UVA BIOL 3010 Exam 1

Diversity of life arose from a common ancestor so this means the makeup of organisms living on earth is

inherited and most similar between closely related organisms

Inherited biological info generates

diversity of living organisms

Evolution shows both

diversity (flexible) and similarity (common characteristics)

Phenotype

observable characteristic (green or yellow pea seeds)

Genes

units of inheritance

alleles

alternate forms of single gene, antagonistic

mendel's law of segregation

the 2 alleles for each trait separate during gamete formation and 2 gametes, one from each parent, unite at random during fertilization

why is a heterozygous pea yellow and not yellowish-green

the two alleles of pea color gene are not compatible and cannot exist together

mendel's law of dominance

trait that appears in F1 progeny is dominant form

trait that's hidden in F1 progeny is recessive form

mendel's law of independent assortment

-ratios are predictable

-traits are independent of each other

arrangement of genes

some genes are in a common structure that keeps them together, makes the traits not independent but alleles still always segregate

chromosome theory of inheritance

-chromosomes come in matched (homologous) pairs in an organism

-the members of a homologous pair separate in meiosis, so each sperm/egg receives just one member

-the members of different chromosome pairs are sorted into gametes independently of one another in meiosis

support for chromosome theory of inheritance

mendel's law of segregation

mutation

the change that happens in an organism's genes that produces differences that are passed to new organisms

mutations are

heritable

genotype

pair of alleles in an individual (YY or yy or Yy)

homozygote

2 identical alleles (YY or yy)

heterozygote

2 different alleles (Yy)

radioactively labeled phosphorus

indicates DNA

radioactively labeled sulfur

indicates protein

Hershey-Chase

-radioactively labeled sulfur and phosphorus integrated into bacteriophage

-P radioactivity recovered in host and passed onto phage progeny

-S radioactivity recovered in phage ghosts

-proved that DNA is responsibility for heredity

Avery experiment

-DNase -> destroy DNA -> R cells (no transformation)

-protease/RNA/fats -> S cells (transformation)

-identified transforming principle as DNA

DNA's chemical constitutents

-deoxyribose

-phosphate

-4 nitrogenous bases

purines

A, G

2 rings

pyrimidines

T,C

1 ring

DNA characteristics

-directionality

-set structure

-nucleotides linked in directional chain (5' to 3')

-phosphodiester bonds always form covalent links between 3' C of one nucleotide and 5' C of next

Chargraff

ratios of A:T and G:C are 1:1

Watson, Crick, and Rosalind

-Rosalind's images indicated that DNA had a helical structure and repeating pattern

-Watson and Crick interpreted image

-2 DNA molecules are paired together, uniform across body

-strands are antiparallel

-right-handed helix

-sugar-phosphate backbone on outside

-base pairs in middle

-2 chains held together by H bonds between A-T and G-C base pairs

why does it make sense that A pairs with T and G with C

the 2 pairs are almost the same size

complementary base pairing

-base pairs consist of H bonds (weak electrostatic bonds) between purine and pyrimidine (G with C, A with T)

-consistent with Chargraff's rules

-each base pair has ~same shape

-weaker bond pairing between bases -> able to open and close

-G+C -> 3 H bonds

-A+T -> 2 H bonds

-more G/C bonds -> higher MP (3 H bonds)

where does DNA store info

-sequence of its bases

-most genetic info is "read" from unwound DNA

gene

molecular unit of heredity of an organism

within a chromosome

what's in a chromosome

-compact group of proteins and DNA

-reflected what Mendel saw in plants

-densely packed DNA, packed with protein

promoter

-allows gene to be expressed/made in a specific cell type

-part of gene but not part of protein made

-recruits transcriptional elements, where/where/how much expression

exon

incorporated into protein, genetic info that encodes its product (protein)

introns

stays in nucleus, part of gene, removed after transcription

all contiguous DNA elements that contribute to the proper expression of a hereditary unit

