meowlecular test chp 1-2

what direction do we always describe dna in

5’ to 3’ direction

_______ bonds connect dna nucleotides together

phosphodiester bonds

how many hydrogen bonds are between an A-T base pairing

2

how many hydrogen bonds are between an G-C base pairing

3

which bond is harder to break and y a-t or g-c. why

g-c bc it consists of more (3 compared to 2) hydrogen bonds

1 mega base consists of how many base pairs

1 million

which enzyme helps to separate strands of dna so that each strand can be used as a template

helicase

which enzyme adds base pairs in the 3 ‘ direction so that dna can be replicated

polymerase

what are the 2 functions of polymerase

• adds base pairs in the 3” direction so that dna can be replicated

• proofreading

most of our genes encode what kind of RNA

MRNA

which rna is translated into proteins

mrna

what is the most predominant rna in our cells (hint, it is not mrna)

ribosomal rna

which rna exists in the cytoplasm, aiding in translation of rna to proteins and is not translated itself

ribosomal rna

functional part of the chromosome

gene

the gene is the functional pt of the protein that includes what 2 things 5’ or 3’ to the gene

• coding information

• regulatory regions

gene regulatory rgn usually contains info on what 2 things

time where gene is expressed

place where gene is expressed

non coding rgn of gene that is excised by processing from primary transcript

intron

intron/exon contain the coding rgn

exon

t/f primary transcript has introns and exons

true

t/f: the more complex an organism is, the more exons

f; the more complex= the more introns (the more needs to be excised out)

t/f introns can vary in length and can be the bulk of a primary transcript

t

what is the function of introns

no known function

a gene group in a bacteria is called

an operon (all the genes will be involved in the same biochemical pathway)

as we increase in complexity of organism (eukaryotes/mammalia), what can be noticed about introns

• there is a lot more space between genes

• way more introns

t/f number of chromosomes = genome size

f

amount of genes/ dna in an organism

genome size

the structures around the coiling nuclear dna are called?

nucleosome

nucleosomes are a combination of?

dna and protein (specifically histone proteins)

whats a way to describe how dna wraps around histones

dna double helix wraps, like a string, around beads aka histone proteins.

what is it called when dna is wound around the histone core

octamer

nucleosomes= dna wrapped around histone core (octomer). it is then twisted onto a ____ and are then looped into a protein scaffold that is able to compact the dna into a chromosome shape.

solenoid

at the 5’ position of the ribose sugar, there is what group attached?

phosphate group (OP)

at the 3’ position of the ribose sugar, there is what group attached?

hydroxyl group (OH)

dna synthesis happens in what direction

5’ to 3’

what does it mean: “ dna synthesis happens in a 5’ to 3’ direction”

OH (3’) group always recieves from the incoming nucleotide the 5’ phosphate (PO) group and extends the 3’ end

t/f leading strand is wear synthesis can occur 5’ to 3’

t

the lagging strand is about how many base pairs slower than the leading strand

1000 bp

what are the fragments on the lagging strand called

okazaki fragments

enzyme that is a little piece of nucleotide that is like a gripping of the polymerase

primase (polymerase needs a primer/ pice of dna to prime polymeraseto have it go)

which enzymes in dna metabolization catalyze formation of the phosphodiester
bond

polymerases

which enzymes in dna metabolization unwind and untangle

helicases

which enzymes in dna metabolization synthesizes a short ribonucleic acid (RNA) to
start DNA synthesis

primase (polymerase cant latch on to one strand. it needs to have double strands in order to keep going)

which enzymes in dna metabolization cut dna

nucleases

what enzymes in dna metabolization catalyze formation of a single phosphodiester bond

ligases (glue)

what enzymes in dna metabolization add methyl groups to nitrogen bases

methyltransferases

what enzymes in dna metabolization take amino groups from nitrogen bases

deaminases

what nuclease removes bases from ends of dna strands

exonucleases

what nucleases cut dna strands internally

endonucleases

each restriction enzyme recognizes a specific ___________ double- stranded sequence

palindromic (same forward as back)

restriction endonucleases are isolated from _______

bacteria

AATT on dna cut by endonucleases are termed what and why

sticky ends; are free and can attach to any other complimentary piece (if restriction enzyme j chops it in half, its called a blunt end and it is not as useful)

what are sticky ends sequence

5’AATT3’/3’TTAA5’

