NROS 305 Exam 1

Trait

an observable/ measurable characteristic of an organism

Heredity

the passing on of traits from parent to offspring.

Heredity

being transmissible from parent to offspring

Inheritance

gaining genetic qualities by transmission from parent

to offspring

Gene locus

the physical location of a gene (or other DNA sequence) on a

chromosome

Enzyme

catalyst that speeds up specific biochemical

reactions in living organisms without being consumed or permanently changed in the process

Amino Acid

all proteins are made up of chains of

amino acids.

Polypeptide: l

Peptide

short chain of amino acids.

Polypeptide

long chain of amino acids (entire protein length.

Nucleotide

pentose and a nitrogenous base, linked to a phosphate group. Form the basic structural unit of nucleic acids like DNA

Pentose

a sugar with five carbon atoms, like ribose or deoxyribose

Pyrimidines

contain a single six-membered C ring & 2 N. T & C

Purines

contain a double-ringed nitrogenous base G & A

Polymer

macromolecule made from monomers, linked together like beads on a string, forming long chains.

Phosphodiester bond:

a strong covalent bond linking phosphate group of one nucleotide to the sugar of the next, forming sugar-phosphate backbone of DNA

5’

End of DNA/RNA. Transcription starts

3’

End of DNA/RNA. Transcription Ends.

Complementarity Nature of DNA Double Strand

allows to transmit genetic information from generation to generation

Genome

the complete set of genes present in a cell/organism

Diploid

containing two complete sets of chromosomes, one from

each parent (most cells)

Haploid

containing one set of chromosomes (gametes

Homologue

pairs of chromosomes (one maternal, one

paternal) that carry the same genes in the same loci but

may have different alleles of genes

Autosome

any chromosome that isn’t an X or Y chromosome (22)

Sex Chromosome

X or Y chromosomes (2)

Chromosome

DNA tightly wound around histones found in the cell’s nucleus

Histone

protein that provides structural support for chromosome

Nucleosome

fundamental building block of chromatin, made of tightly wound DNA around 8 histones.

Chromatin

highly

organized condensed structure made up of DNA,

RNA, and proteins that forms chromosomes in cell nucleus

Independent Assortment

gene located on different chromosome

Genetically Linked

genes located on same chromosome

Mutations

defects in metabolic pathways caused by genetic mutations “one gene = one enzyme

Euchromatin

Accessible, loose & unwound. Demethylated DNA, acetylated and H3K4 methylated histones

Heterochromatin

Inaccessible, tight & wound. Methylated DNA, deacetlyated histones that are H3Kp ^ H3K27 methylated

DNA methylation

gene silencing method

Methyl-CpG-binding proteins (MBDs)

read DNA methylation patterns (which genes should be silenced) to induce tighter chromatin packaging and silence gene expression

Rett Syndrome

MeCP2 protein (an MBD) loses its ‘reading’ function. This results in reduced heterochromatin formation, and abnormally high gene expression

DNA Replication

Process by which a cell makes exact copies of its DNA. DNA replication is semi-conservative, meaning that each daughter

cells receives its own copy of each DNA molecule

Assymetric Cell Division

regenerates radial glial cells, while producing new neural

progenitors

DNA Replication STEPS

1. Initiation

2. Priming

3. Elongation

4. Termination

Polymerase Chain Reaction PCR

selective amplification of DNA samples with heat-stable DNA polymerase to synthesize copies of DNA segment of interest from total genomic DNA

PCR Steps

1. Denaturing 95 degrees

2. Annealing 55 degrees

3. Synthesizing 72 degrees

Neural Progenitor Cell

Mature Cortical Neuron

Radial Glia Functions

1. Guide neuronal progenitors to final cortical layer

2. Produce new radial glia & neural progeitors through asymmetric cell division

Asymmetric Cell Division STEPS

1. Par complex in neural progenitors asymetrically localizes at apical pole

2. Par complex binds & recruits partners (inscutaeable process)

3. NUMB protein begins expression

4. Partner of NUMB pulls it to basal pole

5. Cytokinesis → apical cell stays as neuroblast (apical) & Partner of Numb downregulates gene expresion (basal)

Lineage Tracing

technique used to determine when cells are newly formed, by injecting radioactive nucleotides incorporated into the cell’s DNA

Ovum/Sperm

female/male reproductive cell

Primordial Germ Cell

specialized embryonic pre- cursor cells that develop into reproductive cell

Germ Cell

cells giving rise to gametes

Germline Cell

specialized reproductive cells & their precursor cells pass genetic info from I gen to next

Zygote

single cell formed when egg+ sperm fertilize.

Embryo

earliest stage of develop- e n t after fertilization

Cell Fate Determination

pluripotent → multipotent → adult bone marrow → human embryonic cell/ induced pluripotent

Pluripotent Embryonic Stem Cells

Can become another embryonic lineage/ germ layer. No limited cell fate.

