Genetics exam 3

Transposons

Mobile genetic elements

Conjugation

One bacterium transfers genetic material to another through direct contact

Transduction

DNA is exchanged between cells by phage

Transformation

Bacteria take up DNA from the environment

CRISPR

Provides an adaptive immunity for bacteria, used for editing gene sequence

Phosphate

PO4 group, part of a nucleotide

Deoxyribose sugar

Ribose sugar with one OH group, part of a nucleotide

Nitrogenous base

A,T, G, or C part of a nucleotide

Purine

Adenine and guanine, two ring structure

Pyrimidine

Cytosine and thymine, one ring structure

T + A =

= A + G

T =

= A

C =

= G

A + T /=

/= C + G

DNA double helix

Discovered by Rosiland Franklin, struture of DNA

Antiparallel strands

Strands run in opposite direction, have 5’ and 3’ ends

Hydrogen bonds role in DNA

Bonds form based on distances between nucleotides. Allows purines to match with pyrimidines

Complementary base pairing

A binds with T, C binds with G

Semiconvervitive replication

How DNA is replicated, saves one parent strand and makes one new one

Conservative model

False idea of how DNA is replicated where both original strands go into one daughter cell, new strands go into the other

Dispersive model

False idea of how DNA is replicated, somewhere in between semi-conservative and conservative

Meselson Stahl experiment

Experiment that determined the semiconservative nature of DNA, had to do with heavy and light isotopes

Replication bubble

Place where replication happens

Replication forks

Point where strands diverge

dATP, dGTP, dCTP, dTTP

4 tri-phosphorylated nucleotides

5’ to 3’ activity

New residues added to 3’ end

3’ to 5’ exonuclease activity

Removes mismatches

5’ to 3’ exonuclease activity

Degrades single strand

DNA polymerase III

Does DNA replication, can only add nucleotides to 3’ end

RNA primer

Needed to start synthesis in both leading and lagging strands

Leading strand

Only needs one primer, replication done in one strand

Lagging strand

Needs multiple primers, replication done in okasaki fragments

Primase

Enzyme that makes RNA primer

DNA polymerase I

Removes RNA molecules and fills in gaps

DNA ligase

Connects adjacent DNA fragments

Helicase

Opens fork

B clamp

Positions polymerase III

Topoisomerase

Keeps DNA in relaxed formation

SSBP

Bind DNA and prevent re-hybridization

Replisome

Whole replicaiton complex

AT rich region

Located near single origin of replication. Necessary for replication in prokaryotes

Origin of replicaiton

OriC, only in prokaryotes, DNA A proteins bind here

Cdc6 and Cdt1

Synthesized in M and G1, joins ORC with helicase, help start replication, leave and degrade right after synthesis

Telomerase

Adds back non-coding DNA sequence back to 3’ overhang

Exons

Coding DNA

Introns

Noncoding DNA

Ribose sugar

Nucleotide sugar with 2 OH groups, found in RNA

mRNA

messenger RNA, encode proteins

functional RNA

Have some biological function other than encoding for proteins

tRNA

transfer RNA

rRNA

ribosomal RNA

snRNA

small nuclear RNAs, interact with protein subunits to form spliceosomes

miRNA

microRNAs, regulate gene expression

siRNA

small interfering RNA, protects genomes from transposons

lncRNA

long, non-coding RNA

Constitutively expressed

Always on, tRNA, rRNA , snRNA

Transcription

synthesis of RNA from DNA template

coding strand

Nontemplate strand of DNA molecule having the same sequence as that in the RNA transcript

noncoding strand

template strand with the complementary sequence of the mRNA

Initiation

Dependent on promoter sequence upstream of initiation point

Initiation point

First transcribed base, indicated by +1

5’ UTR

Untranslated region that lies between initiation point and first codon

promoter sequence

has conserved consensus sequences at -35 and -10

Elongation

Takes place in transcription bubble, energy comes from triphosphate bond

rho-dependent termination

Termination based on rho-protein binding to specific sequences on 3’ end

factor independent termination

termination based on haripin loop formed in growing DNA

Endonucleases

Cut inside DNA molecule, helps with RNA decay

Exonucleases

Cut from ends, help with RNA decay

RNA polymerase I

transcribes RNA (except 5s rRNA)

RNA polymerase II

Transcribes protein coding genes

RNA polymerase III

Transcribes small functional RNAs and 5s rRNA

GTF

general transcription factors, DNA binding proteins that form the preinitiation complex (PIC) and help RNA Polymerase II bind to the template DNA strand.

TBP

TATA binding protein, binds to TATA box of promoter

PIC

pre-initiation complex, initiated by TFIID

CTD

Carboxy terminal domain of RNA polymerase II. phosphate groups added here at start of elongation, part of PIC

TFIIB

Recruited by proteins bonded to promoter. Recruits RNA polymerase III for transcription

INR and DPE

Promoter elements similar to the TATA box. Both are DNA sequences

CTD phosphorylation purpose

Involved in different stages and modifications that take place on serine residues during elongation

Pre-mRNA

mRNA with no modifications, has introns and exons and no cap or tail

m7g cap

Modified first nucleotide

GU-AG rule

Introns have 5’ GU splice sites and 3’ AG splice sites

U1

snRNP that binds to 5’ splice site. Helps coordinate splicing

U2

snRNP that binds to branch point. Helps coordinate splicing

U4, U5, and U6

snRNPs that join the help form the spliceosome

Lariot structure

Formed to splice out intron

Alternative splicing

Multiple gene products from 1 gene

Isoforms

Multiple proteins made from alternative splicing

Torpedo termination

RNA polymerase II dissociates using exonuclease

CP complex

Cleavage and polyadenylation complex, makes PolyA tail at PloyA site

Dicer

Modifies siNA so it can be loaded into the RISC complex, part of RNA decay

RISC

Binds to and destroys mRNA transcripts in the cytoplasm

siRNA

Important for RNA decay, binds to mRNA in the cytoplasm complementary to its sequence

Amino acid

Building block for proteins

R group

Determines biochemical behavior of an amino acid

Peptide bonds

Bonds that join amino acids in a protein, has amino and carboxyl ends

Primary structure

Linear sequence of amino acids

Secondary structure

Shapes of proteins in local regions (plate and Alpha helix)

Tertiary structure

Overall shape of a protein, dictated b how the secondary structure folds

Quarternary structure

When proteins interact with the subunits and takes on a shape

Suppressor mutations

Mutations used to determine triplet code