Genetics Exam 3 Memorization

Francis Crick

Francis Crick

• Theoretical Biologist, Created the central dogma

• discovered the 64 codons, and the 3 nucleotides for each codon

Marshall Nirenberg

• Cracked the RNA code with his Poly-U RNA

• Discovered each codons respective amino acid

Redundancy of Codons

• With 64 possible codons, but only 20 amino acids their must be synonyms

Start Codons

AUG, Does specify an amino acid (MET)

Stop Codons

UAA, UAG, UGA, do not specify amino acids

Open reading frame

A sequence of DNA/RNA that potentially codes a protein. Starts with AUG, and ends with a stop codon

N-Terminus (Methionine)

Start of the protein or polypeptide chain where the amino group is located.

C-Terminus

End of the protein chain, last codon before the stop codon.

Adapter Hypothesis

Explanation for how information encoded in DNA is translated into proteins. Adaptor molecules or tRNA serve as intermediaries between the genetic code and the amino acids that make up proteins

Transfer RNA

• Small RNA molecules that have a specific 3-nucleotide sequence called an anticodon at one end and attach to a specific amino acid at another end.

• Each molecule is capable of recognizing a particular codon on mRNA through complementary base pairing between the anticodon on tRNA and the codon on mRNA

Amino Acid, R Group Types

• Non polar, Aliphatic

• Polar, uncharged

• Aromatic

• Positive Charged

• Negative Charged

Why does tRNA have an L shape?

• On one end is the L-shaped tRNA structure contains the anticodon loop, which is a sequence that are complementary to the mRNA

• On the other arm contains the site where a specific amino acid is attached to the tRNA molecule

• At the bottom there is a loop called the D or T loop which helps stabilize the overall structure

Aminoacyl-tRNA synthetases

• Responsible for attaching the correct amino acid to its corresponding tRNA

• Once attached, the enzyme links it together

Wobble Hypothesis

Describes how 3rd nucleotide of a codon is variable

30s, Small Prokaryotic Ribosomal Subunit

• 30 Svedberg, Composed of 16s ribosomal RNA molecules and about 21 different ribosomal proteins

• The small subunit bind to the mRNA molecule and the initiator tRNA carrying the formyl-methionine binds to the start codon in the mRNA

50s, Large Prokaryotic Ribosomal Subunit

• 2 rRNA molecules, 5S(stabilize structure), and 23S (catalyze peptide bond formation between amino acids) and 34 different ribosomal proteins

• Contains 3 binding sites for tRNA molecules, the A site, P Site and E site

Ribosome size of a Prokaryote

70S

40s, Small Eukaryotic Ribosomal Subunit

• Responsible for decoding the genetic information carried by messenger RNA during protein synthesis. Contains one rRNa molecule (18S), and 33 proteins

60S, Large Eukaryotic Ribosomal Subunit

• 5S, and 28S rRNA, and 49 Proteins

• Contains 3 binding sites for tRNA molecules, the A site, P Site and E site

Ribosome size of a Eukaryote

80S

rRNA

Responsible for the structure and function of the ribosome, proteins help the RNA change shape as they catalyze chemical reactions

Peptidyl Transferase

Creates peptide bonds between amino acids, attributed to 23S rRNA

Ribozyme

Processes catalytic activity meaning it can accelerate chemical reactions.

Translation Initiation (Prokaryotic)

• The small ribosomal subunit (30S) binds to the mRNA molecule at the Shine-Dalgarno Sequence, which is located a few nucleotides upstream of start codon

• Initiator tRNA charged with formylmethionine(fMet) binds to AUG on mRNA, located within ribosomal P site

• Large ribosomal subunit joins complex, forming 70S ribosome

Translation Elongation (Prokaryotic)

• During Elongation the ribosome moves along the mRNA molecule in the 5’ to 3’ direction carrying specific amino acids bonded to the codons on the mRNA through the anticodon region of the tRNA.

