Molecular Biology Exam 1

what defines an organism

physical barrrier

store genome stably

reproduce generations

requires energy from external

compartmentalization

important because it separates chemical reactions

genome

genetic information packed into chromosomes, has histone proteins

gDNA

genomic dna

plasmid

extra chromosomal pieces that carry important dna usually in bacteria

what is responsible for bacterial resistance

plasmid

episomes

the equivalllent of plasmids in eukaryotes, usually derive from viruses, attach to your chromomses, small cicurlar DNA

what are episodes derived from

transposons

transposons(trasposable elements)

jump around

what percent of the human genome is genes

40

how much of the genome is intergenic(low or high repeat areas)

60

satellite dna

large arrays of repeats 100-1k bp

minisatelites

15-50bp

short tandem repeats or microsattelites

2-6 bp

what do tandem repeats do

we don’t really know but the have been shown to affect sociableness based on length in vols

can you reverse the central dogma

no you can’t go back from proteins to dna

transcription

copying dna into rna, rna polymerase synthesizes rna

translation

mrna translated into proteins, performed by a ribosome, tRNA(transfer) interprets mRNA info into a protein sequence

mRNA

contain information to produce a protein, which are built up of amino acids

what is the start codon

methionine (AUG)

where in the central dogma does regulation take place

it takes place at each step,

gene regulation

temporally and spatially

forward genetics

identify a mutant phenotype and determine what gene caused it, pheontyope → genotype

backward genetics

gene of interest is disrupted and observe what phenotype it produces, genotype→phenotype

policy

number of copies of the genome

loss of function mutation

knock out or knock down

knock out

affecting at the genomic dna(crispr)

knock down

mRNA controlled bu RNAi, not permanent

Gain of function mutation

knock in or over expression

knock in

crispr

over expression

active all the time

Indel

insertion/deletions, can be natural or crispr

insertions are caused by

transposons jumping

SNP

single nucleotide polymorphisms, a single nucleotide substitution, can be used as a marker

how do we keep having mutations

because we are constantly replicating and there can be errors

model organsims

cheap, easy to get, manipulatible, short gestation

examples of model organisms

mice, drosophillia, sea elephants, robidobeus

viruses

have nucleic acids surrounded by protein coating

are viruses alive

no, because they cannot replicate on their own

other than dna and rna, what is another function of nucleotides

energy, ATP

is dna or rna more reactive

rna, because it has the 2’ oxygen

characteristics of base pairs

non polar, hydrophobic, and planar

nucleoside vs nucleotide

nucleotide have a phosphate group

what is the bond between a sugar and base

glycosidic bond

where is the glycoside bond on pyrimdaine vs purine

n1 of pyrmiidine

n9 of purine

adenosine analogs

compounds that look similar to adneosine, can stop cancer, also caffeine, fits into receptors

characteristics of a phosphate group

acidic- can release H+

negative charge makes it insoluble in lipids of a cell membrane

dehydration synthesis

joining two nucleotides together

dna dirrectionality

5 to 3’

what holds two strands of dna together

hydrogen bonds, cand g is 3

a and t is 2

wastcon crick base pairs

a and t, c and g

antiparralel

one side starts at 5 and one at 3

char gaffs rule

a=t, c=g, a+g=t+c

tautomers

a molecule in which a proton has migrated to a different place(tautomeric isomers), can provide genetic variation

what are rna measurd in

nucleotides

dna hydrophilic region

backbone

what occurs when bases are stacked

vanderwal interactions

what does the flat bases allow

steric hinderance, the spiral flat bases keeps water out of the core(hydrophobic)

which regions are more bendable

a and t regions

what is the predominant dna form

B-DNA

a dna

right handed, has even groove sizes, induced by dna binding proteins

z-dna

left handed, result from high salt, torsional strain, and methylation of cytosine

what causes z dna to turn left handed

a base extrudes and flips, making it quite stable, going from anti to syn

where is there potential for z dna to form

areas of active transcription, receives torsional strain during transcription

major groove

the backbone is father apart, where proteins bind because bases are more accessible

can proteins bind to the minor groove

yes but it isn’t often and can cause the dna to unwind and bend to fit it

can rna catalyze reactions

yes

unusual dna secondary structures

slipped(hairpin), cruciform, DUE,triplex

slipped structure

in areas of tandem repeats, basepairs pair unusually and stabilize a loop

is it bad to have slipped structure

it can lead to repeat expansion or deletion during replication

DNA Unwinding elements

A-T rich regions, near replication origins

cruciform

areas of inverted repeat, and it folds at the ir center

triplex h dna

mirror repeat symmetry, hoosten hydrogen bonds, not stable at neutral ph

hoogsteen pairing

the base pairs bond unusually throwing off number of bonds

what are the biological implications of unusual structure of dna

replication blockage, affect nucleosome position, genetic instability

dna supercoiling

dna winds and clumps, needs to be unwound to complete processes

supercoiling functions

compaction, protection, replication, gene expression in z dna

topoisomerase 1 vs 2

1 cuts one strand to unwind(transcription), 2 cuts both strands(for chromosome condensation and separating daughter chromosomes)

two key features of rna

• can form base pairs with other rna or single stranded dna

• or can interact with protiens(ribonucloprotien particles)

rna modifications

usually permanent(not regulatory)

rna 2’ OH

makes the rna more unstable, making it better for short term functions, rna favors alpha helix because of it

what can the 2’ OH do

facilitate a reaction that breaks phosphoiester bonds

sugar pucker

the sugar in nucleotides buckles making different conformations

what is the pucker sugar for a dna (ribose)

C3’ endo, anti

what is the pucker sugar for b dna

C2’ endo(b helix) anti

how does the 2’ oh affect interactions

allows rna to form hydorgen bonds more prolifically than dna, allowing more inter and intramolecular interactions

what is the sugar pucker for z dna purines

c3 endo, syn

what is the sugar pucker for z dna pyrimidines

c2’ endo, anti

what does endo mean

they face up

snoRNA

rRNA processing

tRNA

delivers amino acids to ribosome

rRNA

component of ribosome

microRNA

binds to target mRNA to silence the gene, triggers degradation of gene by blocking translation by ribosome

snRNA

mRNA splicing, prepares mRNA for translation

mRNA

copy of dna sequence, then binds to ribosome

RNPS

ribonucleoproteins

telomerase

add telomeric repeats at the end of chromosomes in replication

spliceosome

removal of introns from nuclear pre-mRNA

RNase P

generates 5’ end of mature tRNAs

ribosome

protein synthesis machinery