Birchler Exam #5

Long Terminal Repeats

identical sequences of DNA that repeat hundreds or thousands of times found at either end of retrotransposons or proviral DNA formed by reverse transcription of retroviral RNA

Homomorphic Sex Chromosomes

Pair of homologous chromosomes that differ for genes that determine sexual differentiation; chromosomes look the same

Gynandromorph

Organism that has different parts from different sexes. Ex: fly starts as XX and one X is lost, part of fly is XX = female and part is XO = male

Transposable Elements

Segments of DNA that can move from one place in the genome to another

Direct Repeats

Sequences in transposons that are the same in the same strand (2 or more repeats)

Terminal Inverted Repeats (TIR)

Sequence of nucleotides followed downstream by its reverse complement. Required for transposition

Transposase

Protein that moves Ac/Ds

Retrotransposons

Related to retroviruses, can't go between cells

Retrovirus

Single-stranded that replicated via double-stranded DNA intermediates (Contains: gag, pol, and env genes)

Reverse Transcriptase

Enzyme used to generate complementary DNA (cDNA) from an RNA template

Heteromorphic Sex Chromosomes

Pair of formerly homologous chromosomes that determine sex and that no-longer look alike

Dosage Compensation

Same levels of gene expression from X chromosome in males and females

Pseduoautosomal Region

- Present at end of X and Y in mammals
- 29 genes in common - high recombination
- Recombination ensures proper segregation in meiosis

Testis Determining Factor (TDF)

Gene that has been cloned from the Y chromosome and is close the pseudoautosomal region. Initiates male sex determination

Lyon Hypothesis

One of the two X chromosomes in female mammals becomes inactive during development and remains inactive. In different developmental lineages, a different X becomes inactive

Fragile X Syndrome

- Genetic disorder involving an abnormality in the X chromosome
- More common in males
- Causes mental retardation

Turner's Syndrome

XO - Female
- Short stature, no ovaries, no pubic hair, webbed neck
- 0 Barr bodies

Klinefelter's Syndrome

XXY - phenotypically male
- Female pubic hair distribution and often breast development
- 1 Barr body

TATA Box

25-30 base pairs before the start of transcription site where transcription initiation complex forms

CAAT Box

80 base pairs before the start of transcription influences promoter activity

Enhancer

Control elements that regulate transcription; can be upstream, downstream, or within the break being regulated

Silencer

Cis-acting elements bound by repressors; decrease transcription of neighboring genes

Zinc Finger

- Histidine and cysteine residues are intervals
- Bind zinc and form loops that bind the major groove of DNA

Leucine Zipper

- Leu amino acid occurs every 7 amino acids
- Forms an alpha helix in protein
- Match the Leu helix associates with DNA

Helix-loop-helix

- 3 helices with two separated by a loop
- Surface for protein interactions

Patern Formation

Cell differentiation decisions to form an organized adult body plan

Totipotent

Uncommitted cells that can give rise to an adult

Mosaic Development

- Cell lineage determination
- Destroying one cell will eliminate that cell lineage throughout development

Regulative Development

Cell differentiation is dependent on signals from neighboring cells

Morphogenic Gradient

- Polarity from front to back in development
- Caused by different molecular concentrations

Homeotic Genes

- Genes that specify a body segment
- Mutations can put legs in place of antennae
- Ex: Hox gene in Drosophila

Inductive Interaction

Signals from one cell that can induce a certain cell type in another

TI Plasmid

In a soil bacterium that causes tumorous growth disease on plants

Biolistic Gun

- DNA to be transformed placed on gold particles
- Compressed gas used to blast the coated particles into cells
- Inside the cells, the DNA comes off the particles and gets incorporated into the chromosomes
- Used to transform plants, algae, yeast, mitochondria, chloroplasts.

Retroviral Vector

- First application of gene therapy in humans
- Modified retrovirus carries the normal enzyme
- Blood cells used to take up vectors and incorporate the DNA

CRISPR-Cas9

A set of Cas proteins recognizes viral DNA pieces and incorporate them as spacers in the CRISPR DNA

M

Mitosis

G1

Gap 1 between the end of mitosis and the start of DNA replication

S

Synthesis - when the DNA is replicated

G2

Gap 2 between replication and the beginning of mitosis

Cyclins

Proteins that determine the progression from one step to the next in cell division; activate CDPK

Cyclin Dependent Protein Kinases (CDPK)

Activated by cyclin and determines the progression from one step to the next in cell division

Oncogenes

Mutations that are dominant for cancer formation

Tumor Suppressor Genes

A gene whose protein product inhibits cell division, thereby preventing the uncontrolled cell growth that contributes to cancer (Recessive)

Poly A Tail

Long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule

G cap

Put on the 5' end of RNA to increase stability

BAC

DNA is contained within an overlapping set of bacterial artificial chromosomes. Stretches of DNA maintained in E. coli cells

cDNA

Complementary DNA. DNA produced synthetically by reverse transcribing mRNA. Because of eukaryotic mRNA splicing, cDNA contains no irons.

Bioinformatics

Sequence can be used to predict start of transcription, start of translation, introns and exons

Single Nucleotide Polymorphism (SNP)

A single base-pair site in a genome where nucleotide variation is found in at least 1% of the population

RNA-Seq

Sequencing technique used to determine directly the nucleotide sequence of a collection of RNAs

Apoptosis

Controlled cell death

Hox Genes

Regulate identity of body segments

siRNA

- Small interfering RNA
- Class of double-stranded RNA at first non-coding RNA molecules
- Typically, 20-24 base pairs in length, similar to miRNA
- Operating within the RNA interference pathway

miRNA

- Micro RNA
- Small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides