AP Biology Unit 6 (copy)

gene regulation

the turning on and off of genes

gene expression

the overall process by which genetic information flows from genes to proteins/genotype to phenotype

promoter

dna sequence upstream of transcription start site where RNA polymerase and transcription factors bind to initiate transcription

operator

DNA control sequence, acts as a switch, determines whether RNA polymerase can attach to the promoter and start transcribing the gene

operon

cluster of genes with related functions, exist ONLY in prokaryotes

repressor

protein that turns off transcription, functions by binding to the operator and physically blocking the attachment of RNA polymerase to the promoter

regulatory gene

located outside the operon, codes for the repressor

regulatory protein

protein that regulates gene expression

activators

proteins that turn operons on by binding to DNA, make it easier for RNA polymerase to bind to the promoter

histones

crucial aspect of DNA packing, account for about half the mass of eukaryotic chromosomes --\> small proteins grouped and wrapped around a DNA strand to form a nucleosome

nucleosome

consists of DNA wound around a protein core of 8 histone molecules

epigenetic inheritance

Inheritance of traits transmitted by mechanism not directly involving the nucleotide sequence of a genome

enhancers

DNA control sequences, part of the first step in initiating gene transcription --\> binding of activator proteins to these

homoeotic gene

master control gene that regulates batteries of other genes that actually determine the anatomy of parts of the body

embryonic stem cells

harvested from the blastocyst, easily perpetuate themselves indefinitely

positive control of transcription

when the regulatory protein is an activator. It binds to the operon and and stimulates transcription.

negative control of transcription

the genes in the operon are expressed unless they are switched off by a repressor protein

recombinant DNA

formed when scientists combine nucleotide sequences (pieces of DNA) from two different sources to form a single DNA molecule

Plasmid DNA

small, circular DNA molecule that replicate and duplicate separately and independently from the much larger bacterial chromosome

gene cloning

the production of multiple identical copies of a gene-carrying piece of DNA

vector

gene carrier

restriction enzymes

enzyme cutting tools used to cut and paste DNA

restriction site

a DNA sequence recognized by a particular enzyme

polymerase chain reaction

Technique for amplifying dna in vitro by incubating it with sepcfic primers, heat resistant dna polymerase, and nucleotides. Any specific segment can be copied many times within a test tube

gel electrophoresis

-The DNA was all cut by a restriction enzyme at the mutated genes because the mutation creates a palindrome that the enzyme can cut; mutation can also take away palindromes

transcription

process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA). occurs in nucleus

transcription template

uses one of the two exposed DNA strands as a template; this strand is called the template strand. The RNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate (or coding) strand.

translation template

synthesis of a protein from an mRNA template where the code in the mRNA is converted into an amino acid sequence in a protein.

translation

process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus

triplet code

a set of three-nucleotide-long "words" that specify the amino acids for polypetide chains

codons

the genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of nonoverlapping three-base "words"

genetic code

the set of rules that relate codons in RNA to amino acid in proteins

RNA polymerase

transcription enzyme, links together the growing chain of RNA nucleotides during transcription, using a DNA strand as a template

terminator

third phase of transcription (termination), sequence of bases in the DNA template that signals the end of the gene

messenger RNA (mRNA)

encodes the genetic information from DNA and carries it from nucleus to

introns

internal non-coding regions

exons

coding regions, the parts of a gene that are expressed

RNA splicing

the removal of introns and joining of exons in eukaryotic RNA, forming an mRNA molecule with a continuous coding sequence, occurs before mRNA leaves the nucleus

transfer RNA (tRNA)

a type of ribonucleic acid that functions as an interpreter in translation --> each molecule has an anticodon, picks up a specific amino acid, and conveys the amino acid to the appropriate codon on mRNA

\-carries amino acids (anticodons) to ribosomes

transduction

Phages carry prokaryotic genes from one host cell to another

conjugation

Dna is transferred between 2 prokaryotic cells that are temporarily joined

anticodon

on a tRNA molecule, a specific sequence of three nucleotides that is complementary to a codon triplet on mRNA

ribosomes

structures in the cytoplasm that position mRNA and tRNA close together and catalyze the synthesis of polypeptides

ribosomal RNA (rRNA)

a type of ribonucleic acid consisting of nucleotide monomers with a ribose suger and the nitrogenous bases A, C, G, U; usually single-stranded, fuctions in protein synthesis, gene regulation

