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BIOL 1101 > Lecture 12: Gene structure and Expression > Flashcards

Lecture 12: Gene structure and Expression Flashcards

1
Q

unique nucleotide sequences are part of what

A

your chromosomes

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2
Q

How do we know that genes encode proteins

A
  1. 1896: Garrod studied alkaptonuria disease

observations:
- metabolic disorder
- produce chemical that turns black in air
- inherited**!!

  1. 1940: Beadle and Tatum studied orange bread mould
  • mould grows on minimal media (make their own amino acids)
  • used x-rays to produce nutritional mutants (they cant grow on minimal anymore because of a mutation)
  • hypothesis: each mutant had defective gene for enzyme needed to synthesize a particular nutrient
  • the enzyme won’t work properly
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3
Q

what is alkaptonuria disease

A
  • alteration in a gene that encodes the enzyme that metabolizes this chemical
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4
Q

What was the beadle and Tatum experiment

A
  • Arginine Synthesis Pathway
  • How Arginine is built (enzyme for each step)

Each step is controlled by a gene that encodes an enzyme for that step
- enzyme catalyzed reaction
- bc x-ray affects chromosomes, so it was caused by a gene defect

- the mutation caused disruptions when building Arginine

1 gene/1 enzyme: each gene can codes for a specific enzyme that has a specific duty

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5
Q

why is the wild type the ctrl group

A
  1. bc it can do everything (a.a, and growth)

appears in every generation

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6
Q

rlnship btwn genes and proteins

A

1) one gene-one enzyme hypothesis
- direct relationship between genes and enzymes

2) one gene-one polypeptide hypothesis (it was updated…)
- not all proteins are enzymes
- functional proteins sometimes contain 1 or more polypeptides
- different genes encode each polypeptide (coded by different genes)

genes can code for individual polypeptide chains

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7
Q

How to get from genes to proteins

A
  1. transcription
    - nucleotide sequence in DNA is copied into a complementary sequence in an RNA molecule
  • template strand of DNA is used to create messenger (mRNA)
  1. Translation
    - sequence of nucleotides in mRNA molecule specifies amino acid sequence in polypeptide
    - ribosome assembles the amino acid sequence
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8
Q

Genetic Code
- how many nucleotides for how many combinations

A
  • 4 nucleotide bases in DNA or RNA
  • 20 different amino acids in polypeptides

Code:
- 1 nucleotide…only 4 combinations
- 2 nucleotides…only 16 combinations
(not enough combinations since we have 20 amino acids, and these are both smaller)
- 3 nucleotides…64 combinations

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9
Q

DNA vs RNA codes

A

DNA: three letter code-triplet
RNA: three letter code- codon
(complementary to each other)

1 CODON encodes 1 AMINO ACID

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10
Q

How do you build vs Read DNA

A

Built: 5-3
Read: 3-5

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11
Q

Features of the Genetic Code

A
  1. 3 LETTER CODE
  2. COMMALESS
    - Nucleic acid codes are sequential
    - no spaces between codons
  3. UNIVERSAL
  4. REDUNDANT (wobble)
  5. START AND STOP SIGNALS
    Sense codons
    - 61 codons specify amino acids
    - most amino acids specified by several codons (redundancy)
    - Ex. CCU, CCC, CCA, CCG all specify proline
    - start AUG establishes the reading frame (repetition)
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12
Q

Start vs Stop codons

A

START
- also called the initiator codon
- AUG (applicable to most proteins)
- 1st codon recognized during translation
- Specifies amino acid Methionine

STOP
- end of a polypeptide encoding mRNA sequence
- UAA, UAG, UGA
* don’t code for any a.a.*

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13
Q

How do we know the genetic code is universal

A
  • same codons specify the same amino acids in all living organisms and viruses
  • genetic code was established very early in the evolution of life and has remained unchanged evolutionary= been around for a long time
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14
Q

Transcription (DNA to RNA) compared to DNA replication

A
  • Info in DNA is transferred to a complementary RNA copy
  • Similar to DNA replication except:
    1) only 1 DNA strand is used as a template and you’re copying RNA
    2) Only transcribes the genes (unlike how in replication the entire chromosome is replicated)
    3) RNA polymerase is used to catalyze the assembly of nucleotides NOT replication
    4) RNA are single strands (replication: 2 by 2 stranded DNA molecules)
    5) U replaces T (replication: uses Thymine)

regulated by signals like promoters, enhancers, and transcription factors that activate specific genes based on the cell’s needs.

