AP Bio Unit 6

DNA and RNA

the primary sources of heritable information, which transmitted from one generation to the next through one of the two.

genetic information

stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.

circular; linear

b. Prokaryotic organisms typically have ________ chromosomes, while eukaryotic organisms typically have multiple ________ chromosomes.

plasmids

Prokaryotes and eukaryotes can contain these, which are small extra-chromosomal, double-stranded, circular DNA molecules.

adenine with thymine/uracil

cytosine with guanine

DNA, and sometimes RNA, exhibits specific nucleotide base pairing that is conserved through evolution

Purines

G and A, have a double ring structure

Pyrimidines

C, T, and U, have a single ring structure.

hydrogen bonds

nucleotide bases are held together by these; 2 A-T, and 3 G-C; they are easily broken

DNA replication

ensures continuity of hereditary information; wants to occur in the direction of the fork

5’ to 3’

DNA is synthesized in the _________ direction

Replication

a semiconservative process—that is, one strand of DNA serves as the template for a new strand of complementary DNA.

Helicase

unwinds the DNA strands second, breaking hydrogen bonds

Topoisomerase

relaxes supercoiling in front of the replication fork first.

DNA polymerase

requires RNA primers (placeholders) to initiate DNA synthesis, and synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand.

leading strand

5’ to 3’ direction of replication fork

lagging strand

5’ to 3’ in opposite direction of the fork; not perfect

Ligase

joins the fragments on the lagging strand.

chromosome

DNA wraps around histones (proteins)

structure; function

The sequence of the RNA bases, together with the _____ of the RNA molecule, determines RNA _________

mRNA molecules

carry information from DNA to the ribosome; messenger

tRNA molecules

bind specific amino acids and have anti-codon sequences that base pair with the mRNA.; recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence; transfer

rRNA molecules

functional building blocks of ribosomes; ribosomal

DNA to mRNA to amino acids

Genetic information flows from a sequence of nucleotides in ____ to a sequence of bases in an ______ molecule to a sequence of ________ in a protein.

RNA polymerases

use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule. This process is known as transcription.

template strand

The DNA strand acting as this is also referred to as the noncoding strand, minus strand, or antisense strand. Selection of which DNA strand serves as the template strand depends on the gene being transcribed.

5’ to 3’; 3’ to 5’

The enzyme RNA polymerase synthesizes mRNA molecules in the what direction by reading the template DNA strand in the what direction.

ATCG → TAGC → AUCG

DNA → DNA → RNA

modifications

In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated _________

addition of poly-A tail (3’) and GTP cap (5’)

modifications protecting DNA

Excision of introns and splicing and retention of exons

can generate different versions of the resulting mRNA molecule; this is known as alternative splicing.

intron

intervening nucleotide

exons

expressed nucleotides

splicing

get rid of introns and put exons together

steps of transcription/translation

initiation, elongation, and termination

initiation

unwind DNA, begin transcribing

elongation

growing of RNA molecule

termination

transcribed entire gene, RNA polymerase breaks away from DNA

Translation

(of the mRNA to generate a polypeptide) occurs on ribosomes that are present in the cytoplasm of both prokaryotic and eukaryotic cells and on the rough endoplasmic reticulum of eukaryotic cells.

translation in prokaryotes

occurs while mRNA molecule is being transcribed.

start codon

Translation is initiated when the rRNA in the ribosome interacts with the mRNA here.

codons.

the sequence of nucleotides on the mRNA is read in triplets called these

amino acid

Each codon encodes a specific _________,which can be deduced by using a genetic code chart. Many of these are encoded by more than one codon.

Nearly all living organisms use the same genetic code

evidence for the common ancestry of all living organisms.

tRNA; codon

this brings the correct amino acid to the correct place specified by the ______ on the mRNA.

polypeptide chain.