• The ribosome catalyzes the formation of peptide bonds between adjacent amino acids

• Translocation occurs after this, tRNA moves from A to P site and the tRNA growing the polypeptide chain moves to the A site.

Translation Termination (Prokaryotic)

• Translation occurs until stop codon is reached on the mRNA molecule

• When a stop codon enters the A site, it dos not code for an amino acid, but signals termination.

• Release factors bind to stop codon, causing the ribosome to release newly synthesized polypeptide chain

Translation Initiation (Eukaryotic)

• Translation begins with the binding of the mRNA to a ribosome

• The small ribosomal subunit (40S) binds to the mRNA at the start codon AUG/Met.The initiator tRNA carrying methionine binds to the start codon

Translation Elongation (Eukaryotic)

• Ribosome moves along the mRNA, codon by codon.

• Each codon on the mRNA is recognized by the complementary anticodon on tRNA which carries the amino acid

• The ribosome catalyzes the formation of peptide bonds between adjacent amino acids, creating a growing polypeptide chain

• As each amino acid is added to the growing polypeptide chain, the ribosome moves along the mRNA shifting one codon downstream, which exposes a new codon

Translation Termination (Eukaryotic)

• Translation occurs until the ribosome encounters a stop codon (UAA, UAG, UGA)

• When stop codon is reached, a release factor protein binds to the ribosome causing ribosomal subunits and the newly synthesized polypeptide chain to dissociate

Polycistronic

• Prokaryotes

• mRNA that contains coding for multiple genes or proteins

Monocistronic

• Eukaryotes

• mRNA that contains the coding sequence for only one gene

Constitutive Expression

• Continuously expressed under normal cellular conditions

Positive Control

• Stimulate gene expressions

  • activators

Negative Control

• Inhibit gene expression

  • repressors

Francis Jacob and Jacques Monod

• Discovered lac operon hypothesis

• In bacteria, gene regulation maintains flexibility turns genes off/on in response to environment

• Gene regulation brings differentiation in Eukaryotes

Transcriptional Unit

• Multiple functionally related genes transcribed into one mRNA

• Structural genes, a promoter, and an operator

Operator

• Region of DNA that controls the expression of adjacent genes

• Acts as a regulatory sequence where proteins, known as TFs bind to either activate or repress transcription of nearby genes

Promoter

• Located at beginning of a gene that signals the start of transcription

• Serves as binding site for RNA polymerase

Regulator gene

• Encodes proteins or RNA molecules involved in controlling expression of other genes

• LacI gene in e.coli. Encodes lac repressor protein.

Regulatory Proteins

• Small molecule binds to protein changing its shape (allosteric) and altering its ability to bind DNA

• An activator/repressor may become active/inactive

Negative Inducible

Inactivates repressor, turns transcription on

Negative repressor

Activates repressor, turns transcription off

Positive inducible

Activates activator, turns transcription on

Positive repressible

Inactivates activator, turns transcription off

Lac Operon

• Negative Inducible

• In the absence of lactose, the lac repressor protein, encoded by the lacl gene is active and binds to the operator site within the lac operon

• The binding of lac repressor to the operator site physically blocks the access of RNA polymerase to the promoter, which in turn represses transcription

Glucose, cAMP process

• Positive repressible

• When glucose is high, cyclic AMP is low

• In the absence of cAMP the CAP protein is inactive and unable to bind, which leaves transcription inactive

TRP Operon

• Negative repressible

• In the absence of tryptophan, the trp repressor protein is inactive and unable to bind, which allows transcription to continue

• In the presence of tryptophan, it binds, causing transcription to stop

Morphogens

• Signaling molecules that regulate the pattern formation and and development of tissues and organs during embryonic development

• Shh(Sonic Hedgehog), BMPs (Bone Morphogenetic Proteins)

• Master Regulator of segmentation, establishes body axis

Gap Genes

Define regional sections

Pair-Rule Genes

Individual Segments

Segment-Polarity Genes

Orientation of segments

Hormones

Target cells/tissues bind to a specific receptor and elicit a physiological response