-exons

-introns

-promoter

-enhancers

the non-coding elements of the genome are important

-introns regulate gene expression

-exon length may be very similar, but intron length varies greatly

C-value paradox or enigma

-size of genome doesn't correlate with complexity of organism

-large part of genome not used at all

-variation suggested that genomes can contain a substantial fraction of DNA other than for genes and their regulatory sequences

pseudogenes

non-functional genes

gene expression

-the flow of genetic info from DNA via RNA to protein

-RNA polymerase transcribes DNA to produce an RNA transcript (serves directly as mRNA in prokaryotes, processed to become mRNA in eukaryotes)

-ribosomes translate the mRNA sequence to synthesize a polypeptide

-translation follows the "genetic code"

DNA vs RNA

-RNA has U and no T

-RNA has hydroxyl group that makes it less stable than DNA because it's more susceptible to hydrolysis

-RNA usually single stranded

pyrimidines

single ring, U, T, C

purines

double ring, A, G

why uracil and not thymine in RNA

-both U and T base pair with A

-T requires more energy to produce

-deamination of C produces U (would mutate genome, confuse repair machinery with DNA)

-U in DNA is repaired back to C

RNA contains genetic info and can fold into unique structures

-secondary, tertiary structures

-double stranded pairing, even if don't match

-versatile

-can couple with amino acids (tRNA)

-ribosomes translate RNA to protein

-OG genetic material?

Beadle and Tatum

-one gene, one enzyme hypothesis

-each mutation abolishes the cell's ability to make an enzyme capable of catalyzing a certain reaction

-by interfering, each gene controls the synthesis or activity of an enzyme

-gene is not the same as an enzyme

-sequence of nucleotides in a gene contains info that encodes structure of enzyme molecule

-genes specify proteins

primary structure

amino acid sequence, directly determines secondary and tertiary

secondary structure

characteristic geometry of localized regions, helixes and B-pleated sheets

tertiary structure

complete 3D arrangement of polypeptide

quaternary structure

associations between multiple polypeptides within a protein complex

maintaining integrity of DNA

-redundancy

-remarkable precision of cellular replication machinery

-enzymes that repair damage to DNA

new combos of existing alleles can arise from 2 different types of meiotic events

independent assortment and crossing over

new combos of existing alleles - independent assortment

-each pair of homologs segregates free from the influence of other pairs via random spindle attachment

-can produce gametes carrying new allelic combos of genes on different chromosomes but on same chromosome will only conserve existing combos of alleles

new combos of existing alleles - crossing over

-2 homologs exchange parts

-can generate new allelic combos of linked genes

a prototypical genetic material needs to

-store info

-express info

-replicate

-accommodate the intro of new variation

RNA!

was RNA first?

-encodes info (1D)

-complex folding (3D)

-some highly conserved across life, deepest evol origins

-can act as enzyme

-self-replicating

evolutionary scenario

-RNA molex with catalytic activities assemble themselves from primordial nucleotide "soup"

-RNA molecules evolve and diversify by self-replication with mutation and recombination providing raw material for selection

-RNA molecules begin to synthesize proteins

-DNA appears more stable info storage because 2 strands allow error correction

Yanofsky experiment using trp- auxotrophic mutants

-observation: each point mutation changes only one amino acid and linear order of DNA mutations correlates with linear order of amino acid change

-each nucleotide is part of a unit that encodes for one amino acid

-the order of nucleotides in DNA must be converted in sequence to the protein

Crick and Brenner experiment with frameshift mutations

-add/delete nucleotides

-combos of 3+ mutations or 3- mutations restore reading frame

-a triplicate of nucleotides encode for an amino acid

using synthesized mRNAs and in vitro translation to crack the genetic code

-added artificial mRNAs to cell-free translation systems

-AUA|UAU|AUA -> polypeptides with alternating amino acids (depends where starts)

-triplet codons of nucleotides represent individual amino acids

-1+ codon -> 1 amino acid (3rd base not always important)

-experiments demonstrated that 3 nucleotides = codon = 1 amino acid

-AUG = start codon (Met)

-UAA, UAG, UGA = stop

correlation of polarities in DNA, mRNA, and polypeptide

-template strand of DNA is complementary to mRNA

-RNA-like strand of DNA has same polarity and sequence as mRNA

-5' to 3' in mRNA corresponds to N-to-C terminus in polypeptide

structure of eukaryotic body gene

-exons contain protein-coding sequence and untranslated sequence (before start, after stop)

