Genetics Review/Outline
Complex Traits: Quantitative Traits, Complex Traits, and GWAS
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Coefficient of relatedness: proportion of genes that 2 people related in a certain way
share
o High within a family = complex trait may be inherited through genetic factors
or environmental factors
o Higher degree = more likely to exhibit similar expressions of that trait
o Helps qualify genetic connections and predict transmission of traits within
families and populations
Complex trait: phenotype that’s either monogenic or polygenic, and influenced by
the environment
o Don’t follow Mendelian inheritance patterns
o Quantitative and show variability across a population
o Monogenic or Polygenic - continuous variability and are quantitative
o Determined by genetics and environment
o High heritability = large portion of variability in traits is due to genetics
o Multifactorial – influenced by genes and environmental
o Association is analogous to linkage – visualized by Manhattan Plot
Genome-Wide Association Study (GWAS): comparison of millions of variants that
form haplotypes between people with a condition and unaffected individuals to
identify parts of the genome that might contribute to a phenotype
o Identifies genetic risk factors for complex traits
o Found: most complex traits are polygenic, revealed specific “risk alleles” and
“protective allels”, and provided insights into biological pathways and
mechanisms underlying diseases.
Heritability: estimate of the proportion of phenotypic variation in a population that’s
due to genetic differences
Polygenic: trait determined by more than 1 gene
SNP (single nucleotide polymorphism): site in DNA that has a different base at least
1% of a population
o Most common type of genetic variation in humans
o Stable and common – used as genetic markers
o Occur in coding regions, non-coding regions, or intergenic regions
▪ coding regions – might cause mutation in protein sequence possibly
changing function
▪ non-coding regions – might influence gene expression or how genes
are regulated
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o synonymous SNPs: in coding regions and do not result in change in protein
sequence
o non-synonymous SNPs: result in change in amino acid sequence of protein –
can alter function
o regulatory SNPs: occur in regions that control gene expression – can affect
level or timing of gene expression
quantitative trait: one that varies in its characteristics and expression
o continuous variation and are measured on numerical scale
o controlled by multiple genes
▪ also affected by environment to varying degrees
o continuous traits given quantitative value
o additive alleles
continuous trait: genetic variation showing an unbroken range of phenotypes in a
population
o no discrete categories
o gradual differences
multifactorial inheritance: hereditary pattern that occurs when more than one
genetic factor is involved in the development of a condition
o polygenic
empiric risk: probability that a trait will recur based upon its incidence in a
population, based on observation
o estimate of risk of recurrence of multifactorial trait
o derived from observations of a population
genetic marker: gene/short sequence of DNA used to identify a chromosome or to
locate other genes on genetic map
Manhattan plot: display data in genetic analysis
o Identifies regions of genome that are significantly associated with the trait
being studies
o X-axis represents genomic locations of SNPs being analyzed
o Y-axis represents statistical significance of the association between the SNP
and the trait or disease
Chromosome Variation/Mutation
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Aneuploid: cell with one or more extra or missing chromosomes
o Results from nondisjunction in meiosis
o Types:
Trisomy – example: down syndrome is where an individual has three
copies of chromosome 21
▪ Monosomy – example: turner syndrome is a female with only one X
chromosome instead of two
▪ Tetrasomy
▪ Polysomy
o Autosomal aneuploidy is a trisomy autosome often leads to serious
developmental disorders like Down Syndrome, Edwards Syndrome, and
Patau Syndrome
▪ Result from nondisjunction during meiosis often lethal long before
birth with three exceptions: Patau, Edwards, and Down syndrome
o Sex chromosome aneuploidy may result in less severe developmental
effects
▪ Result from nondisjunction during meiosis
Chromothripsis: shattering of chromosomes and then reassembled in a random
manner
o Reassembly often results in duplications, deletions, and translocation
o Leads to genetic instability
o Mechanisms include ionizing radiation, DNA replication stress, telomere
