Midterm 2 Geosci 110

junk DNA

genomic DNA that does not encode proteins, and whose function, if it has one, is not well understood.

complex creatures

what kind of animals have larger jujnk DNA

introns

Noncoding segments of nucleic acid that lie between coding sequences. Copied to mRNA only to be removed

non-coding DNA

components of an organism's DNA that do not encode protein sequences. Some is transcribed into functional non-coding RNA molecules while others are not transcribed.

gene expression

process by which a gene produces its product and the product carries out its function

RNA

single-stranded nucleic acid that contains the sugar ribose

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

ribosome

site of protein synthesis

RNAi

RNA interference; injecting double stranded RNA into a cell turns off expression of a gene with the same sequence as the RNA, regulates gene expression by intercepting transcription products, which means that it can strongly affect the phenotype without modifying the genotype

miRNA

a class of functional RNA that regulates the amount of protein produced by a eukaryotic gene

siRNA

class of double-stranded RNAs about 23 nucleotides in length that silence gene expression; act by either promoting the degradation of mRNAs with precisely complementary sequences or by inhibiting the transcription of genes containing precisely complementary sequences

post-transcription regulation

another word for RNA interference (RNAi)

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.

post-transcription and pre-transcriptio

two windows of opportunity for regulating gene-expression

retrotransposons

"fossil" virus DNA Viruses infected our ancestors and thegenetic material of these viruses has been passed along to us.

Noncoding DNA

gets transcribed into many different types of RNA that regulate gene expression.

plasmids

Where did viruses evolve from?

viruses

small amount of genetic material (DNA or RNA) encasedin protein coat• cannot reproduce themselves except inside a host cell• are tiny (~1/100th size of average bacterium

Retrovirus

RNA virus that contains RNA as its genetic information, An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

CCR5

protein on the surface of white blood cells involved in the immune system
- used by HIV to enter and infect host cells

CCR5 delta 32 mutation

Provides near complete * immunity from HIV infection in homozygotes
Heterozygotes-dylaed onset of AIDS

insertion mutation

a mutation in which one or more nucleotides are added to a gene

deletion mutation

a mutation in which one or more pairs of nucleotides are removed from a gene

substitution mutation

A type of point mutation in which a single nucleotide is substituted with (or exchanged for) a different nucleotide that may result in an altered sequence of amino acid during translation, which may render the newly synthesized protein ineffective.

somatic cell mutation

a mutation that occurs in a body cell

pseudogenes

former genes that have accumulated mutations and are nonfunctional

chromosomal mutations

changes in the chromosomes where parts of the chromosomes are broken and lost during mitosis

chromosomal inversion

When part of the chromosome becomes oriented in the reverse of its usual direction

chromosomal duplication

A segment of the chromosome is repeated. It's the opposite of deletion,

chromosomal deletion

loss of a portion of a chromosome

meoisis

The type of cell division where one diploid body cell produces 4 haploid gametes.

homeotic mutations

a mutation that causes one body part to be substituted for another

homeobox genes

ype of homeotic gene that that encode transcription factor proteins that bind to DNA; these proteins tell cells in various segments of the developing embryo what type of structures to make.

cell fate

The type of cell that an undifferentiated cell in an embryo will become in the adult. Determined by hox genes

cetacean evolution

evolution of marine marine mammals
Trading in their front legs for flippers, while losing their hind legs

vestigial structures

structures degenerate or undeveloped; reduced in size and function by natural selection as no longer required, shared in all members of a species

atavism

in biology, the reappearance of a characteristic in an organism after several generations of absence; individual or a part that exhibits atavism; return of a trait after a period of absence

cocyx

tailbone

atavisms

"throwbacks" - genes present but normally turned off, somewhat similar to vestigial features

Embyology

the branch of biology and medicine concerned with the study of embryos and their development.

ontogeny

the process by which an individual changes in the course of its lifetime - that is, grows up and grows old

branchial arches

Series of arches that support the gills of aquatic amphibians and fishes. Present in all vertabrate embryos

what branchial arches develop into

middle ear bones• eustachian tube• carotid artery• tonsils• larynx• cranial nerves

1.5 million

approximately ___ species have been described

Linnaeus

Swedish botanist who proposed the modern system of biological nomenclature (1707-1778)

Family

Group of genera that share many characteristics

Genus

A group of similar species

binomial naming system

the system used for naming organisms. There are two parts to the name: the first is the genus and the first letter is always capitalised, the second is the species name and is not capitalised.

