SAT II Biology Episode 1 Part 7 docx

Bases Four nitrogenous bases make up the bonding sites along the center of the DNA molecule and are bonded to a carbon on the sugar... Guanine A purine, double-ring base with three bondi

The building blocks of DNA, nucleotides are used to make up the repeating units in the strands of DNA that represent the genetic code

A nucleotide consists of a sugar, a phosphate, and a nitrogen base Since there are only four bases, researchers postulated that the enormous amount of genetic variation on the planet had to be in the sequence of the nucleotides within the DNA molecule This sequence then controls the synthesis of precise proteins in the sequence of amino acids On one end of the DNA molecule, the 5-carbon sugar has a phosphate attached and is known as the 58 end On the other end of the sugar is an OH that is identified as the 38 end of the DNA molecule

Bases

Four nitrogenous bases make up the bonding sites along the center of the DNA molecule and are bonded to a carbon on the sugar

mol-A Adenine

A purine, double-ring base with two bonding sites

B Thymine

A pyrimidine, single-ring base with two bonding sites

C Cytosine

A pyrimidine, single-ring base with three bonding sites

D Guanine

A purine, double-ring base with three bonding sites

Ribose

A 5-carbon sugar, as signified by the -ose ending, ribose is considered

the central part of the nucleotide, as the bases and the phosphate bond to it

Phosphate

Bonded to another carbon on the ribose sugar, the last phosphate on the molecule is the 58 end

Histones are proteins that help protect the DNA molecule The DNA molecule is surrounded by eight or nine histones to help it form a protective DNA-histone complex in a tight space in the nucleus

BASE-PAIRING

Base-pairing is the pairing of complimentary bases along the DNA strand The sum of the bonds and the coiling of DNA makes the molecule securely attached along its entire length Analysis of the assays of the DNA from a variety of organisms caused Erwin Chargaff

to note that the percentage of adenine was almost identical to the percentage of thymine in the DNA of a cell A similar relationship was discovered for cytosine and guanine This was later referred to as Chargaff’s rule and led Watson and Crick to the ultimate conclusion that the molecule was directed inward—the result of which was their proposal that DNA was a double helix Linus Pauling, who did so much work with proteins, wrestled with the molecule being directed outward; many others did as well, based on the strength of Dr

Pauling’s reputation

Adenine-Thymine

This purine-pyrimidine bonding is the result of each base having two hydrogen bonding sites Adenine and thymine can bond only with each other in DNA

This purine-pyrimidine bonding in the DNA molecule is the result of these bases having three sites for hydrogen bonds Cytosine and guanine can only bond with each other

H1 bonds

The bonds between the adenine-thymine and cytosine-guanine classes

of chemicals that form the base sequences in DNA, in addition to other places where we find hydrogen bonds

COMPLIMENTARY STRANDS

Since adenine always bonds with thymine and guanine always bonds with cytosine, if one strand of the DNA molecule is known, then the other, complimentary strand can be known This means that if you have one half of the molecule, you can construct the other half, which is exactly what DNA does during replication The main strand

is used as a template to produce its complement The nature of the bonds along the strand make the adenines on one strand line up in the opposite direction of the adenines on the other strand As a result, the molecule is said to be anti-parallel

5* end

“Hanging out” on one end of the base pairs is the phosphate group, which is the end that starts the “reading” of the molecule when it is being replicated The direction of replication along the master strand then is from 58 end to 38 end

3* end

Opposite the base on the master strand with its 58 end is the compli-mentary strand with its 38 end oriented outward at the “beginning” of this strand, in an anti-parallel way

REPLICATION

A combination of the words “reproduce” and “duplicate,” replication

refers to the act of DNA making a copy of itself This precedes mitosis or meiosis Mitigated by enzymes, it proceeds as two concur-rent events, one from the 58 end of what is called the leading strand and the other from the 38 end of the lagging strand The result of replication is said to be semi-conservative, since we end up with half the original DNA in each of the resulting new strands

DNA helicase

DNA helicase is an enzyme that begins the unraveling of the DNA molecule at the sites of the hydrogen bonds

DNA polymerase

This enzyme arranges the new nucleotides next to their complimen-tary base to make the new strand of DNA As the name suggests, it makes a polymer out of individual nucleotides

Leading strand

A leading strand is a strand of DNA that starts at the 58 end and is made continuously It is not named for the fact that it starts first, but for the fact that, since it is made continuously, the construction of it proceeds faster

Lagging strand

A strand of DNA that starts at the 38 end Its production proceeds slower than the leading strand because it is made in pieces that are then bonded to the template to which it will be complimentary These pieces, known as Okasaki fragments, are bonded into place by DNA ligases