**t**he amino acid is transferred to the growing ….

stop codon

**t**he process continues along the mRNA until this is reached.

the newly synthesized polypeptide/protein

the process terminates by release of this

ATG → TAC → AUG → Met → start

non-template DNA → template DNA → mRNA → amino acid → phenotype

retroviruses

Genetic information in these organisms is a special case and has an alternate flow of information: RNA → DNA, made possible by reverse transcriptase.

reverse transcriptase

an enzyme that copies the viral RNA genome into DNA.

integrates

Retrovirus’ DNA ________ into the host genome and becomes transcribed and translated for the assembly of new viral progeny.

HIV

example of a retrovirus

Regulatory sequences

stretches of DNA that interact with regulatory proteins to control transcription; inhibit or allow transcription

Epigenetic changes

can affect gene expression through reversible modifications of DNA or histones.

Epigenetics

the study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype — which in turn affects how cells read the genes.

The phenotype

of a cell or organism, is determined by the combination of genes that are expressed and the levels at which they are expressed

Observable cell differentiation

results from the expression of genes for tissue-specific proteins.

Induction of transcription factors

during development, results in sequential gene expression.

operons

In prokaryotes, groups of genes called these are transcribed in a single mRNA molecule. The lac operon is an example of an inducible system. 

same

In eukaryotes, groups of genes may be influenced by the ____transcription factors to coordinately regulate expression.

inducible operon

naturally off; needs to be turned on; breaks down molecules/metabolize; ex: lac

repressible operon

naturally on; needs to be turned off; builds molecules/manufactures; ex: trp

repressor protein

needed to turn off genes

methlyation

adding a methyl group packs histones tightly together, preventing transcription (inactivating gene)

acetylation

adding an acetyl group loosens chromatin, allowing transcription

operon

genes grouped together with related functions

repressible

usually on; produce a product; must be repressed when enough product is made; ex: tryptophan

inducible

usually off; breaks down products when on; must be induced (turned on) when product is present; ex: lactose

cascade

one gene activates others, another creates specific function

Promoters

(like TATA box) are DNA sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription. 

Negative regulatory molecules

inhibit gene expression by binding to DNA and blocking transcription.

Gene regulation

results in differential gene expression and influences cell products and function.

Certain small RNA molecules

have roles in regulating gene expression.

activator

used in positive regulation to promote transcription; specific transcription factors that enhance transcription to occur

general transcription factors

aid binding RNA polymerase to DNA

transcription can be regulated at…

chromatin structure: methylate or acetylate

mRNA: alternate splicing

degradation by miRNA

ubiquitin

marks protein for degradation in eukaryotes

proteasome

breaks down protein

genotype; phenotype

Changes in ______ can result in changes in ________ 

phenotype

The function and amount of gene products determine the _______ of organisms. 

normal function of genes and gene products

collectively comprises the normal function of organisms. 

disruptions

in genes and gene products, can cause new phenotypes.  

alterations in DNA sequences

can lead to changes in the type or amount of the protein produced and the consequent phenotype. 

positive; negative; or neutral

DNA mutations can be these three options based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.

positive mutations

confers selective advantage

negative mutations

confers selective disadvantage

neutral mutations

no change in phenotype OR phenotype is selectively neutral

substitution

at a point; say one base pair (A-T) is swapped for another (G-C)

insertion and deletion

causes an entire frameshift; one base pair added or delected

random mutations

can be caused by errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals 

environmental context

a. Whether a mutation is detrimental, beneficial, or neutral depends on this

mutations

the primary source of genetic variation.

mutations and what causes them

a random change in the sequence of genes

caused by: mistakes in DNA replication process and/or environmental agents that damage DNA

example of substitution

ATCGA ATCGA TAGCT

→

TAGCT ATCAA TAGCT

mitosis or meiosis

Errors here can result in changes in phenotype 

chromosome number

Changes in these often result in new phenotypes, including sterility caused by triploidy, and increased vigor of other polyploids. 

human disorders

Changes in chromosome number often result in _______________ with developmental limitations, including Down syndrome/ Trisomy 21 and Turner syndrome. 

euploid

one complete set of chromosomes, or exact multiples of complete sets (ex: 1n, 2n, etc)

monoploidy or polyploidy

change in numbers of whole sets of chromosomes

aneuploid

change in numbers of individual chromosomes, so chromosome number is no longer an exact multiple of the haploid set