Homologous structures

Structurally similar featues adapted to serve different functinons, reflecting common ancestry

Analogous structures

structurally dissimilar featies adapted to serve the same function, does NOT reflect common ancestry

Limits of phylogeny

- limited to the fossil record
- shape does noit inform us about the diversity of microbes - many bacteria look pretty much the same in shape

rDNA

most conserved genetic code where small differences could still be seen

rDNA

ribosomal DNA, codes for making SSU rRNA

SSU rRNA DNA sequence

What is modern phylogeny based off of?

incomplete dominance

Situation in which one allele is not completely dominant over another allele

codominance

condiition in which there are multiple alleles and two are dominant

MHC

gene code for molecules that ennable immune sysstem to recognize invaders, most diverse loci known - many hundres of alleles

albinism gene

causes lack of pigmentation, crossed eyes, and slightly larger body size, example that one gene can influence ultiple traits

polygenic trait

trait controlled by two or more genes

true

genes may influence each other

carbohydrates

the starches and sugars present in foods

lipids

Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

proteins

Nutrients the body uses to build and maintain its cells and tissues

nucleic acids

DNA and RNA

ATCG

the 4 DNA bases

nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

DNA replication

the process of making a copy of DNA

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

semi-conservative

in each new DNA double helix, one strand is from the original molecule, and one strand is new

RNA primer (primase)

marks starting locus for building new DNA strand is added

5 prime to 3 prime

The direction in which DNA and RNA are synthesized

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

exonuclease

enzyme that removes RNA primers

DNA ploymerase

fills in gaps formed by removal of RNA primers

ligase

An enzyme that connects two fragments of DNA to make a single fragment, seals the strand

rRNA

ribosomal RNA; type of RNA that makes up part of the ribosome

The structures of its amino acid strand/the folding

What determines the function of a protein?

codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

amino acid

"payload" of transfer RNA

eukaryote

A cell that contains a nucleus and membrane bound organelles

prokaryote

A unicellular organism that lacks a nucleus and membrane bound organelles

archaea

One of two prokaryotic domains of life, the other being Bacteria.

karyotype

the number and visual appearance of the chromosomes in the cell nuclei of an organism or species.

Tom Brock

-UW Madison professor
-worked on characterization of Lake Mendota
-studied hot springs in Yellowstone
-isolates first extreme thermophiles >80°C (Thermus aquaticus)
-DNA polymerase used in PCR

thermophilic

microorganisms that are most active in hot temperatures, typically those over 113 degrees Fahrenheit (45 degrees Celsius).

immortal genes

Genes that are shared by all forms of life. Evolved early in the evolution of life.
Necessary for basic cell functions.

synonymous mutations

nucleotide changes that don't result in amino acid changes

nonsynonymous mutations

changes in nucleotides that change amino acids

Ernst Hackel

discovered the protist kingdom

Edouard Chatton

coined terms "prokaryote" and "eukaryote" based on presence of nucleotides

endosymbiosis

symbiosis in which one of the symbiotic organisms lives inside the other.

merging of achea and bacteria

how did eukaryotes come about?

Carl Woese

three domain based on r RNA (eukarya, bacteria, archaea)

retrovirus

An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.

translation

Process by which mRNA is decoded and a protein is produced

transcription

(genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA

20-22

how many amino acids are there

carboxyl group

A -COOH group, found in amino acids.