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15
Q

RNA Polymerase

A
  • No primers needed to start complementary copy
  • RNA is made in the 5’-3’ direction
  • DNA template strand is read 3’-5’

Eukaryotes: RNA polymerase does not bind directly to DNA, it needs A TRANSCRIPTION FACTOR

Prokaryotes: RNA polymerase binds directly to DNA
- start replication immediately/asap to make RNA copy
-bind to transcription data (indirectly)

Transcription data- information about which genes are being transcribed into RNA under specific conditions

Transcription factor- protein that helps control the rate of transcription by binding to specific DNA sequences near genes.

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16
Q

TRANSCRIPTION OVERVIEW

A
  • begins as RNA polymerase binds to DNA
  • DNA double helix begins to unwind
  • RNA polymerase adds RNA nucleotides sequentially according to DNA template
  • Enzyme and completed RNA transcript are released from DNA template
  • and DNA returns to OG form before transcription started
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17
Q

Organization of a gene

A

PROMOTER:
- control sequence initiates transcription
- upstream of transcritional unit
- where RNA polymerase binds

TRANSCRIPTIONAL UNIT:
- portion of gene that is copied into RNA (don’t transcribe everything)

TERMINATOR:
- signals the end of transcription of a gene

CASE 1: terminator sequence on mRNA uses complementary base-pairing

CASE 2: protein binds to particular terminator sequence on mRNA

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18
Q

3 Stages of transcription

A

1) initiation
- RNA polymerase 2
euk: have TATA box in promoter
transcription factors: binds promoters
RNA polymerase 2, binds both transcription factors
UWINDS DNA + BEGINS TRANSCRIPTION

2) elongation

3) termination
- Termination of transcription differs in eukaryotes (polyadenylation signal, cells cleave to stop it)
- prokaryotes have terminators

TATA- helps recruit RNA polymerase + transcription factors to start

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19
Q

TATA Box sequence

A

5’…TATAAAA…3’
3’…TATAAAA…5’

  • TATA box in the promoter is about 30 base pairs
  • determines where transcription will initiate
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20
Q

what is the poladenylation signal

A
  • marks the end of transcription
  • cells stop it to terminate RNA synthesis and ensure proper mRNA processing
    ITS STOPPED BECAUSE
    -yes, it marks the end but its being stopped so that the RNA can actually leave

mRNA needs proper modifications: addition of 5’ cap and 3’ poly-A tail

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21
Q

Transcription of Non-Coding regions

A
  • Non-coding genes do not code for protein but instead code for rRNA and tRNA

Prok- use RNA polymerase 2 for all transcription
- same promoters

eukaryote: different genes
- coding region flanked 5’ and 3’ untranslated regions (UTRs)
- additional noncoding elements (introns)
- RNA polymerase 3=tRNA and 1/4 of rRNA
- RNA polymerase 1=3/4 rRNA

UTRs are transcribed but not translated, they dont encode for anything

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22
Q

pre-mRNA

A

1) precursor-mRNA (pre-mRNA)
- must be processed in nucleus to produce translatable mRNA, it then eventually leaves the nucleus and is translated in cytoplasm

2) 5’ cap
- reversed guanine containing nucleotide
- site where ribosome attaches to mRNA
- protects it from degradation

3) Poly A tail
- 50 to 250 adenine nucleotides added to 3’ en d by polA polymerase
- protects mRNA from RNA-digesting enzymes
stabilize mRNA to prevent degradation
= made from poly-A polymerase

  • adding in opposite order

5’ protects from exonucleases

(to protect as it processes)-The 5’ cap is added first, shortly after transcription begins
(mark mrna as complete)-while the 3’ poly-A tail is added after transcription is complete.

