Chapter 14 Flashcards
Gene organization
- Colinearity and noncolinearity
- Nucleotides and animo acids in encoded protein should be PROPORTIONAL
- DNA is longer than mRNA (shown in hybridization)
- without proteins, bacterial genes are coli near, but eukaryotic genes are not
Colinearity
Continuous sequences of nucleotides in DNA encodes a continue amino acid sequence in proteins
Noncolinearity
- coding sequences are NOT continuous
- Discovered by hybridizing DNA with the mRNA transcribed from it
- discovered noncoding regions as the loops
Introns
- spliced out in RNA processing
- Vary from gene to gene
- ## common in eukaryotes, less in prokaryotes
Exons
- exit the DNA, exported
- code for proteins
Genes
- includes DNA sequences that code for all exons and introns
- RNA sequences at the beginning and end are NOT translated into a protein (i.e. promoter and terminator)
Start codons
- codes for starting translation
Stop codons
- codes for stopping translation
Pre-mRNA
- found in eukaryotes (WHY? Adds complexity)
- adds the 5’ cap (DESCRIBE?nucleotide, RNA, 7 methylguanine, 5’-5’ bond at the end of 5’ RNA)
- adds the polyA tail (50-250 adenine nucleotides to 3’ end of RNA), most eukaryotic have the 3’ polyA tail
RNA Splicing
- Cutting out the introns out of RNA
- uses consensus sequences: 5’ consensus sequence (GU(A/G)AGU) 5’ splice site, 3’ consensus sequence (CAGG), branch point (adenine A is ~18-40 nucleotides upstream of 3’ splicing site)
- spliceosome: five RNA molecules and 300 proteins
- REQUIRES consensus sequences
Pre-mRNA processing steps
- 5’ end cleaved, folded over and attaches to the branch point (lariat structure)
- 3’ end cleaved, exons brought and spliced together
- Intervening intron removed
- Within the spliceosome
- 5’ end of intron 1 is promixal to the 3’ end of exon 1
spliceosome
RNA splicing takes place here
Assembles sequentially
WHAT? RNA protein complex
IMPACT? removes introns from pre-mRNA
WHERE? found in the nuclei
WHEN? during transcription
Minor splicing
- WHAT? uses minor spliceosome
- IMPACT? splices out special pre-mRNA introns
- WHERE? U12 type (of introns)
- WHEN? during transcription
Alternative splicing
- WHAT? type of alternative processing
- IMPACT? pre-mRNA can form different options for mRNA –> different amino acid sequences –> different proteins developed
- WHERE? pre-mRNA
- WHEN? during transcription
- exons are able to be spliced together in different combination to yield mRNAs to encode different proteins
- create multiple different proteins from the same sequence, increase complexity from one sequence
- different mRNAs produced from a single pre-mRNA
Multiple Cleavage sites
- HOW? mRNAs can be cleaved and add the polyA tail from different places
- WHERE? mRNA on the 3’ end
- IMPACT? Different lengths —> different form —> different structure —> structure means FUNCTION
- WHAT? different mRNAs produced from a single pre-mRNA
- WHEN? transcription
THINK! alternative splicing impacts
Alternative processing
- Alternative splicing
- Multiple cleavage sites
Guide RNA
RNA that adds nucleotides to the mRNA that were not encoded by the DNA
tRNA structure
Rare modified RNA nucleotide bases
‒ Ribothymine
‒ Pseudouridine
- Common secondary structure—the cloverleaf structure
- Anticodon
Ribosome structure
Large ribosome subunit
&
Small ribosome subunit
(Prokaryotes AND eukaryotes have)
50S —> could be large subunit, “S” refers to the unit of ribosomes
rRNA
processed after transcription, subunits are the result of splicing original rRNA
Small interfering RNA function
- RNA interference: protects from invasion of foreign genes, regulates its own gene regulation
- Types of small RNAs
- Processing and function of microRNAs