RNA-RNA

RNA-RNA is a 5-carbon sugar that possesses an extra oxygen atom [compared with DNA] and replaces thymine with the base uracil,

thus enabling it to pass through the nuclear envelope and take the code of DNA to the cytoplasm Three types of RNA are made in the nucleus and reunite in the cytoplasm in the process known as protein synthesis

TYPES

RNA, the carrier of the DNA code from the nucleus to the rough ER

in the cytoplasm, has three forms that play a key role in the synthesis

of proteins These molecules, acting in concert, ultimately produce the proteins that control the life of the cell, even the production of RNA

rRNA

Stored in the nucleolus, rRNA helps make up ribosomes that reside

on the rough ER Ribosomes are composed of rRNA and proteins The mRNA attaches to the ribosomes and thus begins the making of a protein

mRNA

mRNA is the lengthy form of RNA that is coded by the DNA molecule and carries that code for synthesis of a particular protein This

sequence will be “read” in the ribosome and serves as the blueprint for the precise sequence of amino acids that will make up the protein coded for in the mRNA The codon is three consecutive nucleotides

on the mRNA that code for a particular amino acid carried by the tRNA

tRNA contains the anticodon to the mRNA’s codon, just three nucleotides long; the nature of this molecule was hypothesized before the structure was actually known The tRNA carries an amino acid to the ribosome, where it bonds to the codon on the mRNA There are 20 amino acids that make up proteins The sequence of these amino acids, like the sequence of nucleotide bases in the DNA,

is critical If there was one base pair for every one amino acid, this would result in only four amino acids ever being utilized to make proteins Two base pairs for every amino acid will code for a maxi-mum of 16 amino acids, four short of the needed 20 to transport all

of the amino acids needed for life It is now known that the tRNA molecules are, in fact, three bases long, providing more than enough variations to code for 20 amino acids as well as stop, start, and some duplication

Transcriptiontakes place in the nucleus of eukaryotic cells It is the first step in protein synthesis, wherein DNA’s information is copied

on RNA Three RNA molecules, rRNA, mRNA, and tRNA, are made during this phase, each from the separate complementary strands of original DNA They are then transported to the cytoplasm, where the

next step is performed—translation During translation, the sequence

of codons on mRNA orders the sequence of amino acids in the protein Transcription can be likened to what occurs in, say, a court setting, where the court reporter transcribes the spoken word into the written word—same language, different form

In RNA, uracil replaces the thymine found in DNA The uracil, like the thymine it replaces, still bonds opposite adenine Students should

be careful not to associate uracil with thymine in a way that the

uracil replaces the adenine It doesn’t; like thymine, it will bond

oppositeadenine as thymine does in DNA In RNA, we will get A-U pairing, whereas in DNA, we get A-T pairing

Sugar

The 5-carbon sugar, along with the phosphate, is part of the back-bone of nucleotides and is different in RNA The RNA sugar has one more oxygen than the amount found in the DNA sugar This makes this site possess an OH radical with no electrical activity Alterna-tively, DNA possesses an H1 at that site, making its activity different than RNA

Promoters

The site on DNA where transcription of RNA is begun, using only one

of the DNA strands, the sense strand The other strand—called the missense strand—is not used during this process

RNA Polymerase

As the name of this enzyme suggests, its role is to bring RNA nucle-otides into proper position on the sense strand ending in an mRNA strand

RNA modification

The mRNA molecule is not ready to be transported to the cytoplasm yet It undergoes a final processing stage where the nonsense

sequences, called introns, are excised, leaving the meaningful sequences known as exons to make up the final mRNA A tail, called

the poly(A) tail, is added to the 38 end, a cap—58 cap—is added to the 58 end, and the molecule is ready to take part in the making of polypeptides

TRANSLATION

Continuing the court reporter analogy, this stage of protein synthesis

is like translating words from one language into another In the case

of the cell, we will be translating from the language of the nucleus into the language of the cytoplasm or cell on a larger scale DNA has been replicated, it has transcribed its message into RNA, and a

This is known as the codon and reflects the statement of the original code in the DNA This will be placed along the ribosomes for

“reading,” the sequential passing of the base sequence over ribosome and subsequent bonding of tRNAs in proper places on the mRNA

tRNA–tRNA molecules

tRNA–tRNA molecules transfer amino acids to the ribosomes There is

at least one tRNA for each of the 20 amino acids Amino acids bond

to one end of the tRNA The other end contains a three-base anti-codon sequence form of RNA, which codes for specific amino acids While their nucleotide end anticodon bonds with the next sequence

on the mRNA, their amino acid form lines up with the next amino acid

A Start

The mRNA sequence that initiates the construction of all polypeptides

is A-U-G, which is bonded with the tRNA sequence of U-A-C that carries the amino acid methionine