attrition, and apoptotic events in an apoptosis resistant cell
Euploid: a somatic cell with the typical number of chromosomes for the species
Isochromosome: chromosome that has two copies of one arm but none of the
other, as a result of cell division along wrong plane
o Abnormality and symmetric
o Occurs during error during meiosis or mitosis
Monosomy: cell missing a chromosome
Nondisjunction: unequal distribution of chromosomes during meiosis
o Common cause of aneuploidy
o Occurs when chromosomes don’t separate properly during cell division =
gametes have abnormal number of chromosomes that lead to aneuploidy if
fertilization occurs
Reciprocal translocation: chromosome where two nonhomologous chromosomes
exchange parts, conserving genetic balance but rearranging genes
o No genetic material is lost or gained just exchanged
o Involve non-homologous chromosomes
Robertsonian translocation: chromosome where two short arms of nonhomologous
chromosomes break off and are lost and the long arms fuse
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o Reciprocal translocation involving the acrocentric chromosomes
o Long arms of two acrocentric chromosomes fuse together = chromosome
with two long arms and a loss of the short arms
Trisomy: human cell with one extra chromosome
Polyploidy: chromosomal constitution of a cell containing multiples of the normal
number of chromosomes
o Almost always lethal in humans = spontaneous abortion
o Observed in some human tissues or cells – liver, placenta, and cancer
Nonreciprocal translocation: results from movement of a segment of a
chromosome from one location of a nonhomologous chromosome to another
o First chromosome has loss of genetic material the second chromosome has
no loss of genetic material
Rearrangement: mutation that’s a type of chromosome abnormality involving a
change in structure of native chromosome
o Duplications: a segment of the chromosome may be copied and inserted
into a different location
▪ Can be caused by unequal crossover
o Deletions: parts of the chromosome may be lost completely
▪ Deletions can be caused by radiation-induced DNA damage
▪ Can be caused by unequal crossover
▪ Typically deleterious
▪ DiGeorge Syndrome – most common deletion syndrome
o Translocation: pieces of the chromosome may be transferred to a different
chromosome
o Inversions: some fragments may be rejoined in reverse order, flipping the
sequence
Acentric: segment of a chromosome that lacks a centromere
Dicentric: abnormal chromosome with two centromeres
Fluorescence in situ hybridization (FISH): cytogenic technique that uses fluorescent
probes that bind to only certain parts of a nucleic acid sequence with a high degree
of sequence complementarity
o Detects specific chromosome segment involved in nonreciprocal
translocations
Deletion: mutation that removes a part of a DNA sequence
Triploid: three copies of every chromosome instead of normal two
Tetraploid: containing four homologous sets of chromosomes
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Down syndrome: genetic condition caused when an unusual cell division results in
an extra full or partial copy of chromosome 21
o Most common chromosomal condition
Intercalary deletion: deletion that occurs from the interior of a chromosome
o Portion of the chromosome is removed, and the two remaining ends of the
chromosome are rejoined
o Occur as a result of chromosomal breakage or errors during DNA replication
or cell division – the break can be spontaneous or induced by external factors
Ring chromosome: arms fused into a ring following a breakage
o Can occur due to spontaneous errors during DNA replication, chromosomal
breakage, or damage caused by external factors like radiation
o Unstable structure due to not allowing for normal cell division
Turner syndrome (X0 or 45, X): condition affecting females who have only one X
chromosome
o Occurs in about 1 in 2500 live female births – short in stature, infertility, and
heart defects
Klinefelter syndrome (XXY or 47, XXY): males with an extra X chromosome
o Occurs in about 1 in 500 to 1000 live male births – infertility, taller than
average stature, and learning disabilities
Patau syndrome (trisomy 13): rare and severe condition caused by an extra
chromosome 13 – most die within first few months of life dur to severe
developmental abnormalities
Edwards syndrome (Trisomy 18): serious condition caused by the presence of an
extra chromosome 18 – most affected people don’t survive past the first year of life
Terminal deletion: portion of the end of a chromosome is lost or deleted
Chromosomal variation
o When and why we karyotype?
