Part two Chapter 11 DNA Biology

Cells need what to make identical copies of themselves?

Cells need to make identical copies of themselves for the growth and repair of tissues.

A biding site

for a newly arrived tRNA attached to an amino acid

P biding site

for a tRNA attached to a peptide.

E site

for tRNA molecules exiting the ribosome

gene expressions

gene expressions occur when a gene's product- the protein it specifies- is functioning in a cell.

genes are also responsible for what

genes are also responsible for specifying any type of protein in a cell not just enzymes

ribosomes

has a binding site for mRNA as well as for 2 tRNA molecules at a time which facilitate complementary base pairing between tRNA anticodons and mRNA codons.

genetic code

if the code were a singlet code only four amino acids could be encoded if the code were a doublet it still would not be possible to code for 20 amino acids. if the code were a triplet code, the four basses could supply 64 different triplets. This number is far more than you actually need to code the 20 different amino acids

regulatory gene

in an operon, a gene that codes for a protein that regulates the expression of other genes.

triplets

sequence of amino acids in a protein that determines its structure and function.

Epigenetics

the pattern of inactivation is inherited as the cell divides. In an XX cell, the inactive chromosome in the first cell is the same in all of its daughter cells.

transcription

the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA). a portion of DNA that serves as a template for mRNA formation.

replication bubble

the process of DNA replication occurs

trp operon

the regulatory gene codes for a repressor that ordinarily is unable to attached to the operator. Therefore, the genes needed to make the amino acid tryptophan are ordinarily expressed.

translation

the second step by which gene expression leads to protein (polypeptide) synthesis. It requires several enzymes, mRNA, and the other two types of RNA: transfer RNA and ribosomal RNA.

complementary base pairing (Watson and crick)

the pairing of A > T G > C

Finding the structure of DNA was the first step toward understanding how DNA is able to do the following:

1. Be variable in order to account for species differences 2. Replicate so that every cell gets a copy during cell division 3. Store information needed to control the cell 4. Undergo mutations accounting for evolution of new species

Based on the available data they knew the following

1. DNA is a polymer of four types of nucleotides with the bases adenine (A) guanine (G) cytosine (C) and thymine (T) 2. Based on Chargaff's rules the amount of A = T and the amount of G = C 3. Based on Rosalind Franklin's X ray diffraction photography DNA id a double helix with a repeating pattern

Translation has three phases

1. initiation 2. an elongation cycle 3. termination

triplets and codons

61 triplets correspond to a particular amino acid and the remaining three are stop codons that signal the end of a polypeptide.

template

A molecular mold that shapes the structure or sequence of another molecule. example: the nucleotide sequence of DNA acts as a template to control the nucleotide sequence of RNA during transcription

DNA contains four different types of nucleotides based on their nitrogen containing these bases

Adenine = A > T or U Guanine = G > C Thymine = T > A or U Cytosine = C > G Adenine = 31 % in a human cell Guanine = 19 % Thymine = 31 % Cytosine= 19 % A = Amount of T G = Amount of C 1. The amount of A,T,G and C in DNA varies from species to species 2. In each species the amount of A = T and the amount of G = C

mRNA processing

After transcription the removal of introns and splicing of exons occur before mature mRNA leaves the nucleus and passes into the cytoplasm.

How many classes of RNA formed by transcription.

All 3 classes of RNA are formed by transcription.

What forms around each replication fork

Around each replication fork a "replication bubble" forms.

At the ribosome, what process joins the amino acids to form a polypeptide chain.

At the ribosome, a process called translation joins the amino acids to form a polypeptide chain

researchers performed a series of experiments that revealed what?

By comparing the bases in the mRNA with the resulting polypeptide they were able to learn the code. mRNA sequence of repeating guanines (GGG'GGG'....) would encode a string of glycine amino acids. They concluded that the mRNA codon GGG specifies the amino acid glycine in a protein.

transcription factors

DNA- biding proteins that help RNA polymerase bind to a promoter.

transcription activators

DNA-binding proteins that speed transcription dramatically. They bind to a DNA region called an enhancer, that can be quite a distance from the promoter.