\-makes up the ribosome

start codon

specific codon (AUG) that an mRNA molecule binds to where translation is to begin on the mRNA molecule

P site

tRNA binding site, hold the growing polypeptide during translation

A site

tRNA binding site, vacant and ready for the next amino-acid-bearing tRNA

Steps of Translation

1. Initiation
2. Elongation
3. Termination

translocation

the P site tRNA now leaves the ribosome and the ribosome translocates/moves the remaining tRNA in the A site, with the growing polypeptide, to the P site --\> codon and anticodon remain hydrogen bonded and the mRNA and tRNA move as a unit --\> movement brings into the A site the next mRNA codon to be translated

stop codon

in mRNA, one of the tree triplets (UAG, UAA, UGA) that signal gene translation to stop

mutation

any change in the nucleotide sequence of DNA, can involve large regions of a chromosome or just a single nucleotide pair

silent mutation

a mutation in a gene that changes a codon to one that encodes for the same amino acid as the original codon --\> the amino acid sequence of the resulting polypeptide is thus unchanged

missense mutation

a change in the nucleotide sequence of a gene that alters the amino acid seqeunce of the resulting polypeptide --\> a codon is changed from encoding one amino acid to encoding a different amino acid

nonsense mutation

a change in the nucleotide sequence of a gene that converts an amino-acid-encoding codon to a stop codon --\> results in a shortened polypeptide

bacterial transformation

the ability of bacteria to alter their genetic makeup by uptaking foreign DNA from another bacerial cell and incorporating it into their own. Discovered by Griffith

transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription in Eukaryotes

\-Different genes may be regulated by the same transcription factor.

what factors maximize transcription rate

High concentration of positive transcription factors, a high affinity of positive transcription factor for the regulatory region and a high affinity of the rna polymerase for the positive transcription factor attached to the regulatory region

what initiates transcription

RNA polymerase and positive transcription factor bind on regulatory region

what do plasmids have to do with antibiotic resistance

Bacteria can transfer plasmids back and forth allowing them to share these beneficial genes; this allows bacteria to adapt to new environments

protein building process in eukaryote vs prokaryote

\-In a bacterial cell, which lacks a nucleus, mRNA produced by transcription is immediately translated without additional processing.

in eukaryotic cell, nucleus provides a separate compartment for transcription. The original RNA transcript, called pre-mRNA, is processed in various ways before leaving the nucleus as mRNA.

* Prokaryotic protein synthesis is faster than eukaryote

rna polymerase

transcription enzyme that links RNA nucleotides together

Initiation

Initiation: after rna polymerase binds to promoter, dna strands unwind and polymerase initiates RNA synthesis at start point on template strand

Elongation

polymerase moves downstream, unwinding the dna and elongating the RNA transcript 5'--> 3'. In wake of transcription, dna strands reform a double helix

Termination

3. eventually the rna transcript is released and polymerase detaches from dna

TATA box

Dna sequence in eukaryotic promoters crucial in forming the transcription initiation complex

\-it is commonly a nucleotide sequence containing TATA

What is the advantage of the 5' cap and poly A tail?

Facilitate export of mature mRNA from nucleus, protect mRNA from degradation by hydrolytic enzymes, help ribosomes attach to the 5' end of mRNA once it reaches the cytoplasm

poly-a tail

a sequence of 50-250 adenine nucleotides added onto the 3' end of a pre-mRNA molecule

gtp cap

the 5' end modification that aids with attachment to the ribsome

spliceosome

\-large complex made up of proteins and rna molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons

\-Spliceosome binds to several short nucleotide sequences along intron. Intron is then released, and spliceosome joins together the two exons that flanked the intron.

Stages of Translation

Initiation

Elongation

Termination

rRNA

responsible for reading the order of amino acids and linking amino acids together

mRNA

intermediary between the genetic information in DNA and the amino acid sequence of proteins. mRNAcontains codons that are complementary to the sequence of nucleotides on the template DNA and direct the formation of amino acids through the action of ribosomes and tRNA

tRNA

functions as a translator between nucleic acid and protein languages by picking up a specific amino acid and carrying it to a ribosome, where tRNA recognizes the appropriate codon in mRNA. transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome

signal peptide

sequence of about 20 amino acids at or near leading end of polypeptide that targets it to endoplasmic reticulum or other organelles in eukaryotic cell

repressible operon

its transcription is usually on but can be inhibited when a specific small molecule binds allosterically to regulatory protein. Trp operon

inducible operon

usually off but can be stimulated to be on when a specific small molecule interacts with a different regulatory protein. Lactose operon

enhancer

segment of eukaryotic dna containing multiple cntrol elements, usually located far from gene whose transcription it regulates

lytic

phage replication cycle that results in release of new phages by death of host cell

lysogenic

viral genome becomes incorporated into bacterial host chromosome as prophage; replicated along with chromosome and does nto kill host cell

retrovirus

\-virus whose genes are encoded in RNA, and, using an enzyme called reverse transcriptase, replicates itself by first reverse-coding its genes into the DNA of the cells it infects.

