BIOL 241 Midterm 2

Lectures 11-22

aneuploidy

variations in chromosome number when an organism gains or loses one or more chromosomes & has other than an exact multiple of the haploid set

monosomy

the loss of one chromosome (2n-1)

trisomy

addition of a chromosome to the diploid genome (2n+1)

nondisjunction

mistakes in chromosome segregation during mitosis or meiosis, causes aneuploidy, and historically very important in chromosome theory

polyploidy

in which more than two haploid sets of chromosomes are present, is prevalent in plants

deletions

a chromosomal deficiency occurs when a chromosome breaks and a fragment is lost

pseudodominance

the expression of a recessive mutation (due to a deletion) in this configuration

duplication

when any part of the genetic material, a single locus or a large piece of chromosome, is present more than once in the genome

asymmetric pairing and crossing over …

can generate multiple copies of DNA segments

duplication in evolution

essential genes do not tolerate mutation; duplications of essential genes, then subsequent mutations, confers adaptive potential to the organisms; new gene family members are ‘recruited’ to perform new functions

inversions

a chromosome that has a segment that has been flipped to the opposite orientation

paracentric inversion

doesn’t include the centromere, crossing over within inversion with nonviable gametes due to a lack of genes

pericentric inversion

includes the centromere, no crossing over in inversion loop with nonviable gametes because genes are missing or present in too many copies

balancer chromosome

has a recessive lethal mutation, has inversions (lots of them), carries a dominant marker to help identification

translocation

the movement of a chromosomal segment to a new location in the genome

nonreciprocal translocation

genetic material moves from one chromosome to another without any reciprocal exchange

reciprocal translocation

genetic material moves from one chromosome to another with the exchange of segments between two nonhomologous chromsomes

translocation will …

cause semisterility

Robertsonian translocation (centric fusion)

involves breaks in the extreme ends of the short arms of two nonhomologous acrocentric chromosome, small acentric fragments are lost and larger chromosomal segments fuse at the centromeric region

4 characteristics of genetic material

replicate, store info, express info, allow variation by mutation

Avery, MacLeod, and McCarty

Type S DNA extract + DNAse = no transformation

Hershey and Chase

35S and 32P, with 32P in the pellet, proving that DNA is the genetic material

nucleotide structure

a nitrogenous base, a pentose sugar and a phosphate group

nucleoside

a nitrogenous base and pentose sugar

nucleotide

a nucleoside with a phosphate group added

Chargaff’s Rules

amount of A is proportional to T and amount of C is proportional to G, but C+G to A+T percentages don’t have to match

DNA structure

right-handed double helix, antiparallel strands, bases are stacked, connected by A-T and C-G pairing and 10 base pairs per helix turn

A-T

form two hydrogen bonds

G-C

form three hydrogen bonds

central dogma of molecular genetics

DNA → transcription → RNA → ribosome → translation → protein

mRNAs (messenger RNA)

template for protein synthesis

rRNAs (ribosomal RNA)

components of ribosomes for protein synthesis

tRNAs (transfer RNA)

carry amino acids for protein synthesis

RNA serves as …

the genetic material in some viruses

nucleic acids absorb UV light most strongly at ..

260 nm (due to ring systems in bases)

A-T rich DNA has a …

lower melting temperature

supercoiling

compacts DNA

topoisomerases

cut one (Type I) or both (Type II) DNA strands and wind or unwind the helix before resealing the ends

gyrase

is a type II DNA topoisomerase

chromatin

bound up in nucleosomes with histones, are condensed several times to form intact chromatids, and are eukaryotic DNA

nucleosome core particle

147 base pairs

chromatin remodeling

must occur to allow the DNA to be accessed by DNA binding proteins

euchromatin

is uncoiled and active

heterochromatin

remains condensed and is inactive

polytene chromosomes

have distinctive banding patterns, represent paired homologs, and are composed of many DNA strands

majority of eukaryotic genome …

does not encode functional genes, highly repetitive and moderately repetitive DNA constitute up to 40% of the human genome

satellite DNAs

are highly repetitive and present in heterchromatin

minisatellites or variable number tandem repeats (VNTRs)

usually 15 to 100 bps long, found between genes

microsatellites

are short nucleotide (3-5 nt) repeats

short intersperse elements (SINES) & long interspersed elements (LINES)

resemble transposable sequences, are dispersed throughout the genome rather than repeated in tandem

3 possible models for DNA replication

conservative, semiconservative, and dispersive

Meselson-Stahl experiment

used a density gradient to it’s semiconservative replication

semiconservative replication

the complementarity of DNA strands allows each strand to serve as a template for synthesis of the other

replicon

the length of DNA that is replicated following one initiation event at a single origin