DNA replication process

During DNA replication the two DNA strands (held together by hydrogen bonds) separate and each old strand of the parent molecule serves as a template for a new strand in a daughter molecule. DNA replication begins when the DNA's double helix separates and unwinds. Once this happens new nucleotides are added on to the parental template strand. It is completed by using an enzyme complex called DNA polymerase. The daughter strand is then synthesized by DNA polymerase in a 5'-3' direction.

Elongation cycle

During this step the polypeptide chain increases in length one amino acid at a time. 1. The tRNA at the P site contains the growing peptide chain 2. This tRNA passes its peptide to tRNA- amino acid at the A site. THe tRNA at the P site enter the E site. 3. During translocation, the tRNA- peptide moves to the P site, the empty tRNA in the E site exits the ribosome, and the codon at the A site is ready for the next tRNA amino- acid.

what makes up a transcription unit in bacteria?

In bacteria a single promoters serves several genes that make up a transcription unit.

What is in the double helix

In the double helix each strand has a 5^1 end where a free P appears and a 3^1 end where a free -OH appears.

are genes composed of DNA

Investigators had learned in the 1950's that genes are composed of DNA and that mutated genes result in errors of metabolism.

what are the three types of RNA

Messenger RNA, Transfer RNA and Ribosomal RNA

RNA vs DNA

RNA unlike DNA is single stranded. However the single RNA strand sometimes doubles back on itself allowing complimentary base pairing to occur.

what can have a dramatic effect on gene expression

a single transcription activator can have a dramatic effect on gene expression.

Ribosomal RNA is in Ribosomes

Ribosomes are small structural bodies where translation occurs. Ribosomes are composed of many proteins and several rRNAs (ribosomal RNA) In eukaryotic cells, rRNa is produced in a nucleolus within the nucleus joining with proteins that are manufactured in the cytoplasm to form 2 ribosomal subunits( one large, one small). The subunits leave the nucleus and join together in the cytoplasm to form a ribosome right as protein synthesis begins.

Ribosomes remain free where?

Some ribosomes remain free in the cytoplasm and others have become attached to rough ER. In the latter case, the polypeptide enters the lumen of the ER by way of channel, where it can be further processed by the addition of sugars.

what is the end product of signal transduction pathway?

The end product of the pathway (not the signal) directly affects the metabolism of the cell. ex. growth is possible only if certain genes have been turned on by regulatory proteins.

a signaling cell secretes a chemical signal that binds to a specific receptor. The binding activates a series of reactions within a signal transduction pathway. What does the last reaction do?

The last reaction activates a transcription activator that enhances the transcription of a specific gene.

What did Watson and Crick's model of DNA show

The model showed that the deoxyribose sugar phosphate molecules are bonded to one another to make up the sides of a twisted ladder.

helicase

enzymes that bind and may even remodel nucleic acid or nucleic acid protein complexes.

initiation

The step that brings all of the translation components together. 1. the small ribosomal subunit attaches to the mRNA in the vicinity of the start codon (AUG) 2. The anticodon of the initiator tRNA- methionine complex pairs with this codon. 3. The large ribosomal subunit joins to the small one.

What happens to the subunits in Ribosomal RNA (rRNA)

The subunits leave the nucleus and come together in the cytoplasm when protein synthesis is about to begin.

In tRNA how many amino acids are there.

There are twenty different amino acids where each has its own tRNA.

Transfer RNA takes amino acids to the ribosomes

There is at lease one tRNA molecule for each of the 20 amino acids found in proteins. The amino acids bind to one end of the molecule. The opposite end of the molecule contains anticodon. During translation, the order of codons in mRNA determines the order in which tRNAs bind at the ribosomes. When a tRNA- amino acid complex comes to the ribosome, its anticodon pairs with an mRNA codon. After translation is complete a protein contains the sequence of amino acids originally specified by DNA.

What did James Watson and Francis Crick do

Together they set out to determine the structure of DNA and to build a model that would explain how DNA varies from species to species, replicates, stores information, and undergoes mutation.

DNA polymerase

enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA

When lactose is present and glucose is absent what protein assists

When lactose is present and glucose, the preferred sugar, is absent, a protein called CAP assists in the binding of RNA polymerase to the promoter.

MyoD

a DNA binding protein they an activate the genes necessary for fibroblasts to become muscle cells in various vertebrates.