ECHOR1 was isolated from what organism

ecoli

central dogma of molecular biology

dna is the information storage system. In order to get that info and use that info, it must be transcribed into another molecule that leaves the nucleus = RNA. it is then translated into protein

information stored in dna is transferred to rna by _____ via what enzyme

transcription; rna polymerase

during rna polymerase, the information is copied from how many strands

one strand of dna

during transcription, most genes code for _____ or ____ ____ RNAs used in protein synthesis

protein or untranslated functional RNAs

____ code: what nucleotide sequence codes for what amino acid

genetic code

amino acid ___ will determine the size and the shape of the protein

sequence

the _____ sequence of the gene determines the order of amino acids in a protein, which determines shape, size, and protein function.

nucleotide sequence

rna is transcribed as a _____ stranded molecule

single stranded BUT CAN OFTEN HAVE SECONDARY STRUCTURE (appear to be double stranded as one rna will bind to itself)

is uracil a pyramidine or a purine

pyrimidine

uracil makes a hydrogen bond with what

a

what are the functional rnas

• tRNA

• rRNA

• snRNA

which rna transports amino acids to the ribosome

trna

which rna is the structural and catalytic component of ribosomes, operates with ribosomal proteins

rRNA

what RNA is the structural and catalytic component of spliceosome. functions in rna processing

snRNA

functions of r rna

• structural/catalytic component of ribosomes

fx of trna

transports amino acid to ribosome

function of snRNA (small nuclear rna)

• structural and catalytic component of spliceosome

• functions in rna processing

in order to polymerize an rna transcript, there are how many rna polymerases

3

t/f: all rna polymerases are involved in polymerization and only some of them are involved in proofreading

t

transcription steps

initiation →

• binding of RNA polymerase to promoter rgn (TATA box, CAAT box)

• unwinding via dna helicase

elongation→

• add nucleotides to 3’

• base pairing

• Magnesium needed (COFACTOR)

• energy from ntp substances

termination

• at 3’ end

• processing for mRNA

t/f either one of the strands of the dna double helix can be the template strand for rna transcription

t

the template strand for rna transcription is always determined by what

promoter region

t/f complimentary base pairing of the template strand completely matches the non template strand

f (rna transcript contains “U”)

the 1st codon of a template strand for rna transcription is always?

ATG

why is the template strand for rna transcription also called the antisense strand

the rna transcript that is produced is complimentary and not the same

why is the non template strand sometimes called the sense strand?

because minus the U, it is identical to the rna transcript

as soon as the 5’ end comes off of rna transcription, what is added to it and why

a 5’ cap- 7-METHYL-GUANOSINE- is added so the exonucleases dont come and chomp it off

5’ end of the rna transcript is needed for ____ binding

ribosome binding

what is the sequence for the polyadenylation signal and what does it do

AAUAAA; it indicates that endonuclease can cut the rna polymerase off and that the rna chain can have a poly A tail added to protect/ stabilize it as it is a single stranded molecule.

what is the poly a tail for

protection/stabilization for the unstable single stranded structure

t/f the longer the poly a tail, the longer the rna molecule will last in the cyto

t; the longer it lasts, the more protein can be produced

introns are removed how

by spiceosome (rna is edited b4 leaving the nucleus)

all introns have what kind of recognition sequence

5’GU and a 3’AG

______ of spliceosome recognize 5’GU and 3’AG of introns and splice them out

snRNPs (small nuclear ribonucleo protein)

when snRNPs of spliceosome recognize 5’GU and 3’AG of introns and splice them out, the intron is excised as a ____ and is recycled back into the body and coding exons are spliced together

lariat

what kind of rna act as transporters of amino acids during translation

tRNA (transfer rna)

tRNA ___codon binds to the ____codon of the mRNA

anticodon; triplecodon (the codon that codes for amino acid)

t/f: there are only 20 amino acids therefore different codons are used to code for the same amino acid

true (there are 65 codes)

what is the fx of r rna

translation of mrna

why is the 5’ cap important on the mRNA

• binds r rna aiding in translation

• stabilizes and protects the single stranded molecule

there are 3 ribosomal sites during translation, what are they

A, P, E

ribosomal site- A fx

amino site - accepts incoming charged tRNA

RIBOSOMAL SITE - P FX

polypeptide site - where all the peptide bonds form w all the incoming amino acids

ribosomal site: e fx

exit site - tRNA exits ribosome

at which ribosomal site does the 1st amino acid begin the peptide chain

amino site

t/f amino site/ N TERMINUS of the protein is always synthesized first

true