genetics test 3

how long is an unwound strand of human DNA?

2 meters (6 feet)

histone tails

• part of nucleosome

• flexible

• N-terminal or C-terminal amino acid extensions

• extend from nucleosome core histone proteins

• crucial for chromatin regulation (gene expression)

nucleotide

• monomer of nucleic acids (DNA or RNA)

• 3 components:

  • nitrogenous base

  • pentose sugar

  • phosphate group

nitrogenous base

attaches to 1’ carbon

pentose sugar

hydroxyl attaches to 3’ carbon

phosphate group

attaches to 5’ carbon

pyrimidines

• one ring

• attach via 1st member in the ring

• includes:

  • cytosine

  • thymine

  • uracil

purines

• two rings

• attach via 9th member in the ring structure

• includes:

  • adenine

  • guanine

what bases are found in DNA?

• adenine

• thymine

• guanine

• cytosine

what bases are found in RNA?

• adenine

• uracil

• guanine

• cytosine

ribose

• used in RNA

• OH- group

deoxyribose

• used in DNA

• H- group

• without oxygen

difference between nucleoside and nucleotide

• nucleoside

  • composed of pentose sugar and nitrogenous base

• nucleotide

  • composed of pentose sugar, nitrogenous base, and phosphate group

monophosphate

one phosphate group

diphosphate

two phosphate groups

triphosphate

three phosphate groups

how is DNA made?

• two nucleotide join through dehydration synthesis

  • results in the creation of H2O

• elongated as the new nucleotide is attached to the 3’ carbon because of hydroxyl group

Watson-Crick model (Rosalind Franklin’s model)

• two long strands in a double helix

• the two chains are antiparallel

• orientation of the 3’ and 5’ carbons run in opposite directions

• bases are flat, “stacked” on one another

• nitrogenous bases are paired via hydrogen bonds

• each complete turn of helix is 3.4 nm or 10 base pairs

• double helix measures 2.0 nm in diameter

oligonucleotides

• short chains of DNA

• consists of up to 20 nucleotides

polynucleotides

• long chains of DNA

• consists of more than 20 nucleotides

hydrogen bonds

• weak electrostatic attraction between a covalently bonded H atom and another electronegative atom

• weak bond allows strands to separate

  • makes replication and transcription possible

• guanine and cytosine have 3 hydrogen bonds

• adenine and thymine have 2 hydrogen bonds

RNA structure

• ribose replaces deoxyribose

• uracil replaces thymine

• most are single-stranded (ssRNA)

  • animal viruses are double-stranded (dsRNA)

three major classes of RNAs

• rRNA

• mRNA

• tRNA

rRNA

• ribosomal RNA

• structural component of ribosomes for protein synthesis during translation

mRNA

• messenger RNA

• template for protein synthesis

• carry genetic information from gene to ribosome

tRNA

• transfer RNA

• carry amino acids to the ribosomes for protein synthesis

replication

• create identical copies of the cell’s genetic material

• must be precise for genetic continuity

suggested models of DNA replication

• conservative: the two new strands are paired together

• semiconservative: the two new strands are each paired with one original strand

• dispersive: the two new strands are cut and dispersed within the two original strands

semiconservative replication

• accepted model for replication in viruses, prokaryotes, and eukaryotes

• each newly created strand contains one original strand and one new strand

attributes of DNA replication shared by all organisms

• each strand of parental DNA remains intact

• each parental strand serves as a template for an antiparallel, complementary daughter strand

• completion results in two identical daughter duplexes - one daughter strand and one parental strand

origin of replication (ORI)

place where DNA replication begins

replication fork

• where helix is unwound at site of replication

• there are two replication forks

replicon

the length of DNA replicated

DNA polymerase III

responsible for 5’ to 3’ polymerization in vivo

DNA polymerase I

removes primers and synthesizes/fills in gaps produced after removal

DNA polymerase II, IV, V

involved in various aspects of DNA repair damaged by external force like UV light

DNA polymerase III holoenzyme

• active form of DNA polymerase III

• contains core enzyme complexes made up of subunits

• provides catalytic function

processivity

ability of an enzyme to catalyze consecutive reactions dissociated from the substrate

helicase

unwinds helix

gyrase (type of topoisomerase)

reduces coiling generated during unwinding

single-stranded binding proteins (SSBs)

prevents unwound DNA from reannealing

primase

synthesizes RNA primers for initiation

lagging strand and okazaki fragments

discontinuous synthesis of second strand

DNA polymerase I

removes RNA primers

ligase

joins two strand of DNA together; “fills the gap”

DNA polymerase III (epsilon subunit)

proofreading

DNA polymerase a

• adds RNA primers to both leading and lagging strands of DNA

• low processivity

• quickly dissociates - leads to a process called polymerase switching

DNA polymerase ɛ and δ

• extends primers

• adds DNA nucleotides through elongation

• proofreads

telomeres

• long stretches of short repeating sequences

• preserve the integrity/stability of chromosomes

• sequence in humans: 5’ - TTAAGGG - 3’

telomerase

can add more repeats to the end of a telomere

euchromatin

regions that contain actively expressed genes and are less condensed during interphase

heterochromatin

regions that remain condensed in interphase and contain fewer expressed genes

chromatin remodeling

• histone tails extend from histones and pass through the minor groove of DNA

• potential targets for modification

histone modifications

• acetylation

• methylation

• phosphorylation

acetylation

• adds an acetyl group to the tail via histone acetyltransferase (HAT)