▪ Prenatal diagnosis
▪ Cancers
▪ Miscarriages
Prenatal diagnoses
o Steps:
1. Collect cells
2. Culture cells
3. Karyotype and other testing
o Limitations: invasive, cell culture fail, through derived from fertilized egg – CV
can have mutations distinct from fetus can have mutations distinct from CV
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Miscarriage diagnosis
o Recommended after multiple miscarriages
o Test products of conception (POC)
▪ Placental and/or fetal tissue remaining after miscarriage
o Chromosomal abnormalities: aneuploidies, polyploidies, and triploids
Cell-free fetal DNA
o Less invasive: blood tests
o Median fragments size: ~167 base pairs
o Doesn’t require cell culture
o Measures relative abundance of genes
o Limitations:
▪ Most cfDNA is from trophoblasts may not be identical to fetus
▪ Interference by maternal karyotype abnormality
▪ Misses some chromosomal rearrangements
Inversion loops form in inversion heterozygous
o Paracentric inversion loops – no centromere
o Pericentric inversion loops – has centromere
DNA structure
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A-form: right-handed double helix
o Bases are tilted away from helix axis
o More compact
o Exist less of water is present
Antiparallel: head-to-toe orientation of two nucleotide chains of the DNA double
helix
B-form: most common; right-handed double helix with strands going in opposite
direction
o Bases are parallel to helix axis
o Larger diameter and more open
Chromatin: DNA and its associated proteins
Complementary base pairs: pairs DNA bases that form hydrogen bonds; A-T and G –
C
Deoxyribose: a five carbon sugar that’s part of a DNA nucleotide
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Gyrase: enzyme, topoisomerase, that reduces topological strain in an ATP
dependent manner while double stranded DNA is being unwound by enlongating
RNA-polymerase or by helicase in front of progressing replication fork
Histone: type of protein around which DNA coils in a regular pattern
o Rich in positively charged basic amino acids
Nucleoid: irregularly shaped region within prokaryotic cell containing all or most of
genetic material
Nucleosome: unit of chromatin structure consisting of DNA coiled around an octet
of histone proteins
o Fundamental unit of DNA packaging
o DNA wrapped two times around histone octamer
▪ Two of each H2A, H2B, H3, and H4
Nucleotide: building block of a nucleic acid; has P group, nitrogenous base, and a
five-carbon sugar
Purine: nucleic acid base with a two-ring structure – adenine and guanine
Pyrimidine: nucleic acid base with a singe-ring structure – cytosine, thymine, and
uracil
Topoisomerase: enzymes that catalyze changes in topological state of DNA,
interconverting relaxed and supercoiled forms, linked and unlinked species, and
knotted and unknotted DNA
o Can induce or relieve supercoiling
o Topoisomerase I makes single strand break in DNA
o Topoisomerase II makes double strand breaks in DNA
▪ Mechanism:
• Makes double strand breaks
o Attaches end it creates
• Pass uncut section of double helix through break
• Reconnects broken DNA
Z-form: left-handed double helical structure
o Zig zag backbone
o Occur under high salt conditions and when DNA is being transcribed
Chargaff’s rule: demonstrates the complementary nature of DNA
Supercoiling is induced by replication and transcription
o Teritary structure
o Controlled by topoisomerase
o Makes DNA compact
o Helps DNA fit inside cell
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o Induced by replication and transcription
o Overrotation is a positive supercoil
o Underrotation is a negative supercoil
o Cellular default is negatively supercoiled DNA in nucleus
The structure of DNA
o (1°) primary – linear sequence nucleotides
o (2°) secondary – double helix like A-, B-, or Z-form
o (3°) tertiary – higher order folding
Replication and Recombination
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Branch migration: base pairs on homologous DNA strands are consecutively
exchanged at a Holliday junction, moving the branch point up or down the DNA
sequence
Continuous strands: one of the new strands, leading strand, is synthesized
continuously in 5’ to 3’ direction
Crossing over: exchange of genetic material during sexual reproduction between
two homologous chromosomes’ nonsister chromatids resulting in recombinant
chromosomes
o Generates new combinations of alleles
Discontinuous: lagging strand where new DNA is synthesized in short fragments