CAP

a DNA binding protein involved with the transcription of several genes, including those that code for enzymes involved in the metabolism of certain sugars. ex. lactose, maltose, and arabinose

What happens when DNA is transcribed

a chromatin remodeling complex pushes aside the histone portions of nucleosomes so that transcription can begin. euchromatin also needs further modification before transcription begins.

translocation

a chromosomal segment is moved from one position to another, either within the same chromosome or to another chromosome.

polyribosome

a cluster of ribosomes connecter with mRNA; they play a role in peptide synthesis.

anticodon

a group of three bases that is complementary to a specific codon of mRNA

alternative mRNA processing

a mechanism by which the same primary m RNA can produce different protein products according to which exons are spliced together from mature mRNA's

euchromatin

a more loosely packed form of chromatin that contains active genes

nucleosome

a portion of DNA wrapped around a group of histone molecules.

proteasomes

a protein complex in cells containing proteases; it breaks down proteins that have been tagged by ubiquitin.

release factor

a protein that allows for the termination of translation by recognizing the terminatioin codon or stop codon in an mRNA sequence.

promoter

a region of DNA with a special nucleotide sequence that marks the beginning of a gene.

rung

a rod or bar forming a step of a ladder

exons

a segment of DNA or RNA molecule containing information coding for a protein or peptide sequence.

introns

a segment of DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.

operator

a segment of DNA to which a transcription factor binds to regulate gene expression by repressing it.

triplet code

a sequence of three nucleotides in a DNA or RNA molecule that codes for a specific amino acid in protein synthesis.

codon

a series of three adjacent bases in one polynucleotide chain of DNA or RNA molecule which codes for a specific amino acid. Most amino acids have more than one codon which offers some protection against possibly harmful mutations that might change the sequence of the amino acids in a protein

promoter

a short DNA sequence where RNA polymerase attaches.

enhancer

a short region (50-1500 bp) of DNA that can be bound by proteins to increase the likelihood that transcription of a particular gene will occur

bacteria

a single promoter serves several genes making up a transcription unit. rely mostly on transcriptional control.

crystal

a solid substance whose atoms are arranged in a definite manner. When a crystal is X rayed, the X ray beam is diffracted (deflected) and the pattern that results shows how the atoms are arranged in the crystal. Rosalind Franklin made a concentrated viscous solution of DNA and then saw that it could be separated into fibers. Under the right conditions the fibers were enough like a crystal that when they were X rayed a diffraction pattern resulted.

DNA ligase

a specific type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.

transcription

a strand of RNA forms that is complementary to a portion of DNA.

(mRNA) Messenger RNA

a type of RNA that carries the code or chemical blueprint for a specific protein. it is produced in the nucleus of eukaryotes as well as in the nucleoid of prokaryotes. Once formed mRNA carries genetic information from the DNA in the nucleus to the ribosomes in the cytoplasm where protein synthesis occurs through a process called translation.

operon

a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.

Chromatin Condensation

a way to keep genes turned on or off. The more tightly chromatin is compacted, the less often genes within it are expressed.

arabinose

a white, crystalline, water soluble solid, obtained from plant gums or made synthetically from glucose.

1. which type of RNA carries the instructions for building proteins a. mRNA b. tRNA c. rRNA d. xRNA

a. mRNA (messenger ribonucleic acid)

3. In DNA replication, one of the two old strands of DNA remains as it was. Therefore DNA replication is called a. semiconservative b. unwinding c. templative d. template redundant

a. semiconservative

Four nucleotides that make up RNA molecules

adenine = A uracil = U cytosine = C guanine = G A(adenine) > (guanine) G C(cytosine) > (Uracil) C

house keeping genes

also known as active genes since thy govern functions that are common to many types of cells. ex glucose metabolism

alternative mRNA splicing

also known as differential splicing. it is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process particular exons of a gene may be included within or excluded from the final processed messenger RNA produced from that gene.

chargaff's rule

amount of A,T,G, and C in DNA varies from species to species in each species the amount of A=T and the amount of G=C

vitellin

an mRNA that persists for three weeks instead of 15 hours if it is exposed to estrogen.

lac operon lactose operon

an operon required for the transport and metabolism of lactose in Escherichia coli and many other enteric bacteria

repressor

any protein that binds to DNA and thus regulates the expression of genes by decreasing the rate of the transcription.

doublet

any two bases standing for one amino acid.