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23
Q

INTRONS VS EXONS

A

Introns
- Non-protein coding sequences in pre-mRNA
- must be removed before translation (to go from pre-mRNA to mature mRNA transcript)

Exons
- Amino acid coding sequence sequences in pre-mRNA
- Joined together sequentially in final mRNA

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24
Q

How do we remove introns

A
  • mRNA splicing
  • eukaryotes need to process mRNA for translation, prokaryotes don’t
  • removal of introns and joining exons consequentially

prokaryotes have UTRs but they only code for trna + mrna NOT INTRONS

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25
Q

strands are

A

“recall: strands and complementary and antiparallel”

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26
Q

mRNA splicing

A
  • introns in pre-mRNAs are removed

SPLICEOSOMES DO THIS (molecules)
1) pre-mRNA: remove introns from it to make mature-mRNA
2) made up of: small ribonucleoprotein particles (snRNP)
- small nuclear RNA (snRNA) + several proteins

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27
Q

snRNPs

A
  • bind to introns
  • loop them out of the pre-mRNA
  • clip the intron at each exon boundary
  • join adjacent exons together
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28
Q

What part does the mRNA splicing

A
  • the RNA part does the cutting from the sNRPs
  • previously, It was thought only proteins (enzymes) could do this but nucleic acids can too!

(enzyme activity in large ribosomal subunit=ribozyme)
= RIBOZYMES (nucleic acid enzyme)

29
Q

Why do we have introns

A

1) Alt Splicing
- different version of mRNA can be produced due to different regions being identified as introns and removed in different combinations to make different mature mRNA
(regions in exon in one case may be an intron in another)

2) Exon Shuffling
- generates new proteins

= PROTEIN VARIABILITY
- increasing the coding capacity of existing genes through alternative splicing and evolutionary advantage through exon shuffling

30
Q

Protein Variability

A
  • occurs at the genomic level, and refers to diversity created through introns allowing for gene shuffling

for example:
- humans and worms have the same number of chromosomes, but introns allow for gene shuffling=protein variability
- hence introns create variability

31
Q

Alternative Splicing

A
  • Exons joined in diff combinations to produce different mRNAs from the same gene
  • Different mRNA versions translated into different proteins with different functions (bc of different structure)
  • More information can be stored in the DNA

= EFFICIENCY

Example:
- a-tropomyosin in smooth and striated muscle
- spliced in various ways in different tissues
a) similar protein but different structure=different function

32
Q

Exon shuffling

A
  • Intron-Exon junctions often occur between major functional regions in encoded protein

Exon shuffling: mixes protein regions or domains into novel combinations
- allows quicker and more efficient evolution of new proteins

(complete shuffling bc allows entire exons, which encode specific protein domains, to rearrange or combine during evolution, creating entirely new genes or protein functions)

33
Q

Translation
- going from what to what and explain process

A

mRNA to protein

  • assembly of amino acid into polypeptides
  • occurs on ribosomes
  • P, A, and E sites on ribosome used for stepwise addition of amino acids to polypeptide as directed by mRNA

Small ribosomal subunit, THEN AUG, then Large ribosomal subunit

34
Q

What do adapter molecules do

A
  • bring in amino acids to link onto polypeptide chains

type of trna

35
Q

tRNAs

A

transfer RNAs (tRNA)
- bring specific amino acids to ribosome
- cloverleaf shape
* Bottom end of tRNA contains anticodon, which pairs with codons in mRNA*

Top end contains=amino acid

36
Q

difference between codon and anticodon

A

codon: x3 nucleotide
anticodon: complementary version of codon

37
Q

how is anticodon read

A
  • because mRNA is read 5’ to 3’
    anticodon is read 3’ to 5’
38
Q

Do we have 61 tRNAs?

