DAT Bootcamp: Chapter 6: Molecular Genetics

central dogma

theory that states that, in cells, information only flows from DNA to RNA to proteins

nucleotide

the basic unit of DNA

sugar, phosphate group, nitrogenous base

a nucleotide is composed of a _____ bonded to both a _____ _____ and a _____ _____

purines, pyrimidines

What are the two types of nitrogen bases found in nucleic acid?

adenine, guanine

the purines in DNA include _____ and _____

cytosine, thymine

the pyrimidines in DNA include _____ and _____

hydrogen bonds

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

adenine

in DNA, thymine forms two hydrogen bonds with _____

cytosine

in DNA, guanine forms three hydrogen bonds with _____

antiparallel arrangement

one side of the DNA helix runs in the opposite direction to the other 5' to 3' and 3' to 5'; this is know as an _____ _____

Watson, Crick

the DNA structure was discovered by _____ and _____

topoisomerase

enzyme that uncoils the strands of DNA during replication

DNA helicase

enzyme that breaks the hydrogen bonds between the nitrogenous bases of each nucleotide during DNA replication

replication fork

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

semiconservative

type of replication in which new DNA consists of one parental strand and one daughter strand

DNA polymerase

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

three, five

DNA polymerase always reads the parent strand in the _____ prime to _____ prime direction

five, three

DNA polymerase creates the daughter strand in the _____ prime, _____ prime direction

leading strand

DNA strand that is continually synthesized by DNA polymerase as it moves down the parent strand and adds nucleotides

lagging strand

DNA strand synthesized discontinuously due to limited reading direction of DNA polymerase

Okazaki fragments

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

uracil

in RNA, thymine is replaced with _____

codons

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

amino acids

codons are translated from mRNA into _____

degeneracy, redundancy

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

messenger RNA (mRNA)

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

transfer RNA (tRNA)

assists in the translation of mRNA's nucleotide code into a sequence of amino acids by bringing the amino acids coded for in the mRNA sequence to the ribosomes during protein synthesis

anticodon

in tRNA, a triplet of nitrogenous bases that is complementary to a specific codon in mRNA

ribosomal RNA (rRNA)

a structural component of ribosomes; the mRNA sequence passes through two subunits of this structure and is translated into amino acids at this time

transcription

the organic process whereby the DNA sequence in a gene is copied into mRNA

promoter region

where RNA polymerase binds to the DNA; it's a short DNA sequence found upstream from the site where transcription of a specific RNA is going to take place; in humans commonly known as a TATA box

RNA polymerase

enzyme that binds to the DNA molecule and initiates transcription; recruits and adds complementary RNA nucleotides based on the DNA sequence; creates a new daughter strand of RNA in the 5-3 direction

introns

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

exons

the nucleotides necessary to make the protein

spliced, splicesome

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

guanine cap, poly-A tail

a _____ _____ and a series of adenines known as a _____ _____ are added to the ends of the new molecule to provide protection from enzyme degradation once the RNA leaves the nucleus

translation

process through which mRNA codons are translated into a sequence of amino acids; occurs in the cytoplasm

initiation, elongation, translocation, termination

four distinct stages of translation

initiation

stage of translation in which the ribosome binds to the mRNA near its 5 prime end; the ribosome scans the mRNA until it binds to a start codon; the initiator aminoacyl-tRNA complex, methionine-tRNA base pairs with the start codon

elongation

stage of translation in which hydrogen bonds from between the mRNA codon in the A site of the ribosome and its complementary anticodon on the incoming aminocyl-tRNA complex; a peptide bond is formed between the amino acid attached to the tRNA in the A site and the amino acid attached th=o the tRNA in the P site of the ribosome; after the peptide bond formation , a ribosome caries uncharged tRNA in the P site and peptidly-tRNA in the A site

translocation

stage of translation in which the ribosome advances three nucleotides along the mRNA in the 5-3 prime direction; the uncharged tRNA from the P site is expelled and the peptidyl-tRNA from the A site moves into the P site; the ribosome then has an empty A site ready for the entry of the aminoacyl-tRNA corresponding to the next codon

termination

stage of translation in which one of three special mRNA codons, or stop codons, arrives in the A site; these codons signal the ribosome to stop translation; they do not code for amino acids

polyribosome

A group of several ribosomes attached to, and translating, the same messenger RNA molecule

stop codon

signals the end of the amino acid chain;

UAG, UAA, or UGA

start codon

AUG; the codon that signals the start of translation

ribosome

where translation takes place

A site

binding site for tRNA; binds to the next incoming tRNA complex

P site

binding site for tRNA; where the tRNA contributes its amino acid to the growing polypeptide chain

