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Introduction to medicine (Year 1) > F cell II- Gene expression, protein synthesis and antibiotics and fate of newly synthesised proteins > Flashcards

F cell II- Gene expression, protein synthesis and antibiotics and fate of newly synthesised proteins Flashcards

- Outline cellular components required for protein synthesis - Describe key structural features of DNA and RNA - Outline the key steps involved in DNA replication - Outline the basic steps involved in transcription and mRNA processing - Describe the main types of RNA found in mammalian cells and their functions - Outline how the genetic code functions to enable protein synthesis, including the concept of reading frames - List the steps in the biosynthesis of proteins - Explain how antibiotics

1
Q

What are the cellular components required for protein synthesis?

A
  • Ribosomes
  • Nucleus
  • DNA
  • DNA strand
  • DNA nucleotides
  • RNA nucleotides
  • tRNA
  • mRNA
  • rRNA
  • mRNA processing enzymes
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2
Q

Describe the key structural features of DNA

A
  • Double stranded (double helix)
  • Polymer comprised of nucleotides.
  • Each nucleotide has 3 components:
  • Sugar molecule deoxyribose, attached to 1 of the bases
  • Phosphate (phosphate forms backbone with deoxyribose due to alternating deoxyribose and phosphate subunits in chain)
  • Base (A, G , T ,C). Bases join complimentary bases on opposite strand via formation of hydrogen bonds, holding 2 strands together

Adenine + thymine = 2 H bonds
Guanine + cytosine = 3 H bonds

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3
Q

Describe the key structural features of RNA

A
  • Single stranded
  • Ribose sugar (has extra hydroxyl group), instead of deoxyribose
  • Uracil (lack of methyl group present in thymine) instead of thymine
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4
Q

Why is DNA replication semiconservative?

A
  • Due to fact that one of strands of newly synthesised DNA is from one of the strands from the parent DNA. Each copy contains one original strand and one newly synthesised strand
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5
Q

Outline the key steps in semi-conservative DNA replication

A
  • 2 strands of DNA ‘melt’ (The 2 strands split). Enzyme DNA helicase breaks down H bonds between DNA strands, double helix unzips
  • Nucleotides on daughter strands used as a template to incorporate the complementary bases.
  • New strands formed by complementary base pairing. The nucleotides of the new strands are joined by enzyme DNA polymerase, forms the sugar-phosphate backbone. H bonds form between the complementary bases on original and new strand, strands twist to reform double helix.
  • This daughter DNA is then distributed into the daughter cells during cell division
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6
Q

Outline the basic steps involved in transcription

A
  • DNA strands melt
  • RNA strand form complementary base pairs with DNA antisense template stand
  • Once transcription complete, RNA strand dissociates from DNA strand, now a pre-mRNA strand (or primary transcript), ready for processing
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7
Q

What is the antisense strand?

A

Begins with 3’ ends with 5’

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8
Q

What is the sense strand?

A

Begins with 5’ and ends with 3’

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9
Q

Outline the basic steps in mRNA processing

A
  • RNA splicing- RNA units called introns are removed
    RNA units that remain are exons, but exons are not synonymous with the coding sequence, this depends on where the start and stop codons are. Because of this, some exons contain both coding and non-coding regions
  • 5’ capping- An extra molecule is added to the 5’ end of transcript, this is 7-methyl-guanosine (derived from GTP) , and once this has been attached, the guanine bases are methylated and often additional methyl groups are attached to the first and second base of the transcript
  • 3’ polyadenylation - This is attachment of 50-200 copies of adenine nucleotides to the VERY END of the transcript. This is essential for transcription termination, release of mRNA from the site of transcription, and export to cytoplasm
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10
Q

What are introns?

A

Segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes, hence they’re removed

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11
Q

What are exons?

A
  • Region of genome that end up within an mRNA molecule, some exons coding, others are not
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12
Q

What is the part of pre-mRNA before translation begins called?

A

5’UTR (untranslated region), which are the exons that are not translated. This region is all the exons before the start codon (AUG) initiates translation

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13
Q

What is the part of the mRNA strand that hasn’t been translated after translation has been completed?