Mitosis

2 genetically identical diploid daughter cells

Meiosis

4 genetically unique haploid daughter cells

Transcript

single-stranded RNA molecule created from a

DNA template during transcription.

Transcription

process of duplicating segment of DNA into RNA for the purpose of gene expression

Translation

process of translating sequence of messenger RNA (mRNA)

molecule to sequence of amino acids during protein synthesis

Central Dogma

DNA → RNA → amino acids/polypeptide

Reverse Transcription

RNA → DNA. RNA is template for DNA synthesis

Codon

sequence of three consecutive nucleotides in DNA or messenger RNA (mRNA) that specifies particular amino acid

mRNA

single- stranded molecule of RNA that corresponds to the genetic sequence. Used for protein synthesis

Universal Genetic Code

1 gene = 1 mRNA = 1 protein nucleotide triplets specify sequence of polypeptide.

Start Code

AUG. Initiation of transcription

Stop Codon

UAG, UGA. Termination of transcription

Small Nuclear RNAs (snRNAs)

structural components of spliceosomes, excising introns from pre-mRNA

Ribosomal RNAs (rRNAs)

structural & catalytic components of ribosomes for protein translation

Transfer RNAs (tRNAS)

adaptors between amino acids and codons of mRNA during translation

Messenger RNAS (mRNA)

contain genetic information from DNA for protein translation

micro RNAs (miRNAs)

regulate mRNA expression by degradation/ repressing translation.

Small Nucleolar RNAs (snoRNAs)

guide modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs

Long Non-Coding RNA lncRNA

control RNA transcription in nucleus, modulate mRNA stability, translation and post-translational modifications in cytoplasm (

RNA Polymerase I

rRNA genes

RNA Polymerase II

transcribes mRNA, miRNA, snRNA, snoRNA

RNA Polymerase III

transcribes tRNA & rRNA

Transcription Bubble

locallt unwound DNA segment where mRNA synthesis occurs

mRNA strand

complementary to antisense of DNA & identical to 5’ sense strand

Promoter

RNA polymerase binding site to initiate RNA transcription,

5’ Untranslated Region (UTR)

facilitating ribosome assembly for translation

3’ Untranslated Region UTR

facilitating “circularization of mRNA” → more efficient translation

Open Reading Frame (ORF)

DNA sequence between start and stop codons.

Double Helix

2 antiparallel strands → 6 reading frames total

Regulatory Elements

Regions of non-coding DNA which regulate gene

transcription. (TATA box, TSS, CAAT Box, silencers, enhancers)

Transcription Factors

Proteins that bind to specific DNA sequence controlling transcription. Directly interact with RNA polymerase (ex. TATA-binding protein, activators, repressors)

DNA Modifications

Changes to DNA, altering chromatin structure to control gene access for transcription (DNA methylation, histone mods)

Distal Regulatory Elements

located thousands of base pairs away from the promoter and contact core/proximal promoter by looping out the DNA in between (silencers, enhancers, locus control regions).

Core Promoter

Defines TSS. Required to recruit RNA polymerase and dictate accurate position & direction of initiation (TATA Box, downstream promoter element, TRFIIB)

General Transcription Factor

assemble on core promoter to form preinitiation complex (PIC),

which directs RNA polymerase II to the transcription

start site (TSS)

Trasncriptional Activator

transcription factor increasing transcription of a specific gene. Consists of a DNA-binding domain (DBD) and a separable activation domain (AD).

Transcription Activator MECHANISM

bind to regulatory promoter elements and stimulate PIC

formation by altering chromatin structure and

recruiting other co-activators

Enhancers

specific DNA motifs that bind transcription factors (TF) to upregulate assembly of the pre-initiation complex

Silencers

DNA motifs that bind TFs to downregulate RNA transcription by either actively interfering with PIC assembly or passively prevent binding of TFs to their enhancer motif.

Insulators

block interactions of enhancers & silencers with multiple genes

Interpreted differently for nuclear vs. mitochondrial DNA

AGA, AGG, AUA, UGA

Partially Denegerate Code

first two bases are identical, but the third base is either a pyrimidine (U or C) or a purine (A or G) specifying the codon for 2 different amino acids. (AGU, AGC = Ser; AGA, AGG = Arg)

Completeley Degenerate Code

first two bases are identical but any of the bases can

be at the third position specifying the same

amino acid (GGU< GGC< GGA< GGG = Glycine)

Degeneracy

All amino acids except methionine and tryptophan are specified by more than one codon

Ribosomes

provide the structural framework for polypeptide

synthesis. Large 80S RNA–protein complexes composed

of two subunits: large 60S & small 40 S (80S = 80 proteins)

60S Subunit

28S rRNA, 5.8S rRNA, and 5S rRN