bio ch.8

purine pyrimidine

2 ring structure (adenine and guanine) 1 ring structure (thymine and cytosine)

anticodon

3 base sequence on the tRNA complementary to the codon on mRNA

types of genetic info transfer

3 general transfers, 3 special transfers, 3 unknown transfers

discuss what is meant by the universal genetic code

64 codon combinations for 20 amino acids the same code is utilized by the simplest prokaryotic organism and by humans

relatively large chromosomes that never leave the nucleus are made of

DNA

Central dogma of molecular biology

DNA --> RNA --> protein

1952- Hershey and Chase demonstrated

DNA is genetic material used T2 bacteriophage- a virus that infects bacteria virus= DNA (or RNA) surrounded by a protein coat, to reproduce, a virus must infect a cell and use that host cell's machinery to make more viruses, a replicative process known as lytic cycle

function of RNA

DNA makes RNA makes protein gene-segment of DNA that contains the info necessary to encode an RNA molecule or protein, genes are embedded within the DNA in nucleus RNA moves to cytoplasm, DNA stays in the nucleus 3 types of RNA involved in protein synthesis and all 3 work together to produce a protein

central dogma of molecule biology

DNA makes RNA makes protein- Crick and Watson and Nirenberg- cracked the genetic code describes the fundamental process that makes us all different we all have same genes and proteins, but we have different alleles of those genes

order and type of amino acids that make up the protein are determined by

DNA sequence

general transfers

DNA-> DNA= DNA replication DNA-> RNA= transcription RNA-> protein= translation

transcription is

DNA-> RNA transfer of genetic instructions from DNA to RNA divided into 3 stages - initiation, elongation, termination

discuss work of Griffith, Avery, Hershey, and Chase demonstrated that DNA is the genetic material

Griffith- discovered process of transformation, was studying a bacterium that infects mammals, used virulent S strain and harmless R strain, infected mice with heat killed S strain and harmless caused death Avery- tried to identify material involved in transformation, treated S strain with protease enzymes Hershey and Chase- demonstrated DNA is genetic material

special transfers

RNA-> DNA= reverse transcription RNA->RNA= RNA replication DNA-> protein= Direct translation

TATA box is

a highly characterized core promoter sequence found in most eukaryotic promoters binding site for a transcription factor known as TBP

in eukaryotes, pre initiation of transcription is

a step that determines if transcription will proceed this step is involved in the regulation of gene expression RNA polymerase briefly binds to a promoter sequence in the presence of specific transcription factors RNA polymerase II and therefore the initiation of transcription requires the presence of a core promoter sequence in DNA, requires the presence of a core promoter sequence in the DNA

DNA replication begins as

an enzyme- DNA helicase, breaks the hydrogen bonds holding the 2 strand together and forms a replication fork the resulting structure has 2 branching strands of DNA backbone with exposed bases these exposed bases allow the DNA to be "read" by another enzyme, DNA polymerase, which then builds the complementary strand as DNA helicase continues to open the double helix, the replication fork grows

2 strands in DNA backbone run in

anti parallel direction of each other one of the DNA strands is built in 5'->3' direction, while the complementary strand is built in the 3'->5' direction in the DNA backbone, the sugars are joined together by phosphate groups that form bonds between the third and fifth carbon atoms of adjacent sugars in a double helix, the direction of the nucleotides in one strand is opposite to their direction in the other strand 5' and 3' each mark an end of a strand

the lagging strand

at opposite of replication fork from the leading strand 3'->5' DNA polymerase cannot build a strand in this direction this strand is synthesized in short segments known as Okazaki fragments on this strand an enzyme known as primase builds a short RNA primer

Griffith's experiment

bacterium- Streptococcus pneumoniae- infects mammals 2 strains of bacteria virulent S strain (smooth) and a harmless R strains (rough) the S strain is surrounded by a polysaccharide capsule, which protects it from the host's immune system, resulting in the death of the host R strain- does not have a protective capsule, is defeated by the host's immune system when mammalian cells are infected with R strain, the host does not die heat killed S strain and live R strain killed the mice- Griffith felt that the R strain had "transformed" into the lethal S strain the material transferred between strains had to be heredity material

explain Watson and Crick's double helix model of DNA

built model of DNA double helix, like a spiral staircase as a nucleic acid, DNA is composed of nucleotide monomers, containing sugar, phosphate group, nitrogenous base (A,C,G,T) 2 sides to the double helix- sugar phosphate backbone- made from alternating phosphate groups and sugars the "steps" of the double helix are made from the base pairs formed between the nitrogenous bases DNA double helix is held together by hydrogen bonds between the bases attached to the 2 strands

discuss potential outcomes of point mutations

can have no effect, a minor effect, or a dramatic effect

DNA repair

cell identifies and corrects damage to DNA

define transformation

change in genotype and phenotype of a cell/organism due to the assimilation of external DNA (heredity material) by a cell

define mutations

change in the DNA or RNA sequence, and many mutations result in new alleles some mutations have no effect on the protein, whereas others are either beneficial or harmful evolution could not take place without the genetic variation that results from beneficial variations harmful mutations can result in genetic variations

