bio 108 quiz 3

what are monomers of nucleic acids

nucleotides

what sugar does RNA and DNA have.

• RNA has ribose

• DNA has deoxyribose

what is the structural difference between ribose and deoxyribose

• ribose has an OH bond at C2’

• deoxyribose has an H bond at C2’

can RNA be double stranded? what is the structure known as

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

• this is known as a stem loop

what is need to form a stem loop

you need all the 4 bases to form a stem loop

describe the strands of DNA

• DNA is double stranded and antiparallel

what are the DNA nucleobases

• Guanine (G)

• Adenine (A)

• Thymine (T)

• Cytosine (C)

what are the RNA nucleobases

• Guanine (G)

• Adenine (A)

• Uracil (U)

• Cytosine (C)

what are pyrimidines? what bases are considered pyrimidines

pyrimidines refers to bases with single ring structures

• Cytosine, Thymine, and Uracil are considered pyrimidines

what are purines? what bases are considered purines

purines refers to bases with double ring structures

• Adenine and Guanine

what are the components that made up a nucleotide

base + ribose or deoxyribose + phosphate

what are the components that made up a nucleoside

base + ribose or deoxyribose

what is the difference between thymine and uracil

• at C5, thymine has a methanol group,

• at C5, uracil has a hydrogen group

describe the complementary base pairing in DNA

• A - T

• G - C

describe the complementary base pairing in RNA

• A - U

• G - C

describe how complementary base pairing occurs

purines pair with pyrimidines by hydrogen bonding

which base pair is harder to separate?

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

describe the regions of DNA where a separation happens

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

what does two DNA strands form

they form a double helix

• all DNAS

what is the name of the strand that is synthesized during DNA Replication

its called the primer strand

what is the name of the strand that is copied during DNA replication

its the template strand

how does the primer strand elongate during DNA replication

by the addition of DNA precursor molecules called deoxynucleotide triphosphate

what falls under deoxynucleotide triphosphate? what are they referred to as?

they are referred to as dNTPs

• dATP,

• dCTP,

• dGTP

• dTTP

what does the “d” stand for in dNTPs

it stands for deoxyribose

what does the “N” stand for in dNTPs

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

describe the reaction and the mechanisms involved in dna replication

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

what is the name of the direction of DNA synthesis

it is called 5’ to 3’

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

what length is getting longer in the primer strand

the 3’

what happens to a dNAP during DNA synthesis

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

what does DNA synthesis begin with?

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

what must occur in order to convert two strands of DNA into four

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

what is a replication fork

the site where both strands of DNA are being replicated

describe what happens with the top strand in a replication fork. what is the name given to it

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

describe what happens with the bottom strand in a replication fork. what is the name given to it

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

what is the name given to the fragments seen in discontinuous DNA synthesis

okazaki fragments

what causes the difference between continuous and discontinuous DNA synthesis

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.

what is the site where DNA synthesis begins known as

its known as replication origin

how does replication begin and proceed? what does this lead to

it begins and proceeds bidirectionally (both ways)

• this leads to two replication forks

what is the first protein added to a DNAP replication fork? what does it do

its called DNA helicase

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

what does DNA helicase creates while separating the strands

it creates knots as its is separating the strands

what is the an additional protein added to a DNAP replication fork after the DNA helicase? what does it do

its called DNA topoisomerase

• it removes the knots created by the DNA helicase

is DNA topoisomerase in the replication fork

no its not directly associated with the replication fork.

what does the term SSB refer too? what do they do?

it refers too Single Strand (DNA) Binding proteins

• it protects and organizes single stranded DNA

what are the proteins involved in leading and lagging strand synthesis

• DNAP III- Core

• Clamp

• Clamp Loader

• DNA Primase

what does DNAP III - Core do?

it does DNA synthesis and has 3 peptides

what does the clamp do

• surrounds DNA strands and prevents DNAP from dissociating

• donut shaped and is behind core

what does the clamp loader do

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

• interacts with core

has 5 peptides

what does DNA primase do

it synthesize the RNA primers needed to start DNA syhthesis

describe the coupling between leading and lagging strands

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

what proteins although involved in the synthesis aren’t in the fork

SSB and Topoisomerase

what need to occur for lagging strand synthesis to happen

a loop

what term is referred to all of the DNA in an organism

genome

what synthesizes RNA

RNA polymerase (RNAP)

describe transcription

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

what type of RNAs are made during transcription?