Helicase: unwinds and separates double stranded DNA or RNA during replication
allowing each strand to be copied
Heteroduplex: double stranded molecule formed from complementary strands that
come from different sources
Holliday Junction: branched nucleic acid structure that contains four double
stranded arms joined
Ligation: joining of two nucleotides into single polymeric chain via ligase
Okazaki fragments: short sequences of DNA nucleotides, synthesized
discontinuously and later linked by ligase
Initiator protein: recognize a specific DNA sequence within origin of replication
Primase: catalyzes the synthesis of a short RNA segment to a single stranded DNA
template
Proofreading: occurs in mRNA translation for protein synthesis
Replication: producing two identical replicas of DNA from original DNA molecule
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Replication bubble: region of DNA that has been unwound and separated during
DNA replication
o Each bubble states at an origin of replication
▪ Prokaryotes have one origin of replication
▪ Eukaryotes have many origin of replications
o Proceeds outward in a bidirectional fashion
Replication fork: a locally opened portion of a replicating DNA double helix
Strand displacement: single stranded DNA invades a double stranded DNA leading
to replacement of one strand of the double stranded DNA
Telomere: region of repetitive nucleotide sequences associated with specialized
proteins at end of linear chromosomes
Telomerase: adds a species-dependent telomere repeat sequence to 3’ end of
telomeres
Translesion synthesis: DNA repair process that allows cells to replicate DNA past
damaged sites
5’-3’ polymerase activity: addition of a new nucleotide at 3’ end of a strand –
determine speed of an enzyme
3’-5’ exonuclease activity: enzymatic function that removes nucleotides from 3’ end
of a DNA, primarily to correct errors during DNA replication
5’-3’ exonuclease activity: enzymatic ability to remove nucleotides from 5’ end of a
DNA or RNA molecule; 5’ -> 3’
Central Dogma
o DNA replication → DNA → transcription → RNA → translation → protein
Competing models of replication
o Conservative – old strand come together; new strands come together
o Semiconservative – old strands pair with new strands
o Dispersive – mix of old and new parts within each single strand
Leading vs. lagging strand
o Leading strand – continuous DNA synthesis
o Lagging strand – discontinuous DNA synthesis
▪ Okazaki Fragments
Steps of replication
o (1) initiator proteins begin separating strands
o (2) helicase further unwinds DNA
o (3) primase makes RNA primers
o (4) DNA pol III extends primers
o (5) primase makes new primers to fill gap in lagging strand
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o (6) new primers also extended by DNA pol III
o (7) strands fully separated
o (8) DNA pol I replaces RNA primers with DNA
o (9) DNA ligase seals nicks in sugar phosphate backbone
Prokaryotic DNA replication
o Initiator proteins DnaA bind to origin of replication and begin unwinding DNA
o Helicase further unwinds DNA
o SSBs bind to ssDNA
o Gyrase alleviates supercoiling caused by strand separation
RNA primer provides 3’ -OH for DNA pol to add on to
DNA pol I – removes and replaces primers
o Active in 5’-3’ polymerization, 3’-5’ exonuclease, and 5’-3’ exonuclease
DNA pol II – DNA repair, restarts replication after damaged DNA halts synthesis
o Active in 5’-3’ polymerization and 3’-5’ exonuclease
DNA pol III – enlongates DNA
o Active in 5’-3’ polymerization and 3’-5’ exonuclease
DNA pol IV – DNA repair
o Active in 5’-3’ polymerization
DNA pol V – DNA repair, translesion DNA synthesis
o Active in 5’-3’ polymerization
o Error prone
DNA pol α – forms a complex with primase and initiates synthesis
o Active in 5’-3’ polymerase
DNA pol ε – leading strand synthesis
o Active in 5’-3’ polymerase and 3’-5’ exonuclease
DNA pol δ – lagging strand synthesis; primer removal
o Active in 5’-3’ polymerase and 3’-5’ exonuclease
Connecting fragments
o DNA pol I takes primer away
o Ligase fills gap
The problem with linear chromosomes
o Telomeres shorten with each round of replication in somatic cells
o Shortening of telomeres is associated with aging
Telomerase replicates chromosome ends
o Happened in germ line cells and many cancers
o Telomerase contains its own RNA template
o Template pairs with existing or newly synthesized telomere sequences