-introns occur between exons, don't code from protein

-exons and introns together sometimes termed "gene body"

genes (can) code for proteins

-bread mold can't synthesize own Arg due to mutations in different genes

-biochemical pathway of Arg in mold -> each of 4 genes are required to convert one intermediate to the next, different responses of different mutants implies the corresponding genes encode proteins with distinct enzymatic activities and function in a linear pathway

-> "ONE GENE, ONE ENZYME" hypothesis, not broad enough

one gene, one polypeptide (or many polypeptides)

-some proteins aren't enzymes

-some protein subunits are encoded by different genes (can't function in isolation)

proteins are chains of amino acids linked by peptide bonds

-20 main amino acids

-R group is side chain that's unique to each amino acid and determine chemical properties

-COOH group and -NH2 group of adjacent amino acids are joined in covalent peptide bond

polypeptides have N terminus and C terminus

levels of polypeptide structure

-nonpolar/uncharged -> inside

-charged -> outside

-interactions that determine the 3D conformation of a polypeptide and water

-primary, secondary, tertiary

missense mutation

change a codon for one amino acid into a codon for another amino acid, whole protein product is still made

frameshift mutations

-shift reading frame for all codons beyond the point of insertion or deletion, almost always abolishing the function of the polypeptide product

-alter grouping of nucleotides into codons

-almost always results in stop codon at some point

intragenic suppression

-the restoration of gene function by one mutation canceling another in the same gene

-only occurs in the region between 2 frameshift mutations of opposite sign

-a gene still dictates appearance of amino acids (no stop codons)

-occurs often because some amino acids are produced by more than 1 codon (GC is degenerate)

5'

N terminus

3'

C terminus

nonsense mutation

point mutation that changes a codon for an amino acid into a stop codon (UAG, UAA, UGA), termination of protein product at that point

initiation codon

AUG

Griffith experiment

in bacteria there exists some "transforming principle" such that live bacteria can be affected by components of other strains

single nucleotides are

building blocks of DNA and RNA

polynucleotide

strand of DNA or RNA

template strand of DNA

complementary to mRNA

RNA-like strand of DNA

same polarity and sequence as mRNA

5' to 3' in mRNA corresponds to

N to C terminus in polypeptide

hydrophobic amino acid

inside

hydrophilic amino acid

outside, charged, interacting with environment

evolution is smart and

reuse functional domains making protein domains modular

scientists take advantage of this feature and

synthesize novel proteins

DNA info is linear

protein that ends up being translated carries that linear info

mutation may not change that amino acid sequence because

multiple triplets -> same amino acid

cell will degrade proteins

if mistakes are made, lots of repair mechanisms to fix mistakes and/or degrade

how can protein synthesis be restored by a cell in cases of pre-mature stop codon in a protein

use a drug to skip the stop codon during translation (read-through undesired stop codons). RNA is transient so you can't mutate the RNA stop codon

to study what a gene does

scientists clone it

cloning

the process of producing genetically identical individuals of an organism either naturally or artificially

whole or any part of a gene can be cloned

exons, promoter, enhancers, introns

enhancers

modify transcriptional level

genes

all the components that allow RNA to be made in a particular cell type at a particular time

protein making bits

-exons (encode protein sequence)

-sometimes promoter (allows expression of a certain gene in a certain cell type, when and where a gene will be expressed)

gene cloning

-an indispensable molec bio technique that allows scientists to produce large quantities of their gene of interest

-links eukaryotic genes to small bacterial or phage DNAs and inserting these recombinant molecules into bacterial hosts

-can produce large quantities of these genes in pure form

you can clone a single gene

-cutting out insert

-cutting vector

-ligation

-transformation

restriction enzymes

-bacterial defense against viral infection

-recognize and cleave viral DNA

-modification enzymes keep host DNA methylated

-prevent invasion by foreign DNA by cutting it into pieces

restriction endonucleases

recognize a specific DNA sequence, cutting only at that sequence

what prevents these enzymes from cutting up the host DNA

-restriction-modification system

-they're paired with methylases

-these enzymes recognize, methylate same site

-methylation protects DNA, after replication the parental strand is already methylated

-restriction enzymes know that methylated sequences aren't phage so won't cut it