B Stop

There are several stop codons on the mRNA, namely U-A-A, U-A-G, and U-G-A, which bond opposite the tRNA anticodons of A-U-U, A-U-C, and A-C-U, respectively

Polypeptides

The chains of amino acids that make up the polypeptides are, in sum, formed in the following way Once the mRNA is attached to the

rRNA in the ribosomes, the tRNA anticodon, with its accompanying amino acids, moves into position on the codon of mRNA The mRNA

is then shifted by three bases along the rRNA and makes room for another tRNA-amino acid complex to move into position Once this occurs, the two adjacent amino acids are bonded to each other in a peptide bond at the amine and the carboxyl groups Once again, mRNA is shifted, and another tRNA-amino acid moves into place Another peptide bond is formed between this third amino acid in the sequence and the second amino acid As the process continues, the tRNAs are immediately rejected from the mRNA—the tRNA-amino acid complex is the substance that was moved into position on the

mRNA, not the tRNA by itself It is now available to leave the area

and pick up another amino acid specific to itself In addition, the molecule is continually moved along the rRNA sites, and, thus the polypeptide elongates When codons U-A-A, U-A-G, or U-G-A are encountered, the process stops and a polypeptide is formed The formation of a protein may not be complete and depends on the interaction among the amino acids as to what form this protein will take Some, like insulin, are actually shortened in order to become active Not all proteins will become enzymes—some will be struc-tural, as in the proteins in the plasma membrane or those that make

up part of other biological molecules Originally, the thinking was characterized as “one gene—one enzyme,” but is now thought to be more accurate with the phrase “one gene—one polypeptide chain.”

MUTATIONS

Characterized as “errors” in the genetic code, these cause a change in the functioning of the cell, either as a structural anomaly—as in the case of sickle cell anemia—or as a functioning anomaly, such as a defective enzyme There are so-called micro-mutations and macro-mutations Both form the basis for much of our evidence for evolu-tion The causes of mutations can be almost anything from radiation

to physical disruption of the cell—a rare one—to environmental factors to chemicals Pollution is feared to be the potential cause of

These mutations tend to affect larger numbers of DNA sequences, even up to whole chromosomes, as in the case of the first type discussed below

Non-disjunction

Chromosomes fail to separate properly during the process of meiosis,

as in the cases of Down’s, Turner’s or Klinefelter’s syndromes

Translocation

A segment breaks off of one chromosome and moves to another chromosome

Inversion

A segment of a chromosome breaks off and is inserted in reverse order

Deletion

A segment of a chromosome breaks off and is lost

Duplication

An extra copy of a segment of a chromosome is produced along the chromosome

RECOMBINANT

DNA

Recombinant DNA is the transferring of DNA segments from one entity to another, whether it is DNA molecules or chromosomes Recent technology uses restriction enzymes from bacteria to slice DNA in very specific places for the purposes of recombining se-quences or assaying the nature of a sequence

BACTERIAL GENETICS

Variation is introduced into bacteria cells in several ways One is by conjugation, the exchange of DNA between bacteria Another, transduction, occurs when DNA is introduced into the bacteria by a

virus Transformation occurs when bacteria absorb free pieces of DNA from their environment

VIRAL GENETICS

Non-living substances, viruses can nonetheless take over a living cell

in two stages The first, called the lytic stage, is when the virus penetrates the cell, uses cellular enzymes to duplicate viral particles, transcribes the DNA into RNA, and then uses the RNA to make proteins The second, called the lysogenic stage, occurs when an infected bacterium does not immediately duplicate viral particles The viral DNA is temporarily incorporated into the cellular DNA

EVOLUTION

Evolution is the changes in the frequencies of certain genes in a population over a period of time; 11 percent of the SAT II Biology exam has questions on this subject Genetic variation is what drives evolution Much of what involves evolution also involves knowledge

of several fields of geology, as will be seen We will provide the highlights of this concept and make reference to areas that the student will want to be conversant with outside the specific area of biology, such as paleobiology or biogeography

JEAN-BAPTISTE DE

LAMARCK

Lamarck popularized the notion that acquired traits were passed on

to future generations Changes in the body cells are not capable of being passed on Only sex cell changes achieve this Lamarck’s theory became known as the use-disuse theory and was soon seen by many

as fruitless If one loses a finger prior to having children, those children will not be missing a finger as a result of the parent losing a finger Especially with our knowledge of the nature of mutations, we can reject this idea outright Darwin did also