BIOL 101 Chapter #9 Notes

what are the two types of nucleic acids?

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

what are the three parts of a DNA nucleotide?

deoxyribose (5-carbon sugar), phosphate group, and a nitrogenous base

what's the phosphate group?

a molecular group consisting of a central phosphorous atom bound to four oxygen atoms

what's the nitrogenous base?

nitrogen containing molecule that acts as a base

what are the four types of nitrogenous bases? (DNA)

Adenine (A), Thymine (T), Guanine (G), Cytosine (C)

are adenine and guanine purines or pyrimidines?

they're double-ringed purines

is cytosine and guanine purines or pyrimidines?

they're small single-ringed pyrimidines

carbon atoms of the five-carbon sugar are numbered as?

1' (one prime), 2' (two prime etc...), 3' , 4' , 5'

what is a double helix (In DNA)?

the molecular shape of DNA in which two strands of nucleotides wind around each other in a spiral shape

- structure is proposed by Francis Crick & James Watson

- originally found by Rosalind Franklin though*

what is Chargaff's rule?

A pairs with T, G pairs with C

- equal amounts of both base pairs

how is adenine and thymine connected by?

how is cytosine and guanine connected by?

- connected by two hydrogen bonds

- connected by three hydrogen bonds

what is the direction of the DNA strands?

they are anti-parallel (going opposite directions) with 3' carbon going upward position (always the arrow) and a 5' carbon at an upward position

what's the structure of RNA?

single strand of nucleotides, consisting of a nitrogenous base, five-carbon sugar, and a phosphate group

- five-carbon sugar is called ribose

- ribose has a hydroxyl group at 2' carbon

RNA contains what? what doesn't it have?

contains nitrogenous bases Adenine (A), Cytosine (C), Guanine (G), and Uracil (U); it does NOT contain Thymine (T)

In RNA, what is Thymine replaced with?

with Uracil (U)

- new base pair is (AU)

what are the three types of RNA mentioned in the chapter?

messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)

- all majorly involved in the production of proteins

what do most prokaryotes contain (chromosome related)?

a single, circular chromosome that is found in an area in the cytoplasm (nucleoid)

how does DNA contain all these millions of base pair combos?

through super coiling

- special proteins & enzymes help maintain the structure

what are histones?

the protein that DNA is wrapped around

- imagine DNA as a string and the histones as beads on the string

what are metaphase chromosomes?

during cell division, chromosomes are at their most compacted state, held together by scaffold proteins

what is semi-conservative in DNA replication?

each DNA strand of the double helix is used as a template strand for the synthesis of two new strands

- results in DNA composed of one new and one old strand

what is DNA polymerase?

an enzyme that joins individual nucleotides to produce a new strand of DNA by adding complementary base pairs to DNA strands

- can only add to the 3' strand

what is the replication fork?

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

what is RNA primer?

a short segment of RNA, normally about 10 nucleotides long, required to start a new chain

- adds nitrogenous bases A, U, G, C to DNA strand

- later sealed by DNA ligase

what happens on the leading strand in DNA replication (5' to 3')

DNA polymerase builds to the replication fork

- synthesized continuously in the 5' to 3' direction

what happens on the lagging strand

DNA polymerase builds away from direction of replication fork; the DNA segments left behind are called Okazaki Fragments

- synthesized discontinuously (segments) in the 3' to 5' direction

what is the telomerase?

enzyme that has a built-in sequence of DNA/RNA that goes at the end of a DNA strand (3' to 5' strand) to add pairs to 5' to 3' strand

- eukaryotes have this; prokaryotes DO NOT

- founded by Elizabeth Blackburn

what is a telomere?

the DNA sequence at the end of linear chromosomes

- repetitive sequence that doesn't code for any specific gene

what is a helicase?

an enzyme that helps open up (unzips) DNA double helix during DNA replication by breaking hydrogen bonds

what is primer (RNA)?

a short stretch of RNA nucleotides that are required to initiate replication and allow the binding of DNA polymerase

- gives complementary bases to a DNA parental strand

what is DNA ligase?

an enzyme that catalyzes the joining/formation of DNA fragments together

what is the process of DNA replication summarized? (three steps)

I. DNA unwinds at origin of replication

II. new nitrogenous bases are added to the complementary parental strands; one strand continues, and the other strand lags

III. Primers (RNA) are removed, new DNA nucleotides replace primers and spaced-segments are sealed by DNA ligase

what is mismatch repair?

the form of DNA repair where non-complementary nucleotides are recognized, excised(removed), and replaced with the right complementary bases

what is nucleotide excision repair?

DNA repair process, where the damaged section of DNA is removed and replaced with nucleotides using the complementary strand 5' to 3'

- incorrect bases are removed!

what is a mutation?

a permanent change in the DNA sequence of a genome (nucleotide/gene wtv)

what is polymerase mistakes?