• works to open the chromatin

• allow for gene expression

methylation

• adds a methyl group to the tail via methyltransferase

• can either increase or decrease transcription

phosphorylation

• adds a phosphate group to the tail via a kinase enzyme

• related to cycle of chromatin unfolding and condensation that occurs during and after replication

central dogma

• the flow of information in a cell

• DNA to RNA to protein

transcription

uses DNA template to create a gene copy that is held in mRNA

translation

creates a polypeptide chain from the mRNA gene copy

genetic code

• written in linear form

• uses ribonucleotide bases that compose mRNA

• each “word” consists of three ribonucleotide letters

• unambiguous

unambiguous

each triplet specifies only one amino acid

codon

every three ribonucleotides in mRNA

degenerate

• a given amino acid can be specified by more than one triplet code

• redundancy in the code

the wobble hypothesis

• relaxed base pairing is required in the third position (wobble)

• initial two ribonucleotides of the triplet code are often more critical than the third

• third position is less spatially constrained

  • does not adhere as strictly to established base-pairing rules

start and stop signals

triplets that initiate and terminate translation

methionine (AUG)

• initiator codon

• first amino acid added to the protein

UAG, UAA, UGA

• termination codons

• don’t code for an amino acid

commaless

once translation begins, codons are read with no break/no skips

nonoverlapping

any single ribonucleotide within mRNA is part of one triplet

overlapping genes

• a single mRNA can have multiple initiation points

• creates different reading frames

RNA polymerase

• directs RNA synthesis

• uses a DNA strand as a template

• assembles a complementary, antiparallel strand of ribonucleotides

• no primer necessary

• contains subunits α, β, β’, and ω (omega)

coding strand of DNA

• called nontemplate or complementary strand

• complementary to the template strand

σ (sigma) factor

• holoenzyme of RNA polymerase

• plays regulatory function in the initiation of RNA transcription

essential steps of transcription in E. coli

1. promoter recognition

   1. sigma factor recognizes specific start sequence in template DNA

2. transcription initiation

   1. RNA binds to promoter

   2. DNA unwinds

3. chain elongation

   1. RNA polymerase synthesizes a complementary RNA strand

4. chain termination

   1. transcription stops

   2. RNA polymerase reaches terminator sequence

   3. polymerase detaches

promoter

• immediately upstream (5’)

• referred to as the +1 nucleotide

• controls access of RNA polymerase to the gene

coding region

portion of the gene that contains the information needed to synthesize the protein product

termination region

• regulates cessation of transcription

• immediately downstream (3’)

transcription termination in bacteria

• termination sequence in RNA causes newly formed transcript to fold inwards on itself

  • hairpin secondary structure

• sometimes depends on rho termination factor

transcription in eukaryotes

• occurs in nucleus

• mRNA must leave nucleus for translation

• 3 forms of RNA polymerase are needed

• chromatin remodeling occurs

• RNA polymerases rely on general transcription factors (GTFs) to bind DNA

• enhancers and silencers control transcription regulation

chromatin remodeling

chromatin must uncoil to make DNA accessible to RNA polymerase (acetylation)

RNA polymerase I (RNAP I)

transcribes 3 ribosomal RNA genes

RNA polymerase II (RNAP II)

• transcribes protein-coding genes and most small nuclear RNA genes

• dependent on cis-acting and trans-acting transcription factors

• core promoter determines where RNAP II binds to DNA

RNA polymerase III (RNAP III)

transcribes tRNA, one small nuclear RNA, and one rRNA

cis-acting transcription factors

• adjacent parts of same DNA molecule

• includes promoters, enhancers, and silencers

trans-acting transcription factors

• bind to cis-acting DNA elements to influence gene expression

• includes factors, activators, and repressors

eukaryotic promoter elements

• TATA box (Goldberg-Hogness)

  • most common promoter sequence

  • 5’ - TATAAA -3’

• CAAT box

  • often found near -80 position

• GC-rich box

  • 5’ - GGGCGG - 3’

  • located at -90, further upstream

four cis-acting DNA elements regulate transcription initiation

• core promoter (TATA box)

• proximal-promoter elements

• enhancers

• silencers

general transcription factors (GTFs)

• essential

• RNAP II cannot bind without them

transcriptional activators and repressors

bind to enhancer and silencer to regulate transcription

termination of transcription in eukaryotes

• no specific sequence

• polyadenylation signal sequence

  • RNAP II transcribes until it reaches poly-A tail (AAUAAA)

  • transcript is cleaved

5’ capping

• 7- methylguanosine

• added by guanylyl transferase

• stabilizes and protects mRNA from nuclease attack

• facilitates transport and splicing

• orients ribosomes during translation

3’ polyadenylation

• poly-A polymerase catalyzes addition of poly-A tail at 3’-OH end

• protects from degradation

• facilitates transport

• aides ribosomal recognition

intron splicing

• removal of non-coding regions of mRNA

• removes introns

• joins together exons

introns

noncoding internal sequences that are removed during RNA processing

exons

sequences that are retained and expressed

alternative splicing

• single mRNA transcript is processed into multiple mRNA isoforms

• allows one gene to code for multiple proteins

translation

• polymerization of amino acids into polypeptide chains

• requires ribosomes and tRNAs

transfer RNAs (tRNAs)

• adapt specific triplet codons in mRNA to a correct amino acid

• tRNA anticodons complement mRNAs

ribosomes

• have essential role in expression of genetic information

• consist of ribosomal proteins and ribosomal RNAs (rRNAs)

• consist of large and small subunits