What is #' in sugar?

it is counting carbons clockwise from the oxygen, going from 1' to 5'

nucleotide components

phosphate group linked to 5-carbon sugar linked to nitrogenous base

phosphodiester bonds (AP)

link sugars and phosphates in nucleotides (forming the sugar-phosphate backbone)

purines

double ringed nitrogenous bases (A and G - two rings as Pure as Gold)

pyrimidines

single ringed nitrogenous bases (C, T, U)

What is attached to the 5' end of DNA?

phosphate group

What is attached to the 3' end of DNA?

OH (hydroxyl) group

antiparallel

the DNA strands run in opposite directions, each with a 5' end and a 3' end (5' always opposite 3' of complementary strand)

plasmids

small, double-stranded, circular DNA molecules in prokaryotes and eukaryotes

nucleosome (AP)

bunches of histones, package eukaryotic chromatin

euchromatin (AP)

loose DNA in the nucleus, active for transcription

heterochromatin (AP)

genetic material is fully condensed into coils, inactive

DNA helicase

unwinds the double helix by breaking the hydrogen bonds in DNA replication

replication bubbles

DNA strands exposed in a y-shape from helicase opening them, with DNA replication proceeding in both direction from the origin

origins of replication

where DNA replication begins, proteins attach here to begin strand separation

DNA topoisomerases (AP)

cut and region the helix to prevent it from tangling, stop helix from twisting in DNA replication

DNA polymerase

adds the nucleotides to the freshly built strand, only 5' 3 for new strand and 3' to 5' for old strand in DNA replication

What happens to RNA primase after DNA replication kicks off?

it is degraded by enzymes and replaced with DNA

RNA primase

adds a short strand of RNA nucleotides (RNA primer) to start off replication

leading strand

one DNA strand is made continuously in DNA replication by DNA polymerase, 5' to 3' towards forking point

lagging strand

made discontinuously in pieces by DNA polymerase, 5' to 3' direction away from forking point

Okazaki fragments

the pieces of nucleotides that make up the lagging strand

DNA ligase

links the Okazaki fragments to produce a continuous strand in DNA replication

semiconservative

half of each new molecule was a part of the original one, while the other half is a new strand in DNA replication

telomeres (AP)

the ends of the DNA molecule, contains unimportant DNA and gets shorter over time since chromosome loses base pairs at the end

central dogma

DNA --> mRNA --> protein --> expression

Where do transcription and translation occur in prokaryotes?

both in the cytoplasm at the same time

messenger RNA (mRNA)

temporary RNA version of DNA, exits nucleus

ribosomal RNA (rRNA)

makes up parts of the ribosomes, produced in nucleolus

transfer RNA (tRNA)

shuttles amino acids to ribosomes, matches amino acids to anticodons to codons by reading mRNA

What is the structure of tRNA?

anticodon on one side, amino acid on the other,

wobble pairing

anticodons in tRNA can pair against base matching with their third nucleotide

interfering RNAs (RNAi)

small snippets of RNA naturally made in the body, bind to specific RNA sequences to mark for destruction (e.g. siRNA and miRNA)

polycistronic transcript

prokaryotes will transcribe a recipe used to make several proteins, unlike eukaryotes

monocistronic

eukaryotes tend to have one gene that gets transcribed to one mRNA translated into one protein

initiation (transcription)

unwind and unzip DNA using helicase

promoters

special sequences in the DNA strand where transcription begins (like docking sites at a runway), no primer in transcription

What are promoters made up of?