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o DNA polymerase synthesizes complementary strand
Recombination
o Mechanism:
▪ (1) homologous chromosomes align
▪ (2) single strand breaks are formed
▪ (3) strand displacement/invasion/exchange
▪ (4) ligation and formation of Holliday junction
▪ (5) branch migration
o Biological role of recombination
▪ Help homologous chromosomes pair and segregate during meiosis
▪ DNA repair
▪ Immune system development
o Impact of inherited defects in recombination machinery
▪ Infertility – aneuploidy
▪ Elevated cancer risk
▪ Immunodeficiency
o Resolution of Holliday Junction
▪ Final outcome (crossover vs. noncrossover) depends on plane of
resolution
▪ Resolution in vertical plane = crossover
▪ Resolution in horizontal plane = no crossover
Transcription and mRNA processing
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Capping enzyme: catalyzes addition of 5’ cap structure to the 5’ end of mRNA
Downstream: region of DNA or RNA sequence that’s located towards 3’ end relative
to reference point
Exon: sequence of DNA that’s transcribed into RNA and retained in final, mature
mRNA, ultimately coding for proteins
Intron: non-coding DNA sequences within a gene that are removed from pre-mRNA
during RNA splicing, leaving exons
Isoform: different variants of a gene produced form same locus from alternative
splicing leading to proteins
Lariat intermediate: introns are removed in form of a circular RNA that bears a short
tail
Nontemplate strand: same sequence of RNA molecule it produces, except for uracil
replacing thymine
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Poly-A polymerase: enzyme that catalyzes the template-independent addition of
adenine nucleotides to 3’ end of RNA
Polyadenylation: post-transcriptional modification in eukaryotes where poly-A tail is
added to 3’ end of mRNA, enhancing their stability and facilitating nuclear export
and translation
Promoter: DNA sequence located upstream of a gene that signals the start of
transcription, allowing RNA pol and others to bind and initiate process of creating
RNA molecule from DNA
RNA polymerase: transcribes DNA into RNA
snRNA: non-coding; found in nucleus playing crucial roles in pre-mRNA splicing by
forming snRNPs
snRNP: play vital role in removing introns from pre-messenger RNA
spliceosome: crucial in eukaryotic cells that removes non-coding introns from premRNA resulting in exons joining and forming mature mRNA
TATA box: conserved DNA sequence in promoter region of many eukaryotic genes
that helps initiate transcription
TBP: binds DNA and harbors two repeats with an internal structural symmetry that
show sequence asymmetry
TFIID: recognize and bind to the TATA box
TFIIH: required for basal transcription of class II genes and for participation in DNAexcision repair
Template strand: DNA strand used as a template for RNA synthesis during
transcription
Terminator: signals end of a gene or operon during transcription, instructing RNA pol
to stop and release new synthesized RNA transcripts
Transcript: RNA produced when a gene’s DNA sequence is copies during
transcription
Transcription: converting DNA into RNA
o RNA synthesized int eh 5’ to 3’ direction
o Template strand read in the 3’ to 5’ direction
Upstream: location toward 5’ end
5’ cap: modified nucleotide structure (m7G) that’s added to 5’ end of some primary
transcripts
Eukaryotic transcription
o RNA pol I: rRNA
o RNA pol II: mRNA – transcribes protein encoding genes
o RNA pol III: tRNA
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Eukaryotic transcription initiation
o Eukaryotic RNA pol II requires general transcription factors
o TFIID contains the TATA binding proteins (TBPs)
o TFIIH has helicase and kinase activity
o Kinases phosphorylate targets by transferring a phosphate from ATP
o Binding of TBP to the TATA box distorts the DNA structure
o Distortion may help recruit other general transcriptional factors
o RNA pol I
▪ Requires termination factor – protein the binds downstream of
transcription unit
o RNA pol III
▪ Terminates after synthesizing a series of uracils
o RNA pol II
▪ Complex
▪ associated with dephosphorylation of RNA pol II=
▪ associated with cleavage of mRNA and addition of polyA tail
mRNA processing
o occurs in eukaryotes only
o 3 major types:
▪ Capping
▪ Splicing/Cleavage – by ribosomes
• Requires specific sequences
o Catalyzed by spliceosome that is made up of 5 snRNAs
and ~300 proteins
o Arranged into 5 different snRNPs