A

-No because of Wobble Hypothesis

39
Q

Wobble hypothesis

A
  • 61 different sense codons don’t require 61 DIFFERENT tRNAs
  • first two nucleotides of anticodon and codon must match exactly but the third nucleotide has more flexibility

Ex. tRNA carrying glutamine
- matches codons CAA and CAG
where the CA are necessary to match but the A (on CAA) and G (on CAG) are flexible

40
Q

Aminoacylation

A
  • adds amino acid to tRNA
  • aminoacyl-tRNA (amino acid linked to tRNA)
  • aminoacyl-tRNA synthetases catalyze reaction

WE NEED ATP FOR THIS

Aminoacylation is a two-step process performed by aminoacyl-tRNA synthetase:

Activation: The enzyme binds an amino acid and ATP, forming an aminoacyl-adenylate intermediate (amino acid + AMP) and releasing pyrophosphate (PPi).

Transfer: The activated amino acid is transferred to the 3’-OH group of the corresponding tRNA’s terminal adenine, forming aminoacyl-tRNA.
This ensures the correct amino acid-tRNA pairing for protein synthesis.

41
Q

Synthetases

A
  • an enzyme that requires ATP
    for any suffix: tases
42
Q

What will happen if the wrong tRNA binds during aminoacylation

A
  • it’ll disassociate
43
Q

Ribosome composition

A
  • made of RNA (rRNA) and protein

2 subunits: large and small
- ribosomes are free or bound

44
Q

Stages of translation

A

1) INITIATION
- ribosome assembled with mRNA molecule and initiator Met+RNA (AUG CODON= start codon)

2) ELONGATION
- amino acids linked to tRNAs added 1 at a time to growing polypeptide chain

3) TERMINATION
- new polypeptide released from ribosome
- ribosomal subunits separate from mRNA

45
Q

Initiation process for translation

A
  1. Initiator tRNA (Met-tRNA) binds to small subnit
  2. Complex binds to 5’ cap of mRNA (to recruit translational assembly), scans along mRNA to find AUG start codon
  3. Large ribosomal subunit binds to complete initiation

Met-tRNA is in the ‘P’ site (unique no other a.a. will do this, only 1 will go directly to P site)
No 5’ Cap in prokaryotes
They use a specific nucleotide sequence instead

46
Q

Do prokaryotes have 5’ Cap

A

No

47
Q

What does initiation establish

A

reading frame
- GTP energy is consumed: to catalyze recruitment of large subunit

48
Q

Elongation process for translation

A

1) aminoacyl-tRNA matching the next codon enters A site
- Peptide transferase (internal enzymatic activity of a large subunit) catalyzes formation of first peptide bonds and cleaves tRNA in P site

2_ Ribosome moves along mRNA to next codon
- empty tRNA moves from P to E site, then released
- newly formed peptidyl-tRNA moves from A to P site
- A site is empty again (for the next tRNA to enter)

49
Q

How many sites of energy expenditure are needed in elongation

A

2

  1. when an aminoacyl-tRNA binds to the codon in A site; GTP is hydrolyzed in this step
  2. The ribosome moves along the mRNA to another codon, using energy from GTP hydrolysis

gtp for prokaryotes, atp for eukaryotes

50
Q

termination process in translation

A
  • Begins when A site reaches stop codon
  • Release factor (RF) or termination factor binds to A site (recognizes STOP codon but they aren’t protein synthesizers)
  • Polypeptide chain released from P site
  • Remaining parts of complex separated
51
Q

Polyosomes

A
  • multiple ribosomes can simultaneously translate a signal mRNA
  • mature protein sequence
52
Q

Where does simultaneous transcription and translation occur

A
  • prokaryotes (no nuclear envelope)

Prokaryotes lack a nucleus, so transcription and translation occur simultaneously in the cytoplasm. Thus, no need to transport

53
Q

Polypeptide Processing

A

Processing reactions convert polypeptides into finished form

  • removal of one or more amino acids from the protein chains (regulate the function of the protein)
  • Addition of organic groups (macromolecules)
  • Folding guided by chaperones (to determine the structure and function)
  • Alt pathways to different mature polypeptides
54
Q

what happens to proteins in the secretory pathway

A
  • proteins are distributed within cells by sorting signals
  • signals are coded in the DNA, and appear when protein is made
  • Can’t find another exit site w/o shuffling proteins and nucleotide signals
55
Q

Sorting signals in ER

A

polypeptides that sort to EM begin synthesis on free ribosomes on cytosol and produce short segment of amino acids=signal peptide

  • proteins sorted at RER

1) signal peptide (signal sequence)
- at beginning of polypeptide chain (occurs in cytoplasm, DM system)

which binds to….