TATA box, weak bonds (double instead of triple) allows RNA polymerase to break through

antisense strand / noncoding strand / minus-strand / template strand

the strand that serves as a template for RNA, only copy one of the 2 DNA strands

sense strand / coding strand

dormant strand not copied in transcription

elongation (transcription)

RNA polymerase builds RNA, adding to 3' side of template strand (build new mRNA 5' to 3')

promoter region

upstream of actual coding part of gene so polymerase can get set up before the bases it needs to transcribe, no need for a primer

termination (transcription)

RNA separates from the DNA template

terminator

special sequence of bases in DNA template that signals end of the gene, lots of C's and G's (STRONGER triple bonds) causes RNA polymerase to release

Do eukaryotes or prokaryotes need extra mRNA processing?

eukaryotes

heterogeneous nuclear RNA (hnRNA) (AP)

freshly transcribed RNA in eukaryotes, still needs to be processed

exons

coding regions of hnRNA, are EXpressed and EXit the nucleus

introns

non-coding regions of hnRNA, INtervening sequences and stay IN the nucleus

splicing

when introns are removed from the mRNA in processing, can splice in different ways with different exons

spliceosome

the RNA-protein complex that does the splicing of introns in mRNA processing

small nuclear ribonuclear proteins (snurps)

part of spliceosomes that recognize the start and end of introns

poly (A) tail

a long string of adenine nucleotides at the 3' end of processed mRNA

5' GTP cap

one guanine nucleotide at the 5' end of processed mRNA

exit (E) site (AP)

holds deactivated tRNA so it can exit after its amino acid has been added

adding (A) site

holds tRNA with next amino acids to be added to the chain

primary (P) site

holds tRNA carrying the growing polypeptide chain

large subunit of ribosome

tRNA binding site, binds with small subunit after it attaches to mRNA, has E, P, and A sites

small subunit of ribosome

mRNA binding site

initiation (translation)

ribosome attached to mRNA, shuttles from A to P to E binding sites

How is tRNA linked to amino acids?

charged tRNA and enzymes need ATP to link AA and tRNA

start codon

AUG (methionine), first to go into ribosome in initiation

elongation (translation)

addition of amino acids to the growing polypeptide chain by tRNA reading mRNA

stop codons

UAA, UGA, UAG (do not code for an amino acid)

termination (translation)

the ribosome runs into one of three stop codons

pre-transcriptional regulation

largest point of gene expression regulation, occurs before transcription, transcription factors encourage or inhibit transcription's start

transcription factors

can encourage or inhibit the start of transcription by adjusting difficulty for RNA polymerase to get to start site, influence expressed genes

epigenetic changes

changes to the packaging of DNA that alter the ability of transcription machinery to access a gene, occurs through histone tightness modification

operons

a cluster of genes used to control a single promoter in bacteria

lac operon

controls expression of enzymes that break down lactose

structural genes

code for enzymes needed in chemical reaction, usually transcribed at the same time to produce particular enzymes

promoter gene

where RNA polymerase binds to begin transcription

operator

region that controls where transcription will occur, where repressor binds

regulatory genes

codes for specific regulatory protein called the repressor

repressor

can attach to operator and block transcription, binds = transcription will not occur

inducer

binds to the repressor and causes it to fall off, turns on transcription

post-transcriptional regulation

when the cell creates RNA, then decides it should not be translated into a protein, RNAi binds to RNA with BP = double stranded RNA which is destroyed

post-translational regulation

cell has made a protein, but doesn't need it; mostly enzymes made ahead of time, turn off as needed

morphogenesis

the succession of stages the cell changes in shape and organization throughout its development

undifferentiated cells

can develop into any type of cell

differentiated cells

once cells become specialized, their futures options are limited (no dedifferentiation; a future muscle cells can't turn into a bone cell)

homeotic genes

the early genes that turn certain developing embryonic cells into future specialized cells, make sure the right gene is activated or part is modified at the right time

Hox genes

a subset of homeotic genes

apoptosis

programmed cell death, destroys scaffolding parts of developing embryo (toe webs)

mutation

an error in the genetic code

causes of mutation

chemicals, radiation, polymerase mistakes

What has proofreading abilities?