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

• messenger RNA (mRNA)

• ribosomal RNA (rRNA)

• transfer RNA (tRNA)

• Noncoding RNA (ncRNA)

what is the only RNA, that is translated into proteins?

mRNA

describe translation

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

what does the term central dogma refer to?

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

how many types of RNAP are in bacteria

one

how many types RNAP are in eukaryotes

three

what does RNAP 1 transcribe

rRNA

what does RNAP 2 transcribe

mRNA

what does RNAP 3 transcribe

tRNA

describe the mechanisms of RNAP

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

describe the direction of RNAP during RNA synthesis

5’ to 3’ - same as DNAP

what is one notable differnce between RNAP and DNAP

RNAP does not require a primer, while DNAP does.

what are the RNA precursors

• ATP

• CTP

• GTP

• UTP

is the RNA precursor ATP, the same as the one used in high energy reaction

yes

what is the name of DNA strand being copied during RNA synthesis

transcribed strand

what is the name of DNA strand not being copied during RNA synthesis

non-transcribed strand

which of the DNA strands does the newly created RNA sequence correspond to in RNA synthesis

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

describe RNAP in all species

it is similar in all species

what are the three phases of transcription

1. initiation

2. elongation

3. termination

what is RNAP aided by during the initiation phase of transcription

RNAP is aided by auxiliary transcription factors which are proteins

• often abbreviated “TF”

describe the process of transcription in bacteria

• RNAP has 6 subunits (polypeptides)

  • one of the subunits is called sigma

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

at what position is the transcription start site (TSS) in bacteria

+1

what are the consensus sequences and what is their importance during transcription in bacteria.

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

• -35 sequence

• -10 sequence

what does the term promoter refer to in transcription in bacteria

it refers to the RNAP binding sites:

• -50 to +20

  • it includes the consensus sequence

what does sigma also do during transcription in bacteria

it also separates DNA strands

is the position of TSS the same in eurkayotes

yes, it occurs +1 position

describe the process of trancription in eukaryotes

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

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

what are two examples of GTFs and where do they bind in eukaryotes

• TBP: its binds at -30

• TF(2)B: it binds at -35 and -25

  • upstream and downstream of TBD

what do GTFs form in eukaryotes

GTFs form a huge complex of approx a 100 peptides

what are DNA strands at TSS separated by in eukaryotes?

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

what is the eukaryote promoter definition at BU?

its goes from - 150 to +40

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

what are nucleosomes

• protein complex with 8 histone proteins

• DNA is wrapped around histones in eukaryotic celles

which nucleosome is removed?

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

what is the purpose of nucleosomes

• organize and condense DNA

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

what controls when transcription starts?

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

• activators

• repressors

describe the role of activators

it has a positive role

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

describe the role of repressors

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

what is term is applied when no transcription is occurring

OFF

what is term is applied when transcription is occurring

ON

using the example of lactose metabolism, describe what happens when a repressor is bound to the DNA

• no transcription is occurring

• there is no lactose inside or outside the cell

using the example of lactose metabolism, describe what happens when a activators is bound to the DNA

• transcription is occuring

• lactose outside the cell

• no glucose oustide the cell

what does having no lactose outside a cell correlate to in terms of transcription in lactose metabolism

its means that it is repressor bound

what does having lactose outside a cell correlate to in terms of transcription in lactose metabolism

its means that the repressor is released

what does having no glucose outside a cell correlate to in terms of transcription in lactose metabolism

it means that the activator is binding

what are two instances when transcription is highest in lactose metabolism

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

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

what are the two regions in a gene in a eurkaryote

• regulatory region

• transcribed region