UW Madison Bio 151 Exam 2

x-ray crystallography

makes DNA crystal, shines X-rays to form a scatter pattern that gives information about the structure of DNA

double helix structure

describes two interlinked strands of DNA making a spiraling "ladder"

DNA strand

a single series of nucleotide bases covalently linked in any order

dNTPs

deoxynucleotide triphosphates

sugar-phosphate backbone

an alternating chain of sugars (ribose or deoxyribose) and phosphates that make up the outside of the DNA or RNA

phosphodiester bond

antiparallel

opposite arrangement of helix strands -- parallel in opposite directions

5' end of DNA

one end of a DNA chain, refers to a sugar with a 5' phosphate group attached to it

3' end of DNA

one end of a DNA chain. refers to a sugar with a 3' hydroxyl attached to it

complementary/matching base bairs

A and T (or U in RNA), C and G

semi-conservative

the process of replicating DNA "conserves" one template strand and makes one new strand

DNA polymerase

enzyme that matches complementary nucleotides with the template strand

Helicase

enzyme that "unzips" the DNA

single strand binding proteins

proteins that stabilize the single strands of DNA to prevent them from re-binding to one another

origin of replication

specific DNA sequence where helicases and polymerase begin the replication process

replication bubble

region of DNA between the two "unzipped" strands, where the origin of replication is

replication fork

y-shape created by unzipped sections of DNA

supercoiling

phenomena that occurs as the DNA strands are unwound where the still-wound pieces tighten increasingly

topoisomerase

enzyme that prevents supercoiling by cutting the strands and allowing them to unwind and then re attaching them

primase

enzyme that makes the RNA primer

RNA primer

indicates where the RNA polymerase should start replicating the DNA

DNA ligase

enzyme that links the two replicated NDA fragments

leading strand

strand of DNA being replicated continuously - "bottom" strand of replicated DNA

lagging strand

strand of DNA being replicated DIScontinously - "top" strand of replicated DNA

okazaki fragment

short segments of DNA synthesized in the lagging strand during DNA replication

telomere

the end of a linear chromosome that contains a repeated sequence of DNA

telomerase

enzyme that adds nucleotides to the template strand, extending it where the RNA primer can bind

transcription

turning DNA into RNA by RNA polymerase

messenger RNA (mRNA)

RNA that carries information from DNA. Has a similar nucleotide content/percent to DA

RNA polymerase

enzyme that makes RNA from DNA

promoter DNA

nucleotides bound by RNA polymerase and cofactors -- where transcription begins

terminator DNA

where transcription ends (ish)

transcription unit

region of DNA between specific promoter and terminator DNA

nuclear envelope

lipid bilayer that surrounds the nucleus of eukaryotic cells

primary transcript (pre-mRNA)

first form of RNA formed through transcription in protein synthesis

mature mRNA

final product of spliced RNA - processed from transcribing pre mRNA

polyA tail

3' end of DNA that has a long stretch, around 250, A's. binds proteins that help stabilize RNA and export RNA from nucleus

exon

parts that remain after non-coding sections of DNA are removed

intron

non coding sections of DNA - removed from strand

spliceosome

proteins and small nuclear RNAs (snRNAs) that remove introns

snRNA

small nuclear RNAs that bind, recognize specific nucleotides at exon-intron junctions

genetic code

triplet codon

series of 3 nucleotides that code for amino acids

transfer RNA

small, stable RNAs that bind a specific type of amino acids at its attachment site

anticodon

complementary 3 nucleotide sequence for each tRNA

aminoacyl tRNA synthetase

tRNA that has bound to its amino acid

small ribosomal unit

unit of ribosome made of rRNA and proteins. catalyze

large ribosomal unit

unit of ribosome made of rRNA and proteins

ribosomal RNA (rRNA)

non coding RNA that makes up most of a ribosome

A slot

amino acyl site

P slot

peptidyl site

E slot

exit site

start codon

tells ribosome where to initiate translation along mRNA

initiator tRNA

anticodon that matches start codon

stop codon

tells ribosome where to end translation along mRNA

release factor protein

protein that causes termination of translation by releasing polypeptide

5' UTR

untranslated region 5' to the start codon

3' UTR

untranslated region 3' to the stop codon

transposable element (transposon)