DNA to prevent inheritance of them, RNA does not have

base substitution (point) mutations

single nucleotide base is substituted for another

nonsense mutation

point mutations that lead to a stop codon (terminate translation early)

missense mutations

point mutations that lead to a different amino acid

silent mutation

point mutations that code for the same amino acid with no change to the overall protein sequence

insertions / deletions

gene rearrangement that results in gain / loss of a gene(s) and frameshift

frameshift mutation

changes the sequence of codons (triplets) used by the ribosome to make proteins, everything after is affected

duplications

gene rearrangements that result in an extra copy of genes from unequal crossing over or chromosome rearrangement, results in new traits

inversion

changes in orientation of chromosomal regions

translocation

two different chromosomes break and rejoin in a way that causes the DNA sequence or gene to be lost, repeated, or interrupted (can also be one chromosome breaking in 2 places)

transposons

gene segments that can cut / paste themselves throughout the genome

conjugation

swap DNA with other bacterial cells

transformation

uptake of DNA for bacteria

transposition

movement of DNA within and between DNA molecules for bacteria

What increases the genetic variation of bacteria?

conjugation, transformation, transposition

viruses

nonliving agents capable of infecting cells, use host cell machinery to replicate, made of protein shell (capsid) and genetic material

viral genome

carries genes for building the capsid and anything else the virus needs that the host cannot provide

How can viral genomes mix?

if two viruses infect the same cell

lytic cycle

the virus immediately starts using the host cell's machinery to replicate the genetic material and create more capsid proteins, lyse to release viruses

lysogenic cycle

virus incorporates itself into host genome and remains dormant until it is triggered, can remain dormant for a long time until triggered, means cell can divide with viral DNA

prophage

host cell's genome before phage

transduction

the transfer of DNA between bacterial cells using a lysogenic virus. host DNA is packaged into new viral particles so next infected cell has previous host DNA and viral genome

enveloped viruses

viruses with a lipid envelope, no need to break out of cell but bud out of membrane instead

retroviruses

use enzyme reverse transcriptase to convert their RNA genomes into DNA (e.g. HIV), high mutation rates and no proofreading = hard to treat

recombinant DNA

generated by combining DNA from multiple sources to create a unique DNA molecule not found in nature

genetic engineering

produces new organisms or products by transferring genes between cells

polymerase chain reaction (PCR)

lab technique for making billions of identical gene copies in hours, DNA used for phylogenetic analyses

amplification

the process of making many copies of genes

thermocycler

the machine used that mimics the process of DNA replication

transformation in lab

the process of giving bacteria foreign DNA (e.g. making insulin from bacteria or for gene expression studies)

gel electrophoresis

separates DNA fragments by weight and charge

restriction enzymes

create a molecular fingerprint by cutting in specific, personally unique patterns

restriction fragment length polymorphism (RFLP)

the unique restriction fragments of individuals

DNA fingerprinting

when RFLPs from DNA at the crime scene are compared to the suspects' RFLP

DNA sequencing

used to determine the order of nucleotides in a DNA molecules

CRISPR Cas-9

clustered regularly interspaced short palindromic repeats, molecular scissors that cut and paste

Who discovered CRISPR-Cas 9?

Jennifer Doudna and Emmanuelle Charpentier, 2 female scientists

uses for CRISPR Cas-9

cure lifelong, inherited diseases; don't use on gametes or early development embryos; only stem cells

Cas-9

protein, DNA cutting enzyme, has RNA guide inside with the necessary sequence, surrounded by enzyme

How accessible is CRISPR?

very, any Joe Schmoe can make in 3 weeks

supernatant

lighter components of a solution, in the liquid after centrifuging

lysozymes

naturally occurring enzyme used to break open cells

freeze cells overnight

water expands, leads to breakage

fluorescent protein tail

negatively charged his amino acids

elution buffer (imidazole)

breaks bond between nickel bead and fluorescent proteins by making nickel beads more negative and the R groups of the his more positive