1 error made in nucleotides every 100,000 nucleotides (10 to 5), but an enzyme later fixes most mistakes, so the final error is 1 error per 10 million nucleotides (10 to 10)

what are some of the causes of DNA sequence mutations?

radiation (UV damage), replication, and chemicals

does mutation help with evolution, how?

yes; mutations drive natural selection

- most will be harmful; small amounts of mutation are beneficial

what is the central dogma?

- DNA encodes RNA (transcription process)

- RNA encodes Protein (translation process

what's the overall function of the central dogma?

gene expression; it takes one gene and expresses it into a protein

what is mRNA?

messenger RNA; it's a form of RNA that carries the nucleotide sequence code for a protein sequence that is later translated into a polypeptide sequence (central dogma function)

what is transcription?

DNA to mRNA

- occurs in the nucleus of a cell & mRNA must be transported to the cytoplasm (occurs in only eukaryotes)

- for prokaryotes, this occurs in the cytoplasm of a cell

what are the three stages of transcription?

initiation, elongation, and termination

what is initiation?

DNA double helix partially unwinds in the region of mRNA synthesis

what is the transcription bubble? (sub-set of iniation)

the region of unwinding on the mRNA, allowing transcription to occur

what is the promoter? (sub-set of iniation)

a sequence on DNA where RNA polymerase and its associated factors (proteins and enzymes) bind to & initiate transcription

- it determines whether a corresponding gene is transcribed all the time, some of the time, or hardly at all

what is elongation?

the addition of nucleotides to the new DNA strand

what are the factors in elongation?

the template strand, non-template strand, and RNA polymerase

what is the non-template strand?

strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except for the nitrogenous base T which is replaced by nitrogenous base U in mRNA

what is the template strand?

strand of DNA that specifies the complementary mRNA molecule

what is RNA polymerase?

an enzyme that synthesizes (combines), an RNA strand from a DNA template strand

what is termination?

stops transcription, (prokaryotic) soon as the mRNA is made, ribosomes start making proteins

- eukaryotic cells processes of transcription and translation occur at different times

what are eukaryotic genes composed of?

exons and introns

what are exons?

the segments of a gene that remain in the mRNA after the pre-mRNA has been spliced. They contain the coding sequences that are translated into proteins. Essentially, exons are the parts of the gene that "exit" the nucleus and are expressed as proteins

what are introns?

non-protein coding intervening sequences that are spliced from mRNA during processing

what is splicing?

the process of removing introns & reconnecting exons in pre-mRNA

what is pre-mRNA? (not in notes)

the initial, unprocessed RNA transcript of a gene, containing both coding regions (exons) and non-coding regions (introns)

what is the promoter? (video notes**)

controls the rate of transcription

what is elongation? (video notes**)

RNA polymerase opens up gene, and adds its nucleotides (A, U, C, G)

what is alternative splicing?

a gene regulation mechanism in eukaryotes that allow different protein products to be produced from one gene when different combinations of introns (sometimes exons) are removed from the transcript

- allows for many diverse genes

what is the Poly-A tail?

a sequence approximate 200 adenine nucleotides added onto the 3' end of a pre-mRNA molecule

what are ribosomes?

part of rRNA, has stabilizing proteins

- made up of small sub-unit & large sub-unit

what is the small sub-unit?

binds the mRNA (only holds onto mRNA)`

what is the large sub-unit?

binds tRNA

what is tRNA?

transfer/translation RNA, a form of RNA that reads mRNA codon and brings the appropriate amino acid

- translates language of RNA into the language of proteins

what are codons?

sequence of three mRNA nucleotides which together form a unit of genetic code in a DNA or RNA molecule

what is the genetic code?

the amino acids that correspond to three-nucleotide codons of mRNA

- is universal; can be applied to every living organism

what are stop codons?

one of the three mRNA codons that specifies termination of translation

- UAA, UAG, UGA

what are start codons?

the AUG (rarely GUG) on an mRNA from which translation begins; always specific for methionine

- initiates translation

what is gene expression?

the process of turning on a gene to produce RNA and protein

what is an operon?

a cluster of genes that are transcribed together

what's a lac operon? (prokaryotic gene expression ex.)

enzymes that break down lactose

what happens if there is no lactose present for the lac operon? (prokaryotic gene expression ex.)

repressor binds to operator, turning off the enzymes that break down the lactose

what happens if there is lactose present? (prokaryotic gene expression ex.)

lactose binds to a repressor, and opens up the operator (Make Mo Enzymes!!)

what is epigenetic?

describes non-genetic regulatory factors

- describes changes in DNA that control access to genes in chromosomes