TATA box

cis regulatory element found in promoter region of genes in archeae in eukaryotes

each new strand that is formed is

complementary to the strand used as the template each resulting DNA molecule is identical to the original DNA molecule

gene pool

complete set of unique alleles in a species or population

RNA replication

copying of 1 RNA to another

illustrate common chromosomal alterations

deletion- removal of a large chromosomal region, leading to loss of genes within that region duplications (amplifications)- lead to multiple copies of a chromosomal region, increasing the number of genes located within that region, some genes may be duplicated in their entirety insertions- addition of material from one chromosome to a non homologous chromosome inversions- reversing the orientation of a chromosomal segment translocations- interchange of genetic material between non homologous chromosomes

RNA structure

differs from DNA in 3 specific ways both are nucleic acids and are made out of nucleotides RNA is single stranded while DNA is double stranded RNA nucleotides (like those from DNA) have 3 parts- 5 carbon sugar, phosphate group and a base RNA contains the 5 carbon sugar ribose, whereas in DNA the sugar is deoxyribose RNA contains nitrogenous uracil instead of thymine -uracil pairs with adenine

describe how transcription makes RNA from a DNA template

during transcription, a complementary copy of RNA is made in DNA replication, both strands of DNA double helix are used as templates, in transcription, only 1 strand is needed RNA polymerase enzymatically "reads" a template strand of DNA, known as the coding strand, to synthesize the complementary RNA strand

exon vs intron

exon- region of gene that contains the code for producing a protein, many genes contain exons, with each exon containing the info for a specific portion of a complete protein intron- gene's exons are separated by long regions of DNA that have no identified function, these long regions are introns

describe the importance of the finding that in DNA, the amount of adenine and thymine were about the same and that the amount of guanine and cytosine were about the same

found base pairs showed double helix

humans have 3 billion bases in the

genome

common types of mutations

germline- can be passed onto descendants, change the DNA sequence within a sperm or egg cell, and therefore can be inherited, the inherited mutation may result in a genetic disease somatic- cannot be transmitted to the next generation chromosomal alterations- large changes in the chromosome structure splice site- mutations in coding region for a gene may also alter the splicing of mRNA frameshift- alters reading frame

splicing

humans have 22,000 genes, yet make many more proteins alternative splicing allows 1 mRNA to produce many polypeptides process by which introns are removed

chargaff rule 1

in any double stranded DNA the number of guanine units approximately equals the number of cytosine units and the number of adenine units equals approximately equals the number of thymine units Human DNA- 30.9% A and 29.4% T, 19.9% G and 19.8% C rule constitutes the basis of base pairs in the DNA double helix- A pairs with T, G pairs with C number of purines (A+G) always approximates the number of pyrimidines (T+C), and obvious consequence of the base-pairing nature of the DNA double helix

termination

in prokaryotes and eukaryotes is very different end of transcription involved detachment of RNA from DNA template when ribosome comes to one of the three stop codons, for which there is no tRNA

importance of regulation of gene expression

includes the mechanism to turn genes "on" and transcribe those genes into RNA gives cell control over its structure and function has role in natural selection and evolution

describe the role of DNA

instructions= genetic material

T2 bacteriophage can quickly turn E. coli bacteria

into a T2 producing system

elongation

involves the further addition of RNA nucleotides and the change to a transcriptional complex addition of RNA nucleotides to the growing RNA transcript during transcription; also refers to the process during translation of adding additional amino acids to the growing polypeptide