DNA sequence that can splice in and out of DNA, cause damage and move surrounding genomic DNA

point mutation

change in or loss of a single base

synonymous mutation

"silent" point mutation that codes for the same amino acid

missense mutation

point mutation that codes for the wrong amino acid

nonsense mutation

point mutation that codes for a stop codon

frameshift mutation

deletion or insertion of nucleotides that can have a waterfall change in the way codons are read

deletion

mutation - removal of a nucleotide in a DNA sequence

insertion

mutation - addition of a nucleotide in a DNA sequence

genome

all the genetic information of an organism

non-coding transcription units

created non-mRNA, templates of DNA that are not translated into proteins. Use different promoters and process differently than coding transcription units

gene expression

ways in which genes are visible or characteristically shown on a larger scale (color, texture, etc)

transcription factor proteins

proteins that regulate Inhibit, drive) gene expression and transcription

lac operon promotor

DNA in E.coli makes a single mRNA that codes for two proteins

lactose

sugar that binds the repressor in allosteric inhbition so it no longer functions

CRP

activator transcription factor

cAMP

cyclic AMP - a second messenger used to carry information

difference between -ase an -tase

-tase enzymes require input of ATP, -ase enzymes to not

enhancer DNA

gets bound by transcription factor to stimulates transcription

silencer DNA

gets bound by transcription factor to repress transcription

chromatin remodeling

change in the wrapping of DNA by histone proteins

histone

proteins that wrap DNA into nucleosomes

nucleosome

DNA that's been wrapped by histones

histone acetylation

addition of acetyl groups to histones - causes less compact winding and more transcription

DNA methylation

temporary addition of methyl groups to bases to reduce transcription of nearby genes

microRNA

single-stranded non-coding RNA molecules - complementary to a part of mRNA, blocks translation or triggers mRNA desctruction

epigenetic changes

changes in transcription such as transcription factors, histone modifications, DNA methylation. Do not alter DNA nucleotide sequence but can still last for many cell divisions because of positive feedback loops

protein signal sequence

specific group of amino acids that bind lock-and-key to a specific structure, pore, pump, membrane, motor etc.

nucleus

organelle in the cell where DNA is contained

nuclear envelopes

inner and outer portions, two lipid bilayers that surround the nucleus

nuclear pores

perforate the nuclear envelope, complex transporters

nuclear localization signal sequence

particular sequence of amino acids that binds importin

importin

protein that shuttles back and forth in the nuclear pore, imports proteins bound to it

endomembrane system

network of organelles including the endoplasmic reticulum(s), golgi apparatus, and vesickles

smooth endoplasmic reticulum

network of membrane-enclosed tubes that are continuous with the outer nuclear envelope. does not have ribosomes. protein enzymes for the synthesis of membrane lipids, steroids, carbs

rough endoplasmic reticulum

network of membrane-enclosed tubes that are continuous with the outer nuclear envelope, has ribosomes. Where transmembrane proteins are inserted into the membrane

trafficking

allows insertion through protein in ER membrane

transport vesicle

vesicles that move proteins into the Golgi appatus

secretory vesicle

receive proteins in the Golgi apparatus before being exocytosed

golgi apparatus

stack of flattened membrane-bound disks or layers. Trans (outermost) and cis (innermost) layers, often where proteins are modified

glycosylation

method of processing proteins in which they are covalently linked to other molecules, particularly carbohydrates

lysosome

vesicle that has digestive enzymes. Its membrane has transport proteins to export digested molecules to the cytoplasm

cytoskeleton

intracellular rods and fibers made of many proteins. Moved by motor proteins