Bio unit 4

gene expression

when a gene is used to make a product

gene regulation

turning on or off specific genes as required by the cell, allows cells to become specialized

housekeeping genes

always needed, always turned on, constantly being transcribed and translated

transcription factors

positive (activators) and negative (repressors)

activators

bind to DNA near promoter, help RNA polymerase attach, increases transcription

repressors

block RNA polymerase or promoter, decreases or stops transcription

post-transcriptional regulation

interfering DNA, alternative splicing, mRNA degradation, and masking protein

interfering DNA

bind SiRNA and miRNA to mRNA, siRNA cuts mRNA so no protein is made, miRNA blocks ribosome so no translation occurs, both decrease gene expression

alternative splicing

produces different mRNA versions from the same gene

mRNA degradation

a regulation molecule will directly or indirectly affect the rate of mRNA breakdown less protein produced

masking proteins

keeps mRNA in an inactive from until needed delay protein production

translation regulation

length of Poly-A tail

length of Poly-A tail

specific enzyme can add or delete repeating sequence of adenine at the ends of mRNA molecule

post-translational regulation

processing, modification, and degradation

processing

protein is cu/modified to become active

modification

chemical groups attached to the proteins are affected by or removed changing the chemical activity

degradation

ubitquin tags proteins and they are destroyed, stops protein function

pre-transcriptional regulation

histone acetylation and DNA methylation

histone acetylation

adds acetyl groups to stones and the DNA becomes looser, increases gene expression

DNA methylation

adds methylation groups to DNA, DNA becomes tighter, decreases gene expression

similarities of acetylation and methylation

both help DNA get to mRNA

difference between methylation and acetylation

acetylation increases rate of transcription and methylation decreases

ways to increase gene expression

acetylation, adjust length of poly-A tail, post-transcriptional processing

transcription

making mRNA from DNA

enzyme used in transcription

RNA polymerase

RNA polymerase role in transcription

adds new nucleotide bases without needing a primer

which way does the sense strand run

3’-5’

Sense strand

DNA segment that matches the mRNA sequence, representing the genetic code for protein

which way deos the anti-sense strand run

5’-3’

anti-sense strand

serves as a temple for transcription, forming a complementary mRNA molecule

exon

protien coding nucleotides, stay in mRNA

introns

non-coding intervening sequences removed during RNA splicing

how does RNA polymerase know where to bind

recognizes a seuqnece called a promotor, typically TATA, lies just before the gene

initation

The first step of transcription where RNA polymerase binds to a specific DNA sequence called a promoter, forming an initiation complex.

step 1 of transcription

Initiation : RNA polymerase binds to the promoter to unzip the DNA

step in transcription after initation

exonagation: RNA polymerase builds mRNA

elongation

RNA polymerase builds mRNA

step in transcription after elongation

termination: releases mRNA when termination sequence is reached

termination

releases mRNA when termination sequence is reached

step in transcription after termination

mRNA leaves the nucleus after mRNA is modified (capping, tailing, and splicing)

3 post-transcriptional modifications that happen to mRNA

tailing, capping, and splicing

tailing

adding a chain of adenine nucleotides using poly-a-polymerase to protect mRNA from attacks

capping

5’ cap consists of 7 carbons is added to the start of the pre mRNA molevcules, ribosomes recognize this site and use it for intial attachment

splicing

occurs in a splicesome removes introns and joins exons together

splicesome

enzyme protein complex that removes introns from mRNA

the DNA backbone

The 3 carbons of one nucleotide attach to the phosphate of the next nucleotide, and the phosphate is attached to the 5th carbon in the next nucleotide

purpose of DNA replication

cells need to make a copy of DNA before dividing so each daughter cell has a complete copy of genetic information

anti-parallel

DNA molecule has a direction. complementary strands run in opposite direction

first step of DNA replication

helicase unzips the 2 strands

step in DNA replication after helicase unzips the 2 strands

single-stranded bonding proteins keep the strands apart

step in DNA replication after SSBs keep the strands apartt

gyrase untwists the strands

step in DNA replication after gyrase untwists the strands

RNA primase lays down primer in the 5’-3’ direction

step in DNA replication after RNA primase lays down primer

DNA polymerase III adds bases to the 3’ end of the primer and continues to add bases following helicase, this repeats multiple times for the lagging strand

step in DNA replication after DNA polymerae III lays down bases

polymerase I removes the primer, fixes mistakes, and replaces primer with DNA bases on the lagging strand

step in DNA replication after DNA polymerase I does it jobs

ligase attaches the okazaki fragments together

step in DNA replication after the okazaki fragements are attached

telomerase builds from the 5’ end where the primer was on the leading strand

helicase

unzips the DNA part of helix

gyrase

enzyme that prevents tangling upstream from the replication fork

single stranded bonding proteins

prevents the DNA molecule from closing, binds to each strand at replication fork

primase role in DNA replication

adds small section of RNA primer to the 3’ end of template DNA

leading strand

requires 1 primer, build continueously

lagging strand

requires many primers, built in fragments

DNA polymerase III

enzyme that builds new DNA strand (can only add nucleotides to existing strands of DNA)

DNA polymerase I

removes the primer, fixes mistakes, and adds DNA bases on lagging strand

okazaki fragments

short pieces of DNA made on lagging strand

telomerase

enzyme that replaces telomeres (adds to 5’ end)

ligase

enzyme that glues okazaki fragments together

telomeres

non-coding ends of a chromosome

translation location

ribosomeof cytoplasm

codon

group of 3 messenger RNA bases

the mRNA code

same for all life, strongest support for a common origin of all life

transfer RNA

matches codons to amino acids

first step of translation

in the ribosome the first transfer RNA arrives with an amino acid

step in translation after first amino acid arrives

second tRNA arrives with second amino acid

step in translation after two amino acids are present

the first 2 amino acids form a peptide bond

step in translation after amino acids form a peptide bond

everything shifts down and the process repeats until a stop codon is reached

step in translation after a stop codon is reached

polypeptide is released

mutations

any change in the DNA sequence

two types of small mutations

point mutations and frameshift mutations

types of point mutations

silent mutation, nonesense mutation, and missense

point mutation

a change in one DNA nucleotide

silent muation

change in DNA base but the correct amino acid is placed

nonsense mutation

premature stop codon

missense

the wrong amino acid is placed

frameshift mutations

an insertation or deletion of a nucleotide

types of frameshift mutations

insertion, deletion, and frameshift

insertion

extra base in DNA, everything shifts down

deletion

base is removed

frameshift

after insertion or deletion everythig shifts and amino acids are wrong

chomosomal mutations

any change in the structure or number of chromosomes

types of chromosomal mutations

chromosomal deletion, chromosomal duplication, chromosomal inversion, chromosomal translation, and non-disjunction chromosomes

chromosomal deletion

one or more genes are removed

chromosomal duplication

a segment is copied twice and added to the chromosome

chromosomal inversion

a segment of genes is flipped

chromosomal translation

material is swapped with another chromosome

non-disjunction chromosome

failure to seperate durinig meiosis

basic biotechnology tools

recombinent plasmid, gel electrophoresis, and polymerase chain reaction

plasmids

small supplemental circles of DNA that are self replicating

first step of making a recominant plasmid

choose restriction enzyme that cuts the plasmid once and the DNA twice (but not the actual gene)

step in making a recombinant plasmid after picking the restriction enzyme

the gene is inserted into the plasmid