RNA polymerase

known as DNA dependent RNA polymerase, is an enzyme that produces RNA using a DNA template

general mechanisms of gene expression

lac operon- required for transport and metabolism in lactose of E. coli cis regulatory elements trans acting factors regulatory protein/ transcription factor

polymers that comprise DNA, RNA, and amino acids

linear polymers

discuss consequences of effect on function mutations

loss of function-gene product or protein having less or no function, a null allele has a complete loss of function, mutations are usually recessive haploin sufficiency- when a reduced dosage of a normal gene product does not produce a normal phenotype gain of function- gene product or protein having a new or abnormal function and a dominant phenotype, thyroid hormomes

following transcription, __________ is produced

mRNA however, newly transcribed eukaryotic mRNA is not ready for translation this mRNA requires extensive processing, and so is known as pre mRNA

proteins

made out of amino acids

transcription

making mRNA from info in DNA (gene) sequence

mRNA

messenger RNA takes genetic instructions from the nucleus to the cytoplasm, where the ribosomes are located ribosome- organelles where proteins are made binds to ribosome, bringing the genetic instructions to order the amino acids to the site of protein synthesis the 4 nucleotides (A,C,G,U) are arranged into codons of 3 bases each each codon encodes for a specific amino acid, except for stop codons, which terminate protein synthesis produced during transcription, caries the genetic instructions of a gene from the nucleus to the ribosome in the cytoplasm

chargaff rule 2

molecular diversity added evidence that DNA could be genetic material composition of DNA varies

common causes of mutations

mutagenesis- process by which the genetic info of an organism is changed in a stable manner spontaneous or induced spontaneous- occurs during normal cellular functions - due to mistake during DNA replication or transcription, mitosis, meiosis induced- environmental factor- mutagen- chemicals (like those inhaled while smoking), radiation (X-Rays, UV light, nuclear radiation)

carcinogenesis oncogenes carciongens

normal cells are transformed into cancer cells mutated genes involved in the development of cancer cancer causing agents (tobacco smoke, radiation)

DNA is composed of

nucleotides, each of which contains a nitrogen containing base, a 5 carbon sugar, and a phosphate group 4 possible bases in these nucleotides- adenine, guanine, cytosine, thymine

types of point mutations

occur at a single site within the DNA silent- mutated codon codes for the same amino acid, and has no altered affect on the protein missense- mutated codon codes for a different amino acid and can have a minor or dramatic effect on the protein nonsense- mutated codon is a premature stop codon, has a dramatic effect transition - purine for purine (A<-->G), pyrimidine for pyrimidine (C<-->T) transversion- purine for pyrmidine

initiation

occurs when all transcription factors are aligned along the promoter correctly transcription factors are usually proteins that bind to the DNA sequence of the promoter start of transcription signaled by the transcription initial complex formed by the promoter, transcription factors, and RNA polymerase

identification of the structure of DNA suggested that each strand

of the double helix would serve as a template for synthesis of a new strand

cis regulatory elements

on same side as binding sites of one or more trans acting factors, usually a regulatory protein, which interacts with RNA polymerase in intron, in 3' region regulatory protein bound to this to switch a gene on or off

the 2 new strands of DNA are built in

opposite directions, through either a leading strand or a lagging strand

in eukaryotes, transcription can be divided into 5 stages

pre initiation, initiation, promoter clearance, elongation, termination

describe how DNA is replicated

process in which a cell's entire DNA is copied/ replicated occurs during the Synthesis (S) phase of the eukaryotic cell cycle semi conservative because of the process of replication, where the resulting double helix is composed of both an old and new strand

translation

process where info in genes is converted from the language of nucleotides to the language of amino acids amino acids are placed in a specific order during this the order is specified by the codons in mRNA, which is produced during transcription as mRNA sequence is based on the gene sequence in DNA, the order of amino acids that makes the protein is based on the gene sequence as well

Avery and his colleagues treated the S strain bacteria with

protease enzymes trypsin and chymotrypsin (or ribonuclease or deoxyribonuclease) mixed with the remaining extract with R strain bacteria, and asked if transformation of the R strain bacteria still occurred they found that the proteases, which remove proteins from cells, and ribonuclease, which break apart RNA, did not affect transformation, but an enzyme preparation of deoxyribonuclease, which breaks down DNA, destroyed the transforming power these results showed that neither proteins nor RNA carried the "instructions" (or the genes) which allowed transformation 1944- DNA was heredity material