- Piwi interacting RNAs inhibit transposons, found in GERM cells
- CRISPR RNAs defend against foreign genes (bacteriophages and plasmids from DNA) in PROKARYOTIC cells
Small interfering RNAs and microRNAs
Produced from double-stranded RNAs
Perfectly paired double stranded RNAs
Silencing or cutting
Long noncoding RNAs (lnRNAs)
- do NOT encode proteins
- control gene expression
- enhancer RNAs transcribed from enhancers and play a role in control of gene expression
One gene one enzyme hypothesis
- Genes function by encoding enzymes, each gene encodes a separate enzyme
- One gene, one polypeptide hypothesis (more specific)
amino acids
Common ones have similar structures
Joined together by PEPTIDE bonds
Protein functions
- ATP drives production of light in lightning bugs (bioluminescence)
- ricin, toxic molecules to defend themselves
Types of bonds and WHERE
Protein levels of structures
Primary, secondary, tertiary, quanternary
Structure of a ribosome
Codons
- Triplet RNA code
- 64 possible codons: 3 stop codons, 61 sense codons
- No start codon —> “nitrogen formal methionine” start amino acid, specific enzymes to recognize it
Degeneracy of the Code
- Degenerate code: amino acid specified by more than one codon
- synonymous codons: specify the same amino acid
- isoaccepting tRNAs: different tRNAs that accept the SAME amino acid, but DIFFERENT anticodons (think isosceles triangle)
Codons cont.
- sense codons: encoding amino acids
- initiation codon: AUG
- termination codon: UAA, UAG, UGA
Wobble hypothesis
base at 5’ end of tRNA anticodon can pair with several different bases in codon
mRNA and tRNA pair in an anti parallel fashion
Methionine
AUG
Recognized by other enzymes to allow initiation to occur
Start codon
Reading Frame (Triplet Code)
Sequence is read in groups of three, messing it up messes up all of the amino acids & functions, each different three part sequence encodes a different amino acid
Nonoverlapping (Triplet Code)
A single nucleotide may not be included in more than one codon
The universality of the Triplet code
Near universal across the board
Translation, Steps
Amino acids bind to tRNAs
Initiation (initiation factors, 3, energy factors)
Elongation (elongating polypeptides and creating polypeptide bonds, elongation factors, 2)
Termination (release factors, 1 & 2)
Happens on a ribosome
N
Amino acid end of the protein
C
Carboxyl end
Binding amino acids to tRNAs
Aminoacyl-tRNA synthetases load amino acid onto tRNA (charging it)
Specificity between
20 aminoacyl tRNA synthetases in a cell, corresponds with the 20 amino acids
Amino Acids
Attach to the 3’ end of tRNAs, C-terminase binds to it
Initiation
Initiation factor signals (IF 3, 2, 1…)
TRNA loaded with N-formylmethoin attached = fmet tRNA
Energy molecule GTP
REQUIRES INITIATION FACTORS AND GTP
3’ cap strengthens structure of the ribosome for this process
Shine-Dalgarno Consensus Sequence
IF-3, IF-1
Binds to the small subunit, prevents large subunit from binding
During translation
IF-2
Binds informal methionine,
During translation
Elongation
Factors: Tu, Ts, G (EF-TU (forms complex with GTP and charged tRNA)
, E-Ts, EF-G (works with GTP to move ribosomes down the mRNA))
* Exit site E
* Peptidyl site P
* Aminoacyl site A
GTP drives it
Peptides binding on tRNAs
Termination
When ribosome hits termination codon
UAA, UAG, UGA
Release factors that were bound at initiation, releasing:
– The polypeptide from the last tRNA
– The tRNA from the ribosome
– The mRNA from the ribosome
RF-1 —> release factors
Ribosome Structure cont.
3D structure
Polyribosome: an mRNA with several ribosomes attached
Longest polypeptide chain is the RNA that’s produced first
Spliceosome
The splicing of pre-mRNA takes place within this large complex
snRNAs and proteins present