▪ Polyadenylation – by poly A polymerase
• Influences mRNA stability
o Mature mRNAs are often shorter than the genes that encode them due to
splicing
Splicing mechanism:
o (1) cut at 5’ splice site and take 5’ end and attach to branch site (5’ to 2’
linkage creating a lariat structure)
o (2) cut at 3’ splice site releasing intron
o (3) connect exons
o (4) exons go through translation and the lariat structure gets degraded
mRNA cap
o methylguanine added to 5’ end
▪ catalyzed by capping enzyme
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o transcribed nucleotides also methylated
▪ catalyzed by methyl transferase
o 5’ to 5’ linkage with 3 phosphates
Hybridization of DNA and RNA
o Heat to denature
o Cool so complementary sequences pair
o Observe by electron microscopy
Alternative splicing
o Allows production of different proteins from same DNA sequences
Wobble hypothesis helps explain why there are multiple codons for a particular acid
o Rules:
▪ 5’ end of anticodon → can pair with → 3’ end of codon
• G
U or C
• C
G
• A
U
• U
A or G
• I
U, C, or A
Ribosomes
o Large subunit and small subunit
▪ mRNA binding site is on small subunit
o A site: active site where “charged tRNAs carrying amino acids arrive
o P site: where peptide bond formation happens
o E site: where used tRNAs exit
Genes to proteins: Genetic Code and Translation
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Aminoacyl tRNA synthetase: attach correct amino acid to its corresponding tRNA,
ensuring accurate translation of genetic code during protein synthesis
Anticodon: sequence of 3 nucleotides forming a unit of genetic code in a transfer
RNA corresponding to a complementary codon in mRNA
Codon: sequence of 3 nucleotides in a DNA or RNA molecule that corresponds to a
specific amino acid or stop signal
Degenerate: redundancy in genetic code, where multiple codons can code for same
amino acid
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eEF1A: delivery of all aminoacyl-tRNAs to ribosome, aside from initiator and
selenocytsteine tRNAs
eEF1B: facilitates exchange of GDP for GTP on eEF1A, enabling delivery of
aminoacyl-tRNAs to ribosome
eEF2: catalyzing translocation of ribosome along mRNA during elongation phase of
translation
frameshift: mutation caused by an insertion or deletion of one or more nucleotides
in a DNA sequence that’s not a multiple of 3, thus disrupting normal reading frame
and altering protein sequence
mRNA: ssRNA involved in protein synthesis
peptidyl transferase: form peptide bonds during protein synthesis
reading frame: way a sequence of nucleotides in DNA or RNA is divided into codons
for translation into a protein
release factor: terminate translation by recognizing stop codons on mRNA,
triggering release of newly synthesized polypeptide chain form ribosome
ribozyme: catalytically active RNA or RNA-protein complexes, where solely RNA
provides catalytic activity
tRNA: helps decode a mRNA sequence into a protein
o 3’ end of tRNA where amino acids are attached
▪ Aminoacyl tRNA synthetase is an enzyme that changes tRNA and
requires ATP
o tRNA anticodon is antiparallel and complementary
wobble: flexibility in base pairing at third position of a codon-anticodon interaction,
allowing a single tRNA to recognize multiple codons for same amino acid
Translation initiation
o Mechanism:
▪ (1) small ribosomal subunit binds initiator tRNA and eIF2
▪ (2) complex binds 5’ cap
▪ (3) complex scans for 1st AUG
▪ (4) Ifs leave, large subunit binds
o Energetically expensive
o Helper proteins
▪ Initiation → initiation factors
▪ Initiator tRNA → carries methionine and bind to codon AUG
o Nucleus
▪ Inside nucleus
• Transcription – make pre-mRNA
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• Process mRNA – splice, cap, tail
▪ Export mature mRNA to cytoplasm
▪ Translation
Translation elongation
o Translocation
▪ More one codon closer to 3’
▪ Coupled to peptide bond formation
▪ Requires EF-G which hydrolyzes GTP
o Mechanism:
▪ (1) ribosome attached with anticodon attached to codon
▪ (2) anticodon released and EF-Tu : GTP complex binds to protein at A
site
▪ (3) EF-Tu released and GTP turns into GDP
▪ (4) EF-G with GTP helps move protein out of P site and the new protein
into the P site
Translation termination
o Release factors → promote cleavage of bond between tRNA and protein
▪ eRF1 – molecular mimic
• binds to stop codons
▪ eRF3 – binds GTP and ribosome
• stimulates eRF1 activity