5. Which one of the following examples is the correct base pairing for DNA. a. A-C, G-T b. A-T, G-C c. A-G, C-T d. A-A, C-C, G-G, T-T

b. A-T, G-C

11. loosely packed chromatin in eukaryotic cells is called. a. nucleosome b. euchromatin c. an operon d. heterochromatin

b. euchromatin

12. In eukaryotes, transcription ________ are DNA binding proteins that assist RNA polymerase to bind to a promoter. a. activators b. factors c. enhancers d. translators

b. factors

What is required before division occurs

before division occurs each new cell requires an exact copy of the parent cell's DNA or it will not be able to function as the original cell did

7 which of the following strands of DNA is a complement to T-A-G-G-T-C-A? a. G-C-T-T-G-A-C b. C-G-A-A-C-T-G c. A-T-C-C-A-G-T d. A-T-G-G-A-G-T

c. A-T-C-C-A-G-T

13. In general, a cell signaling pathway begins when a. a chemical signal is emitted from a transmitter protein b. an end product activates reactions within a cells cytoplasm c. a chemical signal binds to a receptor protein d. a transcription activator reacts to the chemical signal

c. a chemical signal binds to a receptor protein

6. During DNA replication, enzymes called DNA ______ help fill in the gaps between the portions of replicated DNA to form a continuous strand. a. polymerase b. replicase c. ligase d. lactase

c. ligase

10. _______ is a DNA sequence that controls transcription in a prokaryote. a. repressor b. polymerase c. an operon d. a cloning factor

c. operon

2. Which one of the following bases occurs only in RNA a. thymine b. cytosine c. uracil d. adenine

c. uracil

4. The Watson and crick model of DNA led to the discovery of a. messenger RNA b. complementary base pairing c. x ray diffraction c. consequential pairing

c. x ray diffraction

Ey

can bring about the formation of not just a single cell type but a complete eye in flies. DNA binding protein

complete cycle

complementary base pairing of new tRNA, transfer of the growing peptide chain, and translocation- is repeated at a rapid rate. Outgoing tRNA is recycled and can pick up another amino acid in the cytoplasm to take to the ribosome.

gene expression

controlled in a cell that accounts for its specialization.

8. In the context of gene mutations, if a codon triplet makes no sense in respect to any protein used by the organism it is called a ______ mutation. a. transposon b. point c. transgenic d. frameshift

d. frameshift

9. The sequence of all the base pairs that compose the genes and intergenic DNA segments of an organism is called a a. DNA sequence b. proteome c. DNA fingerprint d. genome

d. genome

heterochromatin

darkly staining portions of chromatin. represent tightly compacted, inactive chromatin. ex. Barr body in mammalian females.

semiconservative

during DNA synthesis, the two original strands of the molecule separate and each strand acts as a template for the synthesis of a new strand

ER

endoplasmic reticulum.

eukaryotes

in eukaryotes each gene has its own promoter where RNA polymerase binds employ a variety of mechanisms to regulate gene expression. These mechanisms affect whether the gene is expressed, the speed with which it is expressed, and how long is it expressed.

signaling between cells in eukaryotes

in multicellular organisms cells are constantly sending out chemical signals that influence the behavior of other cells. during animal development these signals determine the specialized role of a cell will play in the organism Later the signals help coordinate growth and day to day functions. Plants cells also signal each other so that their responses to environmental stimuli are coordinated. ex direct sunlight

IF-2

inhibits the start of protein synthesis when it is phosphorylated by a specific protein kinase.

RNA is a helper to DNA. What does this allow?

it allows protein synthesis to occur according to the genetic information that DNA provides.

When does DNA and euchromatin become genetically active

it becomes genetically active when histones no longer bar access to DNA.

what turns the operon on when lactose is present?

it binds to the repressor and it changes shape. Now the repressor is unable to bind to the operator and RNA polymerase is able to bind to the promoter.

what happens when tryptophan is present?

it binds to the repressor. A change in shape activates the repressor and allows it to bind to the operator which now the operon is turned off.