E site

binding site for tRNA; having already given up its amino acid, the tRNA is released here

double

adenine and guanine are _____-ringed nitrogen bases

single

thymine, cytosine, and uracil are _____-ringed nitrogen bass

2

adenine bonds with thymine and uracil with _____ hydrogen bonds

3

cytosine bonds with guanine with _____ hydrogen bonds

nucleosome

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

bacterial

histone proteins are not found in _____ DNA

9

each histone contains _____ histone proteins

H1

which histone protein keeps the DNA wrapped around the histone core?

euchromatin

represents parts of your DNA that consists of "loosely-packed" nucleosomes; meaning it is easy for RNA polymerases to access the DNA code and

transcribe our genes.

heterochromatin

represents parts of your DNA that consist of "tightly-packed" nucleosomes; these areas of DNA tend to be inactive in transcription.

positively

histones are _____ charged

negatively

DNA is _____ charged

acetylation

_____ of positively charged amino acids removes the positive charge of histones, relaxing the electrostatic attraction between the histones and the DNA. This relaxation means DNA is more loosely packed and increases transcription levels.

increases

acetylation _____ transcription levels.

deacetylation

_____ makes histones more positively charged, making them more tightly bound to negatively charged DNA. Since the DNA is more tightly bound, there is a decrease in transcription levels.

decreases

deacetylation _____ transcription levels

methylation

______ adds non-polar methyl groups to the histone, and reduces DNA transcription.

decreases

methylation _____ DNA transcription levels

phosphodiester

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

5'

the ______ end of DNA has the terminal phosphate group

phosphate

the 5' end of DNA has the terminal _____ group

3'

the _____ end of DNA has the terminal hydroxyl group

hydroxyl

the 3' end of DNA has the terminal _____ group

AT

Origins of replication tend to occur at _____ rich segments

helicase

_____ is the enzyme that 'unzips' the wound DNA double helix by breaking the hydrogen bonds between complementary purines and pyrimidines

single-strand binding proteins

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

topoisomerase

As helicase unwinds the DNA, it actually creates tension ahead of the replication fork (where the strands separate). To relieve this tension, _____ creates small nicks within the DNA double helix.

DNA gyrase

a subtype of DNA topoisomerase found in bacteria and plants

DNA polymerase

the enzyme which adds new nucleotides during DNA replication

3', 5'

DNA polymerase READS the TEMPLATE strand in the _____ → _____ direction

5', 3'

DNA polymerase EXTENDS the COMPLEMENTARY strand in the _____→ _____ direction

telomeres

sequences of repeated nucleotides at the end of a chromosome that don't code anything; they're basically a 'buffer' for the real genetic code we actually use. This way, as replication occurs and that small segment of DNA at the end is not replicated, we don't lose crucial pieces of genetic information

eukaryotic

telomeres are only necessary in ______ organisms

circular

telomeres are not necessary in prokaryotes because they have _____ chromosomes

telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic cells.

primase

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

DNA sliding clamp

Helps to hold DNA polymerase to the template strand

DNA ligase

Enzyme that covalently links the Okazaki fragments together.

S

DNA replication takes place during the _____ phase of the cell cycle

G₀

If the cell does not meet the criteria for entrance into the S phase, it will remain in _____. This is basically like a waiting room where the cell does not grow, nor will it replicate its DNA.

5', 3'

during transcription, RNA will extend in the _____ → _____ direction

cytosol

in prokaryotes, transcription occurs in the _____

sigma factor

While prokaryotic core RNA polymerase is able to bind directly to prokaryotic DNA, it

lacks the ability to target promoter sites. To work around this, prokaryotic core RNA

polymerase combines with _____ to form RNA polymerase holoenzyme . It provides RNA polymerase holoenzyme the ability to target the promoter region of bacterial DNA.

RNA polymerase holoenzyme

While prokaryotic core RNA polymerase is able to bind directly to prokaryotic DNA, it

lacks the ability to target promoter sites. To work around this, prokaryotic core RNA

polymerase combines with sigma factor to form _____ . The sigma factor provides this new enzyme the ability to target the promoter

region of bacterial DNA.

rho dependent, rho independent

two types of termination in bacteria

operon

An _____ is when a group of related genes are under the control of one promoter site.

They are common in prokaryotes as a way to regulate genes as a group; however, they

are sometimes found in eukaryotes as well. The function is to make sure the cell conserves its resources unless those resources are required.

lac operon

operon that aids in control of transcription of lactose metabolizing genes in E. coli

inducible

An _____ operon is one that is usually inactive , unless it is caused to become active .

constitutively

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

inversely

cAMP is _____ related to glucose levels

repressible

A _____ operon is one that is usually active, unless turned off somehow.