Growth Factors

Regulate cell growth, proliferation, survival, development and more

Cadherin

• Help keep tissues organized and intact, ensuring cells stick together properly

Protocadherin

• Important for building the brain

• Help brain cells connect and communicate

Signal Transduction Pathway

• Signal is received

• Signal is transduced

• Signal is amplified

• Cell Responds

Protein Phosphorylation

• Major mechanism for transfer of energy

• Transmit signals from the cell surface to the nucleus

Protein Kinase

• Transfer phosphates from ATP to protein

• Addition of a phosphate group adds a (-) charge changing shape of amino acid

Doubling muscling phenotype

• Mutation in Myostatin makes a huge muscled animal!

• MYOD produced in response to pax3 is soon to be muscle cells

Reporter Gene

• Cut out enhancer, attach it to a reporter gene and see when/where gene is expressed

Tissue Specific Enhancers

• Regulate gene expression in particular tissues

• 510 tissue specific enhancers lost

Oxytocin

Hormone, helps in childbirth contractions, ejaculation, milk ejaculation, social behavior.

Vasopressin

• Antidiuretic hormone, regulate fluid, blood pressure, stress response, memory

Romantic Love

• Lust, Attraction, Attachment

  • Prairie Vole have receptors for oxytocin and vasopressin in different brain regions than the promiscuous meadow vole`

Epigenetics

• Study of heritable changes in gene expression that do not involve alterations to underlying DNA sequence

• Control when and where genes are turned on and off, via methylation of histones

Lamarckian Genetics

• Proposed by Jean-Baptiste Lamarck

• Organisms can acquire new traits or characteristics during their lifetime as a result of environmental interactions

• Rejected by modern, traits acquired during an individual’s lifetime as generally not passed on to offspring through genetic inheritance

Neolamarckian Genetics

Modern reinterpretation that incorporates modern genetic concept, soft inheritance (acquired traits may influence gene expression patterns)

Epigeome

• Complete set of chemical modifications to the DNA and associated proteins that influence gene expression

• MUCH FASTER THAN MUTATION

The histone code

• Describes the diverse array of chemical modifications that occur on histone proteins which are responsible for packaging DNA into chromatin

Pioneer Factors

• Bind to closed chromatin regions and initiate chromatin opening.

• FOXP2→Plays a role in development of speech/language areas of the brain(master regulator)

Polycomb Complexes (PRC1 + PRC2)

• Involved in gene silencing

• Possess methyltransferase activity, and remodel proteins for gene silencing

CpG Islands

• Areas of DNA that are rich in cytosine and guanine.

• Found at the beginning of a gene and are associated with core promoter

• Methylated cytosine, and block major grooves of DNA, which inhibits transcription

• Epigenetics methylation site

Gene Regulatory Proteins

• Transcription Factors attach to regulatory elements on one or more genes. Once there, a TF acts as a switch, turning off or on genes

• Some gene regulatory proteins (TFs, DAX1, FOXP2) recruit enzymes that add or remove epigenetic tags

Epigenetic Tags

• Cells way of remembering long term what its genes should be doing

Intergenerational

• F0→Parent

• F1→Child

• F2→Grandchild

Transgenerational

• F3→Great Grandchild

The missing heritability problem

• Discrepancy between the estimated heritability of complex traits and the proportion of trait variance that can be explained by known genetic variants

Nutrigenomics

• Study of how genes and nutrition interact

Bees as a model organism for epigenetics

• Larvae fed royal jelly exclusively destined to become queens, suppresses DNMT3

• Those fed a mixture of royal jelly develop into workers

Thrifty Phenotype

• Individuals who experience poor nutrition or other environmental stressors during critical periods of development that alter metabolic processes leading to an increased risk of metabolic disorders

Ecological Epigenetics

• Invasive species lack genetic diversity but quickly adapt to new habitats (CpG islands for rapid evolution)

• Maternal behavior impacts behavior→ a tissue specific enhancer is methylated in hippocampus, and impacts glucocorticoid receptor activity, making a happy rat

Genomic Imprinting

• Differential expression of alleles depending on parental origin

• Mom and dad’s genes are antagonistic

• Examples of these genes include IGF2 (insulin-like growth factor 2), which promotes fetal growth and is paternally expressed, and H19, which is maternally expressed and regulates placental development.