How long can an mRNA last?

it can last a long time or be destroyed immediately. it is the same with proteins.

DNA's sequence of bases

it determines the proteins in a cell and the proteins determine the function of each cell.

origins of replication

it is when DNA begins at numerous sites. At each origin of replication, replication forks form which allows replication to proceed in both directions.

what does transcription lead to

it leads to the translation of mRNA and a protein product that in this case stimulates the cell cycle so that growth occurs

mature mRNA molecule

known as a Poly- A tail and is used for stability and guidance so that the mRNA can exit the nucleus and find the ribosome. RNA splicing then removes the non coding RNA introns leaving behind the exons which are then spliced and joined together to form the final mRNA.

Escherichia coli (E coli)

lives in the human large intestine and can quickly adjust its production of enzymes according to what we eat.

RNA or ribonucleic acid

made up of nucleotides containing the sugar ribose which accounts for its name.

the nitrogen bases A, G, C, T

make up the rungs of the ladder- they project into the middle and hydrogen bond with bases on the other strand.

stop codons

marks the site at which translation ends. also called termination codon or chain termination codon. 3 stop codons 1. UAA 2. UAG 3. UGA

start codon

marks the site at which translation into protein sequence begins 1.AUG 2.CUG 3.AUA 4AUU 5.GUG 6.UUG

Ras (protein)

normally inactive but the reception of a growth factor leads to its activation. If it continually activated cancer will develop because cell division will occur continuously

cell signaling

occurs because a chemical signal binds to a receptor protein in a target cells plasma membrane. The signal causes the receptor protein to initiate a series of reactions within a signal transduction pathway. a signaling cell secretes a chemical signal that binds to a specific receptor located in the plasma membrane The binding activates a series of reactions within a signal transduction pathway.

termination

occurs when a stop codon appears in the A site. Next, the polypeptide and the assembled components that carried out protein synthesis are separated from one another. 1. A protein called a release factor binds to the stop codon and cleaves the polypeptide from the last tRNA. 2. The mRNA, ribosomes, and the tRNA molecules can then be used for another round of translation

psychomotor

of or relating to movement or muscular activity associated with mental processes.

singlet code

one base standing for an amino acid

Ribosomal RNA (rRNA)

produced in the nucleolus of a nucleus where a portion of DNA serves as a template for its formation. Ribosomal RNA joins with proteins made in the cytoplasm to form the subunits of ribosomes(one large one and one small one).

cyclins

proteins involved in regulating the cell cycle and are destroyed by giant enzyme complexes called proteasomes.

proteins synthesized by ribosomes attach to what and are used by what

proteins synthesized by ribosomes attach to the ER which is normally used by the ER

DNA replication

refers to the process of making an identical copy of a DNA molecule. DNA replication occurs during the S phase of the cell cycle. During DNA replication the two DNA strands which are held together by hydrogen bonds are separated and each old strand of the parent molecule serves as a template for a new strand in a daughter molecule .

enteric

relating to or occurring in the intestines.

polyribosomes

ribosomes in the cytoplasm that may be free floating or in clusters

mechanisms of gene expression

some occur in the nucleus; others occur in the cytoplasm. In the nucleus, chromatin condensation, DNA transcription, and mRNA processing all play a role in determining which genes are expressed in a particular cell type. In the cytoplasm mRNA translation into a polypeptide at the ribosomes can occur right away or be delayed. These mechanisms control the quantity of gene product and/or how long it is active.

protein activity

some proteins not active immediately after synthesis. Many proteins are short lived in cells because they are degraded or destroyed.

central dogma of molecular biology

states that genetic information flows from DNA to RNA to protein.

how does tRNA and mRNA help during protein synthsis

tRNA assists mRNA during protein synthesis by bringing amino acids to the ribosomes. Proteins differ from one another by the sequence of their amino acids and proteins determine the structure and function of cells and indeed the phenotype of the organism.

Transfer RNA (tRNA)

tRNA transfers amino acids present in the cytoplasm to the ribosomes. also produced in the nucleus of eukaryotes. single stranded nucleic acid that doubles back on itself such that complementary base pairing results in the cloverleaf like shape.

molecular genetics

tells us that genetic information lies in the sequence of the bases in DNA which through mRNA determines the sequence of amino acids in a protein.