A
  • 3’ UTR, this comes after the stop codon has terminated translation
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14
Q

What is the stop codon?

A

AUG

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15
Q

What additions in mRNA processing are not coded for in the gene?

A
  • 5’ capping
  • 3’ polyadenylation
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16
Q

Describe the main types of RNA found in mammalian cells and their functions?

A
  • rRNA- 80-85% abundance, nucleotides 4800, 1900, 160 + 120. This is a structural component of ribosomes or other large enzymes that catalyse translation. They both have protein and RNA subunits the make up the whole enzymes therefore rRNA catalyses protein synthesis
  • tRNA- 10-15% cellular abundance, nucleotide 75. Essential in translation, central to protein synthesis as adaptors between mRNA and amino acids
  • mRNA- 2-5%, nucleotides highly variable, only mRNA encodes proteins
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17
Q

What is the function of small nuclear RNAs (snRNAs)?

A

Function in variety of nuclear processes, including splicing of pre-mRNA

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18
Q

What is the function of small nucleolar RNAs (snoRNAs)?

A
  • Used to process and chemically modify rRNAs
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19
Q

What is the function of small canal RNAs (scaRNAs)?

A

Small canal RNAs, used to modify snoRNAs and snRNAs

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20
Q

What is the function of microRNAs (miRNAs)?

A
  • Regulate gene expression typically by blocking translation of selective mRNAs
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21
Q

What is the function of small interfering RNAs (siRNAs)?

A
  • Turn off gene expression by directing degradation of selective mRNAs and the establishment of compact chromatin structures
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22
Q

What is the leading strand?

A

The sense strand (5’ -> 3’)

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23
Q

What is the lagging strand?

A
  • The antisense strand (3’-> 5’)
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24
Q

What are genes?

A
  • Stretches of DNA that contain information for making RNA, mostly protein-encoding mRNA
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25
Q

What is the process of gene expression?

A

The process by which the information encoded in a gene is turned into a function, primarily via transcription of RNA molecules and translation of mRNA into an amino acid chain

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26
Q

Describe the genetic code

A
  • Amino acids of final protein determined by triplet of bases (codons) in nucleotide sequence
  • 64 codons that code for amino acids in body
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27
Q

What 3 codons are the stop codons?

A
  • UAA
  • UAG
  • UGA
28
Q

When do you begin reading frames in an mRNA strand to determine amino acid order?

A
  • From the start codon AUG, and you stop reading when you reach any of the codon UAA, UAG, UGA
29
Q

Describe the process of translation

A
  • tRNA molecule matches amino acid to codons in mRNA
  • tRNA molecules contain complementary anticodons for the codons on the mRNA strand. This requires high specificity for the correct base pairing of the codons and anticodons. When the codon and anticodon bind, the amino acid on the tRNA molecule is secreted
  • tRNA molecules are also attached to amino acids via covalent bonding
30
Q

Describe the structure of tRNA molecules

A
  • Single stranded RNA molecules, shaped like 3-leaf clovers, however within a single molecule, there are double stranded regions that form intermolecularly
  • Amino acid attaches to 3’ end of tRNA molecule
  • Anticodon is in anti-codon loop, opposite where amino acid attaches to
31
Q

How does an amino acid bind to tRNA?

A
  • Enzyme amino acyl tRNA synthetase (tryptohanyl tRNA synthase). This catalyses formation of bonds between amino acid + tRNA molecule. This requires energy from hydrolysis of ATP.
  • High energy bond forms between amino acid and 3’ point of tRNA molecule. This complex of amino acid and tRNA is called amino acyl tRNA. This requires high specificity to ensure correct amino acid attaches to correct tRNA molecule.
32
Q

What are the steps of the elongation of the polypeptide chain?

A
  • Charging tRNAs with amino acids
  • Initiation of polypeptide synthesis (assembly of ribosome on mRNA together with first aminoacyl tRNA
  • Elongation of the polypeptide (addition of amino acids one at a time)
  • Termination of polypeptide synthesis (release of polypeptide from ribosome)- this happens when ribosome encounters one of the 3 STOP codons
33
Q

How do peptide bonds form?