DNA replication

DNA polymerase catalyzes DNA synthesis and requires a DNA template and all four dNTPs

7 key issues that must be resolved during DNA replication

the unwinding of the helix, reducing increased coiling generated during unwinding, synthesis of a primer for initiation, discontinuous synthesis for the second strand, removal of the RNA primers, joining of the gap-filling DNA to the adjacent strand, proofreading

telomeres

preserve the integrity and stability of chromosomes

telomerases

directs synthesis of the telomere repeat sequence to fill the gap

transposable elements (transposons)

can move within the genome and can insert themselves into various positions within and between chromosomes

overlapping genes

in some viruses, these have been identified

Prinbow box (E. coli)

two consensus sequences, TTGACA & TATAAT, positioned at -35 and -10 with respect to the transcription initiation site

rho-independent termination

facilitated by two sequences in the RNA: uracil-rich sequence at the 3’ end and a stem-loop structure upstream of the uracil-rich portion

rho-dependent termination

rut recognition site that forms a stem-loop and proceeds the terminator

Pol II is …

responsible for mRNA

TATA box

a core promoter element that binds the TATA-binding protein (TBP) of transcription factor (TFIID) and determines the start site of transcription (eukaryotic)

enhancers

can be upstream, within or downstream of the gene and can modulate transcription from a distance

post-transcriptional modification

the addition of a 5’ cap, the addition of a poly-A tail, and introns are removed by splicing

introns

are regions of the initial RNA transcript that are not expressed in the amino acid sequence of the protein

introns are …

removed by splicing

exons are …

joined together in the mature mRNA

group I intron

self-splicing, rRNA introns, unique

group II intron

self-splicing, some mitochondrial genes, lariat structure

spliceosome

for nuclear-derived pre-mRNA and contains small nuclear RNAs (snRNAs) which complex with proteins to form small nuclear ribonucleoproteins (snRNPs)

the genetic code

is written in linear form, using the ribonucleotide bases that compose mRNA molecules

triplet codons

specify one amino acid, code provides 64 codons to specify 20 amino acids

wobble hypothesis

predicts that hydrogen bonding between the codon and anticodon at the third position is subject to modified base-pairing rules

tryptophan and methionine

are encoded by a single codon

2-D structure of tRNAs

is a cloverleaf

charging tRNA

aminoacyl tRNA synthetase activates tRNAs with the appropriate amino acid

ribosomes have …

a large subunit and small subunit

Shine-Dalgarno sequence

in bacteria, the start codon is preceded by this, which base-pairs with a region of the 16S rRNA of the 30S small subunit

translation elongation

require both ribosomal subunits assembled with the mRNA to form the P (peptidyl) site and A (aminoacyl) site; tRNAs enter the A site, catalyzes peptide bond formation between the amino acid at the A site and the growing peptide chain in the P site, the uncharged tRNA moves to the E site

translation termination

is signaled by a stop codon (UAG, UAA, UGA) in the A site and GTP-dependent release factors cleave the polypeptide chain from the tRNA and release it

gene regulation

may be constitutive, inducible, or repressible

regulation can be …

under positive or negative control

inducible tip

if the gene is expressed in the presence of the agonist

negative tip

if the gene is expressed when the regulatory molecule is mutated

constitutive

always being expressed

lac operon

has 3 structural genes, lacZ, lacY, and lacZ, with an upstream regulatory region consisting of an operator and a promoter

structural genes of the lac operon …

are transcribed as a polycistronic mRNA

catabolite repression

the CAP is involved in repressing expression of the lac operon when glucose is present,

cAMP …

is required for CAP binding and glucose represses the expression of adenylyl cyclase, the enzyme that catalyzes the production

glucose is low …

adenylyl cyclase is active & CAP binds to the lac promoter

glucose is high …

adenylyl cyclase is inactive & CAP doesn’t bind to the lac promoter region

trp operon …

is a repressible system & in tryptophan’s presence, the operon is repressed

tryptophan …

functions as a corepressor, which is required for the repressor to bind to the operator

attenuation in the trp operon

the mechanism by which expression of the rest of the trp operon is repressed after transcription of the leader sequence

trp attenuation works by …

the leader region can form 2 different conformations: in the presence of trp, the 3-4 hairpin structure forms and acts as a transcriptional terminator & in the absence of trp, the 2-3 hairpin forms and acts as an antiterminator, and transcription proceeds

attenuation in other operons

is common to several operons for enzymes responsible for synthesis of other amino acids including threonine, histidine, leucine, and phenylalanine

TRAP

trp RNA-binding attenuation protein (used as a mechanism of attenuation for the trp operon)