What does the X ray diffraction pattern of DNA show

the X ray diffraction pattern of DNA shows that DNA is a double helix.

What colors are parent molecules and daughter molecules and what color does a daughter DNA double helix have?

the backbones of the parent molecule are blue which are the original double strand. then after replication the daughter molecules each have a green backbone which is the new strand and a blue back bone which is the old strand. A daughter DNA double helix has the same sequence of base pairs as the parent DNA double helix had.

signal transduction pathway

the binding of signaling molecules known as ligands to receptors that trigger events inside the cell. The combination of a signaling molecule with a receptor causes a change in the conformation of the receptor (known as receptor activation) A protein called Ras functions in signal transduction pathways that lead to the transcription of many genes, several of which promote the cell cycle.

mRNA translation

the cytoplasm contains proteins that can control whether translation of mRNA takes place. The longer an mRNA remains in the cytoplasm before it is broken down the more gene product is produced. During maturation mammalian red blood calls eject their nuclei yet they continue to synthesize hemoglobin for several months. Differences in the length of poly A tail can determine how long a particular transcript remains active. Hormones may also affect the stability of certain mRNA transcripts.

How at what pace does the eukaryotes replicate DNA?

the eukaryotes replicate their DNA at 500 to 5,000 base pairs per minute. There are many individual origins of replication throughout the DNA molecule. The eukaryotes complete replication of the diploid amount of DNA in a matter of hours. In humans that would be over 3 billion base pairs.

epigenetic inheritance

the inheritance of changes in gene expression that are not the result of changes in the sequence of nucleotides on the chromosome. it explains other psychological processes as well such as genomic imprinting

mRNA splicing

the introns are removed and the exons are joined together.

Today we know that...

the paired bases may occur in any order and the amount of variability in their sequences is overwhelming ex. a chromosome contains 140 million base pairs. Since any of the four possible nucleotide pairs can be present at each pair location the total # of possible nucleotide pair sequences is 4 ^140 x 10^6.

translation

the sequence of mRNA bases, which are complementary to those in templates DNA, determines the sequence of amino acids in a polypeptide. This process follows transcription in which the DNA sequence is copied or transcribed into an mRNA.

genomic imprinting

the sex of the individual determines which alleles are to be expressed in the cell by suppressing genes on chromosomes inherited from the opposite sex.

mRNA is processed

there are 3 steps. 1. capping 2. the addition of a poly-A tail 3. splicing After processing, the primary mRNA is modified by the addition of a cap that is composed of an altered guanine nucleotide. One the 3' end, enzymes add a poly- A tail, a series of adenosine nucleotides. In mRNA splicing, the introns are removed and the exons are joined together. The result is a mature mRNA molecules consisting of continuous exons. After the mRNA strand is processed, it passes from the cell's nucleus into the cytoplasm for translation.

the two strands of DNA are..

they are antiparallel and run in opposite directions. the carbon atoms in deoxyribose are numbered. 5^1 carbon has an attached P group 3^1 carbon has an attached -OH group which is circled and colored pink

viruses

they are composed of an outer capsid made of protein and an inner core of DNA. The use of radioactive tracers showed that DNA, but not protein, enters bacteria and directs the formation of new viruses.

Proteins synthesized by free ribosomes or poly ribosomes are

they are used in the cytoplasm where the protein is carried in a transport vesicle to the Golgi Apparatus for modification and transport to the plasma membrane where it can leave the cell.

transport vesicles do what

they carry protein to other locations in the cell including the Golgi apparatus which may modify and package it in a vesicle for transport out of the cell or cause it to become embedded in the plasma membrane.

gene expressions require two processes. what are they?

transcription and translation.

mRNA is formed

transcription begins when the enzyme RNA polymerase binds tightly to a promoter. RNA polymerase opens up the DNA helix just in front of it so that complementary base pairing can occur. Then the enzyme adds new RN nucleotides that are complementary to the template. The resulting mRNA transcript is a complementary copy of the sequence of bases in the template DNA strand. Once transcription is completed the mRNA is ready to be processed before it leaves the nucleus for the cytoplasm.

what happens if a transcription factor is missing

transcription cannot take place.