bio 108 quiz 3

nucleotides

• RNA has ribose

• DNA has deoxyribose

• ribose has an OH bond at C2’

• deoxyribose has an H bond at C2’

yes, RNA can have double stranded regions which are self complementary

• this is known as a stem loop

you need all the 4 bases to form a stem loop

• DNA is double stranded and antiparallel

• Guanine (G)

• Adenine (A)

• Thymine (T)

• Cytosine (C)

• Guanine (G)

• Adenine (A)

• Uracil (U)

• Cytosine (C)

pyrimidines refers to bases with single ring structures

• Cytosine, Thymine, and Uracil are considered pyrimidines

purines refers to bases with double ring structures

• Adenine and Guanine

base + ribose or deoxyribose + phosphate

base + ribose or deoxyribose

• at C5, thymine has a methanol group,

• at C5, uracil has a hydrogen group

• A - T

• G - C

• A - U

• G - C

purines pair with pyrimidines by hydrogen bonding

G-C base pairs have 3 H-bonds which are harder to separate than A-U or A-T base pairs which have 2 H-bonds

these regions are A-T rich because A-T is easier to separate than G-C

they form a double helix

• all DNAS

its called the primer strand

its the template strand

by the addition of DNA precursor molecules called deoxynucleotide triphosphate

they are referred to as dNTPs

• dATP,

• dCTP,

• dGTP

• dTTP

it stands for deoxyribose

N can stand for A, C, T, or G.

1. the 3’ end of the primer strand has an OH group

2. the oxygen (O) from that hydroxyl group attacks the alpha phosphate of a DNA precursor

it is called 5’ to 3’

• this is because 3’ side is where the new bases are continuously being added

the 3’

1. the alpha phosphate breaks from dNAP, releasing 2 phosphates that are linked together, called pyrophosphate

2. a new bond is formed called a phosphoester bond

DNA synthesis begins with short pieces of RNA (10-15 nucleotides)

DNA synthesis must occur on both strands of DNA in order to convert two strands into four

the site where both strands of DNA are being replicated

it synthesize in a continuous way. this is known as a leading strand

it synthesizes in a discontinuous way (in fragments). this is known as a lagging strand

okazaki fragments

because DNA synthesis only occurs in 5’ to 3’ direction

• continuous DNA synthesis already moves from 5’ to 3’

• discontinuous DNA synthesis occurs in lagging strands because its moving in the wrong direction relative to the direction of the replication fork.

its known as replication origin

it begins and proceeds bidirectionally (both ways)

• this leads to two replication forks

its called DNA helicase

• it separates the two strands by surrounding itself on one strand and moves down.

it creates knots as its is separating the strands

its called DNA topoisomerase

• it removes the knots created by the DNA helicase

no its not directly associated with the replication fork.

it refers too Single Strand (DNA) Binding proteins

• it protects and organizes single stranded DNA

• DNAP III- Core

• Clamp

• Clamp Loader

• DNA Primase

it does DNA synthesis and has 3 peptides

• surrounds DNA strands and prevents DNAP from dissociating

• donut shaped and is behind core

• adds and removes clamps and DNAP III Core from double-stranded DNA when appropriate

• interacts with core

has 5 peptides

it synthesize the RNA primers needed to start DNA syhthesis

only 1 clamp loader which intersects with clamp and core complexes on both DNA strands.

SSB and Topoisomerase

a loop

genome

RNA polymerase (RNAP)

a process by which RNA polymerase (RNAP) copies one of the two strands of DNA to make RNA

all RNAs are made during transcription by a RNAP, some include

• messenger RNA (mRNA)

• ribosomal RNA (rRNA)

• transfer RNA (tRNA)

• Noncoding RNA (ncRNA)

mRNA

a process by which mRNA encodes a sequence that a ribosome copies to make a protein

a term used to describe the two steps transcription and translation, but this term is arcane, and few people use it now. 

one

three

rRNA

mRNA

tRNA

its the same idea as a DNAP

• the oxygen (O) from that hydroxyl group attacks the alpha phosphate of an RNA precursor

• a phosphoester bond also forms

5’ to 3’ - same as DNAP

RNAP does not require a primer, while DNAP does.

• ATP

• CTP

• GTP

• UTP

yes

transcribed strand

non-transcribed strand

it corresponds to the sequence of the non-transcribed strand (except the T is replaced by a U)

• this is because RNA precursors are inserted opposite of the DNA strand by base pairing

it is similar in all species

1. initiation

2. elongation

3. termination

RNAP is aided by auxiliary transcription factors which are proteins

• often abbreviated “TF”

• RNAP has 6 subunits (polypeptides)

  • one of the subunits is called sigma

• sigma recognizes 2 specific DNA sequences near TSS (transcription start site)

+1

the consensus sequences are 6 base pairs that are recognized by sigma. they occur at two specific DNA regions

• -35 sequence

• -10 sequence

it refers to the RNAP binding sites:

• -50 to +20

  • it includes the consensus sequence

it also separates DNA strands

yes, it occurs +1 position

• there is no RNAP subunit that recognizes the transcription start site (TSS)

• RNAP interacts with general transcription factors “GTFs” that bind around TSS

• TBP: its binds at -30

• TF(2)B: it binds at -35 and -25

  • upstream and downstream of TBD

GTFs form a huge complex of approx a 100 peptides

separated by GTFs: TF(2)B and TF(2)H

its goes from - 150 to +40

• corresponds to where nucleosomes must be removed to allow GTFs and RNAP to bind

• protein complex with 8 histone proteins

• DNA is wrapped around histones in eukaryotic celles

-1 nucleosome is removed where GTF and RNAP bind at -150 to +40

• organize and condense DNA

  • human diploid DNA is 2ft long and must fit into the nucleus

two types of transcription factors (TFs) control when transcription starts

• activators

• repressors

it has a positive role

• TF (aka activator) binds with DNA and recruits RNAP, leading to transcription to occur

it has a negative role

• TF (aka repressor) is bound to DNA and prevents RNAP from binding. when TF is released, that’s when RNAP binds

OFF

ON

• no transcription is occurring

• there is no lactose inside or outside the cell

• transcription is occuring

• lactose outside the cell

• no glucose oustide the cell

its means that it is repressor bound

its means that the repressor is released

it means that the activator is binding

• when repressor protein is not bound because it senses high lactose levels

• when activator proteins are bound because it senses low glucose levels

• regulatory region

• transcribed region