Chapter 6 ~ Molecular Genetics

the _____ is a theory that states that in cells, information only flows from DNA to RNA to proteins

the _____ is a theory that states that in cells, information only flows from DNA to RNA to proteins

central dogma

a _____ is the basic unit of DNA

nucleotide

a nucleotide is composed of a ______ bonded to both a ______ and a _______

sugar, phosphate group, nitrogenous base

what are the two classes of nitrogen bases found in nucleic acid?

purines, pyrimidines

the purines include _____ and _____

adenine, guanine

the pyrimidines include _____ and _____

cytosine, thymine, uracil (replaces thymine in RNA)

antiparallel DNA strands are held together by _____ _____ between the bases oriented toward the center

hydrogen bonds

in DNA, thymine forms 2 hydrogen bonds with _____

adenine

in RNA, _____ forms 2 hydrogen bonds with adenine

uracil

in DNA and RNA, guanine forms 3 hydrogen bonds with _____

cytosine

1 side of the DNA helix runs in the opposite direction to the other (5' to 3' and 3' to 5') - this is known as the __________ of DNA

antiparallel arrangement

the DNA structure was discovered by _____ and _____

Watson; Crick

what is the enzyme that breaks the hydrogen bonds between nitrogenous bases during DNA replication?

DNA helicase

the _____ is a Y-shaped region where the parental strands of DNA are being unwound

replication fork

DNA replication is _____, meaning that each daughter strand will have 1 new and 1 old strand

semiconservative

_____ is the enzyme that reads the parent DNA strand and creates a complementary, antiparallel daughter strand

DNA polymerase

DNA polymerase always reads the template strand in the _____ direction

3' --> 5'

DNA polymerase creates the complimentary strand in the _____ direction

5' --> 3'

the _____ is the DNA strand that is continually synthesized by DNA polymerase

leading strand

the _____ is the DNA strand that is synthesized discontinuously, due to a limited reading direction of DNA polymerase

lagging strand

_____ are short fragments that result from the discontinuous synthesis of the lagging strand

Okazaki fragments

in RNA, thymine is replaced with _____

uracil

(both are pyrimidines)

DNA is transcribed into mRNA and arranged into triplets known as _____

codons

codons are translated from mRNA into _____

amino acids

most amino acids have more than one codon coding for them - this is known as _____ or _____

degeneracy; redundancy

_____ carries the complement of a DNA sequence from the nucleus to the ribosomes for protein synthesis

messenger RNA (mRNA)

_____ assists in translation by bringing amino acids to the ribosomes during protein synthesis

transfer RNA (tRNA)

in tRNA, triplet sequences of nucleotides that are complementary to mRNA codons are called _____

anticodons

the nucleotide structural component of ribosomes is _____

ribosomal RNA (rRNA)

mRNA sequences pass through _____ ribosomal subunits during translation

two

what is the process where DNA gene sequences are copied into mRNA?

transcription

the promoter region is where _____ binds to DNA during transcription

RNA polymerase

the _____ is a short DNA sequence found upstream from the site where transcription of a specific RNA is going to take place

promoter region

what is the typical human promoter region?

TATA box

RNA polymerase is the enzyme that binds to DNA and creates a _____

transcription bubble

RNA polymerase recruits and adds complementary _____ based on the DNA sequence during transcription

RNA nucleotides

RNA polymerase synthesizes a daughter strand of RNA in the _____ direction

5' --> 3'

_____ are extra sequences of nucleotides that are not necessary to create the corresponding protein

introns

_____ are the nucleotides necessary to make the protein

exons

the introns are _____ out by the _____ leaving only the exons behind

spliced, spliceosome

the spliceosome is only found in _____

eukaryotes

(most prokaryotes lack introns (archaea have them))

a 5' _____ _____ and a 3' _____ _____ are post-transcriptional modifications to mRNA, which provide protection against enzyme degradation after the mRNA leaves the nucleus

guanine cap, poly-A tail

translation occurs in the _____, and it is the process through which mRNA codons produce a _____

cytoplasm; polypeptide

what are the three distinct stages of translation?

initiation, elongation, termination

initiation is the stage of translation in which the ribosome binds to the mRNA near its _____

5' end

in translation initiation, the ribosome scans the mRNA until it binds to the _____

start codon (AUG)

the start codon is the codon that signals the start of translation - what is it and what amino acids does it code for?