Avery MacLeod McCarty Experiment Proteases ribonuclease deoxyribonuclease

proteases- destroys protein, yes- transformation ribonuclease- destroys RNA, yes- transformation deoxyribonuclease- destroys DNA, no-transformation

unknown transfers

protein-> DNA protein-> RNA protein-> protein

Practically everything a cell does (liver cell, skin cell, bone cell, etc) is because of

proteins

what performs the functions of a cell

proteins

adenine and guanine

purine bases

cytosine and thymine

pyrimidine bases

Oswald Avery, together with his colleagues Maclyn McCarty and Colin MacLeod

removed various organic compounds from S strain bacteria and tested the remaining compounds for the ability to cause transformation if the remaining material did not cause transformation, then that material could not be heredity material

lyctic cycle

replicative process to reproduce a virus must infect a cell and use the host cell's machinery to make more viruses

structure of RNA

ribonucleic acid relatively small easily able to carry info out of the nucleus single stranded DNA differs from RNA in nature of sugars and bases

rRNA

ribosomal RNA together with proteins, composes the ribosome, the organelles that are the site of protein synthesis

proteins are made where

ribosomes

Chargaff's rules

rule 1- in DNA, amount of 1 base (a purine) always approximately equals the amount of a second base (a pyrimidine) CG, AT-base pairs rule 2- composition of DNA- in relative amounts of A,C,G, T bases- varied from one species to another

explain the importance of the fact that during DNA replication, each strand serves as a template to make a complementary DNA strand

semi conservative replication produces 2 copies that each contained one of the original strands and one new strand

define Alu sequences

short segment of DNA originally characterized by the action of the Alu restriction endonuclease occurs in large numbers in primate gametes DNA sequences that can translocate around the genome comprise a significant fraction of the genetic material of plants and animals human genome- more than a million of this sequence

ribosomes

site of protein synthesis

illustrate the process of translation, describing how mRNA, rRNA, and tRNA all work together to complete the process

tRNA brings the proper amino acid to the ribosome based on the genetic code anticodon at the bottom of tRNA binds to the codon on the mRNA codon on mRNA is specific for an amino acid or stop codon the codon on the mRNA is specific for an amino acid or stop codon

1958 Meselson and Stahl identified evidence

that DNA replication was semiconservative

the leading strand

the DNA strand that DNA polymerase constructs in the 5'->3' direction this strand is made in a continuous manner, moving as the replication fork grows

a strand running in the 5'->3' direction that has adenine will pair with

the base thymine on the complementary strand running in 3'->5' direction

purine always combines with a pyrimidine in DNA double helix, so

the distance between the 2 sugar phosphate backbones is constant, maintaining the uniform shape of a DNA molecule

discuss what happens to the polypeptide after translation

the events following protein synthesis often include post translational modification of the peptide chain and folding of the protein into its functional conformation during and after synthesis, polypeptide chains often fold into secondary and tertiary structures

what determines the structure of a protein

the order and type of amino acids

what determines the function of a protein

the structure

sequence of the 4 bases carries

the unique genetic information for each species and each individual

explain how the genetic code is a three letter code, and describe its role in translating nucleotides into amino acids

there are 20 amino acids and 64 possibilities presence of codons, three bases of RNA, code for amino acids in DNA, words are 3 letters long , cracked the genetic code

during prophase of mitosis or prophase I of meiosis

these molecules of DNA condense into a chromosome made of 2 sister "identical" chromatids this process ensures that cells that result from cell division have identical sets of genetic material

proteins give the organism its

traits

DNA-> RNA-> protein

transcription (happens in nucleus and uses DNA sequence to make an RNA molecule, RNA then leaves the nucleus and goes to the cytoplasm where translation occurs on a ribosome and produces a protein) and translation are necessary to make protein from info in DNA

tRNA

transfer RNA brings the correct amino acid sequence to the ribosome during translation specific 3 leaf clover structure - contains a 3 base region called anticodon, which can base pair to the corresponding 3 base codon region on mRNA

reverse transcription

transfer of info from RNA to DNA occurs in retroviruses (HIV) also occurs with retrotransposons (self replicating segments of eukaryotic genomes that use reverse transcriptase to move from one position to another via RNA intermediate)

describe translation, and explain that translation is the process of ordering amino acids into a polypeptide; translation involves changing the language of nucleotides into the language of amino acids

translation- RNA-> protein translation uses the products of transcription (mRNA, tRNA, rRNA) to convert the mRNA sequence into a polypeptide according to the genetic code 3 phases- initiation, elongation, termination

explain that the reading frame is the group of three bases in which the mRNA is read, and describe how interrupting the reading frame may have severe consequences on the protein

words are 3 letters long in DNA reading frame- frame of 3 bases in which the mRNA is read and translated mutations can disrupt the reading frame by insertions or deletions of a non multiple of 3 nucleotide bases are known as frameshift mutations many frameshift mutations result in a premature stop codon - results in smaller protein without normal function some mutations can be beneficial