\-Like other viruses, retroviruses need to use the cellular machinery of the organisms they infect to make copies of themselves.

\-However, infection by a retrovirus requires an additional step. The retrovirus genome needs to be reverse-transcribed into DNA before it can be copied in the usual way. The enzyme that does this backward transcription is known as reverse transcriptase.

cell differentiation

process by which cell or group of cells becomes specialized in structure and function; different kinds of cells are not randomly distributed but are organized into tissues and organs in a particular three-dimensional arrangement

Distribution of cytoplasmic determinants

After fertilization, early mitotic divisions distribute the zygote's cytoplasm into separate cells. The nuclei of these cells may thus be exposed to different cytoplasmic determinants, depending on which portions of the zygotic cytoplasm a cell received. The combination of cytoplasmic determinants in a cell helps determine its developmental fate by regulating gene expression during cell differentiation.

different inductive signals

induction-the process in which one group of embryonic cells influences the development of another, usually by causing changes in gene expression

\-The molecules that pass along these signals within the target cell are cell-surface receptors and other signaling pathway proteins. In general, the signaling molecules send a cell down a specific developmental path by causing changes in its gene expression that eventually result in observable cellular changes. Thus, interactions between embryonic cells help induce differentiation into the many specialized cell types making up a new organism.

determination

Progressive restriction of developmental potential whereby the possible fate of each cell becomes more limited as an embryo develops, at the end of determination, a cell is committed to its fate.

homeobox

Homeobox is a 180 nucleotide sequence within homeotic genes and some other developmental genes that is widely conserved in animals. Related sequences occur in plants and yeast. from these similarities, we can deduce that the homeobox DNA sequence evolved very early and was sufficiently beneficial to organisms to have been conserved in animals and plants virtually unchanged for hundreds of millions of years.

steps of gene cloning

1. Isolation and fragmentation of source DNA
2. Insertion of DNA fragment into cloning vector
3. Introduction of cloned DNA into host organism

nucleic acid hybridization

Base pairing between a gene and a complementary sequence on another nucleic acid molecule.

dimers

a molecule or molecular complex consisting of two identical molecules linked together.

\-The presence of dimers can lead to errors in both transcription and replication.

\

tRNA molecules deliver amino acids to ribosomes where the amino acid next

is covalently bonded to a growing polypeptide

Analysis of DNA sequences from two individuals of the same species results in a greater estimate of genetic variability than does analysis of amino acid sequences from the same individuals because

different DNA sequences can code for the same amino acid

what normally leads to the production of functional messenger RNA in eukaryotic cells?

The removal of portions of RNA known as intervening sequences (introns)

how can different lengths come out of the transcription of one RNA

Excision of different introns and splicing and retention of different exons can generate different versions of the resulting mRNA, which may have different lengths.

alternative splicing

excision of introns and splicing and retention of exons can generate different versions of the resulting mRNA molecule

\-creates different versions of the same gene

luciferase

Enzyme used in bioluminescence

\-produced by ribosomes in the cytoplasm OR in the cytosol of the lymphocytes.

what dictates amino acid sequence

sequence of nucleotides in the mRNA.

\-Sequential triplets of nucleotides called codons specify each amino acid to be added, in order, to the growing polypeptide chain.

what happens to luciferase activity if the plasmid is introduced into nonlymphoid cells

little or no activity because nonlymphoid cells will not contain the transcription factors that bind to the plasmid gene regulatory sequences

regulatory sequence

stretches of dan that interact with regulatory proteins to control transcription

How is phenotype determined?

by combination of genes that are expressed and level at which they are observed

\-observable cell differentiation results from expression of genes for tissue-specific proteins

\-induction of transcription factors during development results in sequential gene expression

what increases variation

mutations

\-horizontal acquisition of genetic info via transformation, transduction, conjugation, and transportation

methylation

\-DNA or histone methylation prevents transcription.

\-Protects against restriction enzymes.