A

Via condensation reaction (removal of water molecule between carboxyl and amine groups of adjoining amino acids)

34
Q

How does the incoming amino acid on the tRNA molecule form a peptide bond with the adjacent amino acid in the polypeptide chain?

A
  • Through a nucleophilic attack from the nitrogen on the amine group and the carbon on the carboxyl group of the existing polypeptide chain.
  • In the nucleophilic attack the incumbent tRNA molecule is released and the new incoming tRNA molecule takes its place.
35
Q

How is the process of protein synthesis catalysed by ribosomes?

A
  • Has 2 subunits, a large and small
  • Ribosomes distinguished by 3 sites, P (primary) , A, E (ejaculation) site
  • The tRNA molecule will attach its codon in the P site, and a newly bound tRNA molecule is in the A site.
  • Once the amino acid from the P site is attached, the tRNA’s move so the unattached one is in the E site, and the newly formed tRNA is in the P site, ready for its amino acid to join the chain.
  • The old tRNA in the E site is ejected when another new tRNA molecule joins the A site
36
Q

How do antibiotics inhibit protein synthesis in bacteria but not eukaryotic cells?

A
  • The antibiotics selectively interact with the 70S bacterial ribosome and do not affect the 80S eukaryotic ribosome particle
37
Q

How do ahminoglycosides inhibit protein synthesis?

A
  • Bind to 30S subunit causing misreading of mRNA
38
Q

How do tetracyclines inhibit protein synthesis?

A

Binds to 30S subunit blocking binding of aminoacyl-tRNA

39
Q

How does chloramphenicol inhibit protein synthesis?

A

Binds to 50S subunit, inhibiting peptidyl transferase

40
Q

How does clindamycin inhibit protein synthesis?

A

Binds to 50S subunit, inhibiting translocation (movement of tRNA from acceptor site to peptidyl site)

41
Q

How do macrolides inhibit protein synthesis?

A

Binds to 50S subunit, inhibiting translocation (movement of tRNA from acceptor site to peptidyl site)

42
Q

How does streptomycin inhibit protein synthesis?

A

Targets small ribosomal subunit, inhibits initiation by interfering with codon recognition, leading to misreading of genetic code

43
Q

How does erythromycin inhibit protein synthesis?

A
  • Targets large ribosomal subunit- inhibits translocation
44
Q

How do neomycins inhibit protein synthesis?

A

Target multiple sites and have several effects

45
Q

What are the limitations of antibiotics acting on protein synthesis?

A
  • No action on viruses, which use host’s protein synthesis machinery to replicate, so antibiotics don’t affect viruses
  • Bacteria may develop resistance, including alteration of the target site and destruction of the antibiotic
  • They may inhibit protein synthesis in mammalian mitochondria which have ribosomes like bacteria
46
Q

Why do proteins need to be targeted to different cellular locations?

A

Because different organelles have different functions, which these proteins specifically target, hence why the proteins must be specifically targeted

47
Q

What is the concept of signal sequences?

A

For every destination (organelle) there’s a specific class of signal sequences.

For each signal sequence class there is a receptor which will recognise it (usually on protein)

48
Q

What is a nuclear localisation signal?

A

A signal or sequence in an amino acid sequence that ‘tags’ a protein for import into the nucleus by nuclear transport

49
Q

What is the structure of a signal sequence of a protein targeting the nucleus?

A
  • The signal location within the protein is internal
  • The signal sequence is not removed after protein enters organelle
  • 1 cluster of 5 basic (alkali) amino acid or 2 small clusters of basic residues separated by roughly 10 amino acids
50
Q

What is a mitochondrial signal sequence?

A

A short peptide bearing positively charged basic residues that directs the transport of a protein to the mitochondria

51
Q

What is the structure of a signal sequence of a protein targeting the mitochondria?

A
  • Signal location within protein at N-terminal (at very beginning of protein)
  • The signal will be removed after the protein reaches its destination
  • The nature of the signal is 3-5 nonconsecutive Arg and Lys residues (these are positively charged amino acids), often with Ser and Thr; no Glu or Asp residues (because these are negatively charged)
52
Q

What is the structure of a signal sequence of a protein targeting the ER?

