum or in cytosol
-Has large and small sub units
.Large: many protein, many rRNA
.Small: many protein, one rRNA

159
Q

Large Sub Unit Sites: Ribosomes

A

A: aminoacyl
P: peptidyl
E: exit

160
Q

Overview of Translation

A

-NRG in AA and tRNA bond in P site make peptide synthesis energetically favorable
-Peptide bond formation catalyzed by peptidyl transferase activity of rRNA in large sub unit

161
Q

Ribozyme

A

-RNA molecules that posses catalytic activity
-RNA catalyzes peptide bond

162
Q

EF

A

Elongation factor

163
Q

EF-Tu

A

EF1 in Eukaryotes
-Checks aminoacyl tRNA
-Goes to A cite checks for proper base pairing
.If base pairing isn’t correct EF-Tu is not released and the peptide bond cannot form, the entire thing is cut off
.If base pairing is correct GTP is hydrolysed and EF-Tu is released

164
Q

EF-G

A

EF2 in Eukaryotes
-Helps ribosome move the small sub unit forward 1 codon and helps speed up elongation of polypeptide chain

165
Q

Initiation of Translation: Prokaryotes

A

-Shine Dalgomi sequences on mRNA base pair with rRNA in small ribosomal subunits
-Positioning of small subunits to initiating AUG codons on mRNA also requires initiation factors (IF)
-fMethionine aminoacyltRNA binds to initation codon
-Large ribosomal subunits bind

166
Q

Initiation of Translation: Eukaryotes

A

-Small ribosomal subunit with tRNA + Met, no mRNA yet
-Find 5’ end looks for AUG, binds
-Large ribosomal subunit comes in

167
Q

Translation: Termination

A

Protein recognizes stop codon, not tRNA

168
Q

Translation: Polyribosomes

A

Chain of ribosomes all translating one after the other

169
Q

Translation: Protein Folding

A

Chaperone proteins

Hsp 60 and 70

170
Q

Post Translational Modification

A

Many proteins require
-phosphorylation
-glycosylation
Covalent modifications may be required to
-make protein active
-recruit protein to correct membrane and organelle

171
Q

How is protein degradation controlled?

A

Proteins tagged for degradation
-Small proteins called ubiquitin covalently attached directs them to the proteasome where they are degraded by proteases

172
Q

Antibiotics

A

-There are many inhibitors that act only on bacteria
-A lot of antibiotics screw up bacterial translation
-Not antibiotic its poison, acts on eukaryotes

173
Q

Beta Sheet

A

-H bonding between carbonyl oxygen, 1AA, and amide hydrogen of the AA in neighboring strand
-R group is not involved and alternate up and down
-Typically 4 or 5 strands parallel or anti parallel

174
Q

How is genetic code organized?

A

-Polar, nonpolar, charges, uncharged
-Groups of amino acids with similar properties

175
Q

Cysteine

A

-Disulphide bonds
-R group CH2SH
-S of the R group forms inter or intro disulphide bonds due to oxidization
-helps brace the structure
-Redox: in cytosome, no bonds, breaking bonds

Y1S2 (2 decks)

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