AUG = methionine

the initiator aminoacyl-tRNA complex, _____, base pairs with the start codon during translation initiation

methionine-tRNA

_____ is the stage of translation in which hydrogen bonds form between the mRNA codon in the A site of the ribosome and its complementary anticodon on the incoming aminoacyl-tRNA complex

elongation

a _____ is formed between the amino acid attached to the tRNA in the A site and the amino acid attached the tRNA in the P site of the _____ during elongation

peptide bond; ribosome

after the peptide bond formation of elongation, a ribosome caries unbound tRNA in the _____ and peptidyl-tRNA in the _____

P site; A site

_____ is the stage of translation in which the ribosome advances three nucleotides along the mRNA in the 5' --> 3' direction

translocation

the unbound tRNA from the P site is expelled at the _____ and the peptidyl-tRNA from the A site moves into the _____ during translocation

E site; P site

a _____ is a group of several ribosomes attached to, and translating, the same messenger RNA molecule

polyribosome

_____ is the stage of translation in which 1 of 3 special mRNA codons, or stop codons, arrives in the A site

termination

_____ do not code for amino acids; rather, they signal the ribosome to stop translation (termination)

stop codons

what are the 3 stop codons?

UAG, UAA, or UGA

(they do not code for amino acids)

what is the machine that carries out translation?

ribosome

the ribosomal _____ binds to the next incoming aminoacyl-tRNA complex

A site

the _____ is the ribosomal binding site for peptidyl-tRNA

P site

the _____ releases empty tRNAs from the ribosome

E site

a _____ is a unit of chromatin consisting of a DNA strand wrapped around histone proteins

nucleosome

histone proteins are not found in _____ DNA

bacterial

each nucleosome contains _____ histone proteins

nine

which histone protein keeps the DNA wrapped around the histone core in a nucleosome?

H1

_____ represents parts of DNA that consist of "loosely-packed" nucleosomes

euchromatin

euchromatin is _____ for RNA polymerases to access and transcribe

easy

_____ represents parts of DNA that consist of "tightly-packed" nucleosomes

heterochromatin

heterochromatin tends to be _____ in transcription

inactive

histones are _____ charged

positively

DNA is _____ charged

negatively

acetylation of histones increases _____ levels and therefore increases _____

euchromatin; transcription

deacetylation of histones increases _____ levels and therefore decreases _____

heterochromatin; transcription

histone methylation _____ DNA transcription levels

both increases and decreases

DNA methylation typically _____ transcription levels

decreases

what is the origin of replication?

particular sequence of DNA where replication begins

how does the origin of replication differ between eukaryotic and bacterial DNA?

bacteria only have one origin, while eukaryotes have multiple

each single strand of DNA is made of a chain of nucleotides, which are linked together by _____ bonds

phosphodiester

the ______ end of DNA has the terminal phosphate group

5'

the _____ end of DNA has the terminal hydroxyl group

3'

origins of replication tend to occur at _____ rich segments

A=T

after helicase unzips DNA during replication, _____ attach to each strand of uncoiled DNA to keep them separated

single-strand binding proteins

_____ creates small nicks within the DNA double helix ahead of the replication fork, to relieve tension created by DNA helicase

topoisomerase

_____ is a subtype of DNA topoisomerase found in bacteria and plants

DNA gyrase

_____ are sequences of repeated nucleotides at the end of a chromosome that don't code anything

telomeres

telomeres are only necessary in ______ organisms

eukaryotic

why are telomeres not necessary in prokaryotes?

they have circular chromosomes

_____ is an enzyme that catalyzes the lengthening of telomeres in eukaryotic cells

telomerase

DNA polymerase can only add DNA nucleotides off an existing _____

3' hydroxyl group

_____ provides a 3' hydroxyl group for DNA polymerase to attach new nucleotides to

primase

a _____ is a protein that helps to hold DNA polymerase to the template strand

DNA sliding clamp

_____ is an enzyme that covalently links DNA ends together, which is important for connecting Okazaki fragments

DNA ligase

in prokaryotes, transcription occurs in the _____ (location)

cytosol

which two elements are present in bacterial promoters that help initiate transcription?

-10 and -35 elements

prokaryotic core RNA polymerase combines with _____ to form _____, which has the ability to target the promoter region of bacterial DNA

sigma factor; RNA polymerase holoenzyme

what are the two types of transcriptional termination in bacteria?

rho dependent, rho independent

an _____ is when a group of related genes are under the control of 1 promoter site, and they function to make sure the cell conserves its resources

operon

the _____ is an inducible operon that aids in control of transcription of lactose metabolizing genes in E. coli

lac operon

an _____ operon is one that is usually inactive, unless it is made to become active

inducible

a gene that is always being transcribed and translated is _____ expressed

constitutively