2) Signal Recognition particle (SRP)
- binds to signal peptide to STOP translation

= SRP binds so it can stall the process allowing for the ribosome-mRNA complex to be shuttled to RER

3) SRP Receptor
- SRP binds to protein receptor in ER membrane
- ribosome bound onto ER membrane
- growing polypeptide pushed inside ER lumen

4) Signal Peptidase
- removes signal sequence
- translation continues until polypeptide is complete

56
Q

Where does the polypeptide go now

A
  • ER, Golgi, Lysosomes, plasma membrane, secreted….etc.
  • some proteins remain in the ER
  • some transported to Golgi, where they can be modified further, proteins are then packaged into vesicles that can deliver them to lysosomes, secrete them from the cell or deposit them in the plasma membrane
57
Q

Mutations

A

changes in genetic material
base-pair mutations change DNA triplet, causing:

  • changes in mRNA code
  • leading to changes in a.a. sequence of encoded polypeptide

fact: exposure to X-rays create ROS

58
Q

Types of mutations

A
  1. Misense: Changes a sense codon to a different sense codon (by changing 1 a.a.)
  2. Nonsense Mutation: Changes a sense codon to a STOP codon (arguably the worst bc of premature termination is can make protein non-functional)
  3. Silent Mutation: Changes 1 sense codons o another sense codon that specifies the same amino acid
    (changed 1 nucleotide to another but not a.a.)
  4. Frameshift Mutation: Base-pair insertion or deletion alters the reading frame after the point of mutation
59
Q

If you add 3 nucleotides and 2 are inserted or deleted then is it a frameshift?

A

Yes, since its not a codon its a frame shift, but if you were to just add 3 nucleotides then it won’t be a frameshift bc ur just adding a codon

60
Q

Sickle-Cell disease

A
  • caused by a single missense mutation leading to change in protein structure and function changing how RBC are affected
61
Q

Are mutation induced or spontaneous

A

SPONTANEOUS MUTATIONS
- errors during DNA replication or repair (from mechanism)

INDUCED MUTATIONS
- physical, chemical, and biological agent (mutagens) that generate mutations=MUTAGENESIS

ex. 5-Bromouracil
- analogue of thymine but has bromomine instead of methyl
- can form x2 H-bond w/ adening
- can form x3 bond w/ guanine
- unstable so it jumps btwn the 2 creating substitution mutation through successive rounds of DNA replication

ex. X-rays, UV radiation, 5-bromouracil (a chemical mutagen)

62
Q

gene

A

a string of nucleotides encoding for rna product or protein
- begins w/ promoter and ends w/ terminator
-

63
Q

what causes dna double helix to unwind and open

A

binding of the rna polymerase onto promoter

64
Q

tRNA on A and P site

A

form a peptide bond

65
Q

protein vs polypeptide

A

protein, the functional collection of polypeptides (quaternary structure)
polypeptide, the molecule encoded by a gene (tertiary structure)

66
Q

transcription initiation complex

A
  • combination of TFs (transcription factors) and RNA polymerase 2

(tf’s are released when the RNA polymerase enzyme begins and moves along)

67
Q

T/F: tRNA has an anticodon that can pair with a stop codon

A

F

A RF binds in the A site instead (shape mimics tRNA)

68
Q

what makes the poly-A tail

A

poly-A polymerase
= process of adding poly-A-tail is POLYMERIZATION

BIOL 1101 (18 decks)

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