A
  • Signal location within protein at N-terminal
  • The signal is removed once the protein has reached the lumen of the ER. This means the signal sequence is detached from the final protein
  • The nature of the signal is a core of 6-12 primarily hydrophobic amino acids, often preceded by one or more basic amino acids
53
Q

What are the components of the nucleus?

A
  • Nuclear envelope - consists of inner and outer nuclear membrane
  • ER membrane (separates ER lumen from cytosol)
  • ER lumen- rER lumen site of protein folding, modification and assembly
  • Nuclear laminate (fibrillar network inside nucleus of eukaryote cells, composed of intermediate filaments and membrane associated proteins, provides mechanical support + regulates DNA replication and cell division)
  • Nuclear pores - made of protein complex called nuclear pore complex, consists of proteins embedded in double membrane, have protein components pointing towards cytoplasm called cytosolic fibril. Contains structure called nuclear basket which is involved in transport + chromatin regulation
  • Perinuclear space- this is space between inner and outer nuclear envelope bilayers that separate nucleus from cytoplasm
54
Q

Describe nuclear import

A
  • Small molecules able to enter through pore complex via diffusion, no energy input
  • Larger molecules require active transport to pass through pore complex:
  • Requires input of free energy
  • Requires specific receptors that facilitate the transport through the pore complex by interacting with components of nuclear pore complex
55
Q

How are proteins targeted for the nucleus?

A

1- Nuclear proteins recognised by nuclear import receptors (proteins comprising this receptor are importin proteins)
2- Cargo protein (this is protein targeted to nucleus) and nuclear import receptor form complex
3- Import receptor facilitates transport of protein across from cytosol into nuclear as importin protein can interact with components of pore complex
4- One complex reacher nuclear lumen, cargo protein replaced by another small protein called Ran-GTP, and that deposits the cargo protein into its destination
5- The import receptor forms a new complex with Ran-GTP and exports it back to the cytoplasm where it can bind to a new carbon molecule, but before it’s able to do this, Ran-GTP must convert into Ran- GDP + pi) (GDP same nucleotide used for synthesis of RNA and guanine bases)
6- Ran- GDP dissociates from import receptor as Ran-GDP cannot bind to import receptor, ready for process to begin again

GTP is a cofactor for Ran protein, which is able to hydrolyse GTP to GDP, allowing it to change its configuration

56
Q

What are the functions of mitochondria?

A
  • Respiration
  • ATP synthesis
  • Heat generaation
  • Fatty acid metabolism
  • Intermediary metabolism (synthesis and breakdown of biomolecules)
  • Apoptosis (programmed cell death)
57
Q

Where does free energy come from to transport proteins in mitochondria?

A
  • Cytosolic Hsp70 protein binds ATP. This must be released so the precursor protein can enter the channel through TOM complex. Hsp70 release requires a change and response to ATP hydrolysis
  • Once protein reaches matrix, there’s another protein called mitochondrial HSP70. As protein emerges from TIM23 complex, HSP70 binds to protein and is released by hydrolysis of ATP to ADP
  • Membrane- ATP synthesis via electrochemical gradient
58
Q

How are proteins targeted for the matrix of the mitochondria?

A
  • Signal sequence on precursor protein recognised by receptor that sits in outer membrane of mitochondria, in are called TOM (transport of outer membrane) complex
  • Once precursor protein attaches to TOM receptor, its handed over to a channel in the outer membrane and is threaded through this channel to the inter membrane space
  • As the protein emerges on the other side of the inter membrane space, it meets TIM23 (transport inner membrane) complex. This mediates the transport of the protein into the matrix of the mitochondria
  • The protein is translocated in the matrix and the original signal sequence is cleaved off by signal peptidase as it is no longer needed, and once this is cleaved, the protein is a mature protein
59
Q

How are proteins targeted for the inner membrane of the mitochondria?