Prader-Willi Syndrome

• Deletion of a part of fathers chromosome 15, mild mental handicapped, impaired satiety and compulsive behavior(Maternal Imprinting; Paternal Gene lost)

Angelman Syndrome

• Deletion of a part of mothers chromosome 15 causes mental handicappedness, lack of coordination, frequent laughter (Mothers genes lost, paternal imprinting)

Paternal Imprintation

• Mest/PEG1 are expressed in an area of the brain that governs mouses reproductive behavior (only paternally active)

• W/o, females have fewer oxytocin receptors and show a severe lack of maternal care

Paternal Genes in Imprinting

• Limbic Brain, feelings are from dad

Maternal Genes in imprinting

• Cortex, thoughts from mom

GRB10

• Does different jobs from mom and dad

• Maternal→ foetal growth, metabolism, fat storage

• Paternal→ social behavior

Small Nuclear RNA (snRNA)

• Eukaryotes

• Nucleus

• Processing of pre-mRNA

Small Nucleolar RNA (snoRNA)

• Eukaryotes

• Nucleus

• Processing and assembly of rRNA

Micro RNA (miRNA)

• Nucleus and Cytoplasm

  • Inhibits translation of mRNA

Small Interfering RNA (siRNA)

• Nucleus and Cytoplasm

• Triggers degradation of other RNA molecules

Piwi-Interfering RNA

• Nucleus and Cytoplasm

• Suppresses transcription of transposable elements in germ-line cells

CRISPR RNA (crRNA)

• Assists destruction of foreign DNA

Long Coding RNA (lncRNA)

• More than 200bp barely translated

• Resemble mRNA with 5’ capping, polya tail, splicing but no reading frame

• guide protein/dna interaction

• Involved in rapid evolution

• Recruit chromatin remodeling proteins to specific genomic loci

• Beckwith Wiedemann Syndrome

How does lncRNA impact genomic imprinting

• Imprinted genes clump together, suggesting imprinting acts on large chunks of chromosome as opposed to individual genes

  • Often contain lncRNA genes that are imprinted, and recruit pRC2 to repress protein coding genes

• Many clusters of imprinted genes are associated with disorders that result faulty regulation of lncRNA

  • deletion of KCNQlOTI leads to the expression of alleles from parents. Produces overgrowth and Beckwith-Wiedemann

Xist Gene

• lncRNA gene located on the X chromosome in mammals

• Plays a critical role in X inactivation

• Xist RNA is upregulated and coats the entire length of the Xi chromosome in cis which recruits chromatin modifying complexes and transcriptional repressors, leading to the silencing of most genes.

• Some genes are not methylated, including Pax6 to regulate processes. These genes are farthest from LINE elements

Antisense RNA

• A single stranded RNA which is a mirror image of the nucleotide bases of another RNA strand

• Binds to complementary sequences of mRNA leading to the inhibition of translation

• Includes lncRNA, and miRNA

RNA interference

• Silencing of individual genes by very small RNAs called miRNA or siRNA

• Small RNAs are generated from double-stranded RNA precursors through the action of Dicer, an enzyme

• Dicer cleaves the dsRNA intro short fragments, which are then incorporated into RNA induced silencing complexes(RISCs)

• 60% of human genes are regulated by RNAi individual miRNA can simultaneously target many functionally related genes usually by targeting 3’ RNA

iRNA→siRNA

• originated from a double stranded RNA

• cleaved at the rna duplex or single strand rna that forms long hairpins

• 21-25 nucleotides

• occurs via the degradation of mRNA inhibition of transcription chromatin modification

• target genes are from which they were transcribed