A
  • Signal sequence on precursor protein makes contract with TOM complex receptor and then when it reaches the intermembrane space, makes contact with TIM23 complex receptor, but the signal sequence is quickly cleaved off and next to the signal sequence is a hydrophobic section of protein called the stop-transfer sequence, consisting of hydrophobic amino acids that form a trans membrane domain, and this remains stuck there
  • This part of the protein will exit the temp channel laterally and enter the bilayer of the membrane
  • Once all of the protein has exited to TOM complex, a mature protein with a trans membrane domain enters the inner membrane, with the bulk of the protein facing the entire membrane space
60
Q

What are the functions of the ER?

A
  • Protein synthesis
  • Folding
  • Glycosylation- the process by which a carbohydrate is covalently attached to a target macromolecule, typically proteins and lipids
  • Disulfide bond formation- covalent interactions formed between the sulfur atoms of two cysteine residues
  • Protein quality control - to ensure proper folding and glycosylated, and correct disulphide bond formation as well as correct assembly of the quaternary structure of the protein.
  • Lipid synthesis- ER contains enzymes for lipid synthesis, specifically membrane lipid synthesis that make up the layers of various organelles.
  • Ca2+ storage
  • Intermediary metabolism
61
Q

What is the composition of ribosomes in the rER?

A

70 S (50S + 30S) - this is what gives the rough appearance, as the rER is abundant in ribosomes

62
Q

Why does the sER appear smooth?

A

-They have very few ribosomes

63
Q

What is the ER signal sequence?

A

The targeting of proteins to the ER. The mRNA will contain a specific signal sequence that directs it to ER by a dedicated receptor.

64
Q

How are proteins targeted for the ER?

A
  • The N terminus of the signal sequence is the first part of mRNA to emerge from the ribosome
  • As it emerges it’s recognised by an SRP (signal recognition particle - this is a ribonucleoprotein)
  • The N-terminus and SRP bind and form a complex, and protein synthesis is paused, only the signal peptide (sequence) has been synthesised
  • The SRP -bound ribosome attaches to the SRP receptor in the ER membrane
  • The SRP receptor facilitates docking off of complex onto protein called protein translocator (or protein translocation channel). At this point, SRP and receptor are displaced and recycled
  • Ribosome has docked onto translocation channel, protein synthesis resumes, and as it continues to be synthesised it’s threaded through the protein translocation channel into the lumen of the ER. The signal peptide is cleaved off and the final protein is released into the lumen of the ER.
65
Q

What is the function of the Golgi apparatus?

A
  • Post-translational protein modifications (glycosylation- further than in the ER, sulfation - attachment of sulphate groups, proteolysis- this when when a protein in partially broken down into peptides or amino acids by proteolytic enzymes).
  • Lipid synthesis- this begins in the ER but is completed in the Golgi due to the enzymes found specifically in this organelle.
  • Protein & lipid sorting (secretory granules, plasma membrane, endosomes, lysosomes) - this is the packaging into vesicles and the vesicles being directed to the correct target such as lysosomes, secretory vesicles, plasma membrane, endosomes.
  • At the trans end of the golgi, vesicles form again that pinch off and transport proteins to the plasma membrane etc
66
Q

Explain vesicular transport

A
  • When vesicles form from ER, transport and targeting mediated by vesicular transport
  • Vesicles form from patch of membrane called donor membrane, which then undergo budding (this is selective incorporation of cargo into forming vesicles while retaining resident proteins in donor compartment)
  • This then pinches off and the vesicle has its own bilayer and any cargo proteins trapped in lumen
  • Vesicle then travels through cytoplasm, often through microtubules, until they encounter their target compartment, where proteins on compartment mediate fusion of vesicle and target compartment, allowing contents of vesicle into target compartment
  • Vesicle formation always mediated by protein complexes called vesicle codes or secular codes
67
Q

Describe the secretory pathway

A
  • Proteins destined for the rER are initially synthesised at the endoplasmic reticulum by the ribosomes on the rER.
  • Once the synthesis is complete, the proteins are packaged into vesicles where they travel through the cytoplasm and fuse with the membranes of the Golgi apparatus.
  • Proteins are modified as they pass through the stacks of the golgi apparatus and exit towards lysosomes or secretory vesicles, plasma membrane etc.
  • This entire series of membrane bound organelles is called the secretory pathway

Introduction to medicine (Year 1) (55 decks)

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