Section 2 Biochemical Building Blocks. Chapter 17 Nucleic Acids.

Section 2

Biochemical Building Blocks

Chapter 17

Nucleic Acids

Scientists have studied how organisms organize and process genetic information, revealing the following principles:

1. DNA directs the function of living cells and is transmitted to offspring DNA is composed of two polydeoxynucleotide strands

forming a double helix

Figure 17.2 Two Models of DNA Structure

Section 17.1: DNA

A gene is a DNA sequence that contains the base sequence information to code for a gene product, protein, or RNA

The complete DNA base sequence of an organism is its genome

DNA synthesis, referred to as replication, involves complementary base pairing between the parental and newly synthesized strand

Figure 17.2 Two Models of DNA Structure

Section 17.1: DNA

2. The synthesis of RNA begins the process of decoding genetic information RNA synthesis is called

transcription and involves complementary base pairing of ribonucleotides to DNA bases

Each new RNA is a transcript

The total RNA transcripts for an organism comprise its transcriptome

Figure 17.3a An Overview of Genetic Information Flow

Section 17.1: DNA

3. Several RNA molecules participate directly in the synthesis of protein, or translation Messenger RNA (mRNA)

specifies the primary protein sequence

Transfer RNA (tRNA) delivers the specific amino acid

Ribosomal RNA (rRNA) molecules are components of ribosomes

Figure 17.3b An Overview of Genetic Information Flow

Section 17.1: DNA

The proteome is the entire set of proteins synthesized

4. Gene expression is the process by which cells control the timing of gene product synthesis in response to environmental or developmental cues Metabolome refers to

the sum total of low molecular weight metabolites produced by the cell

Figure 17.3b An Overview of Genetic Information Flow

Section 17.1: DNA

The Central dogma schematically summarizes the previous information Includes replication, transcription, and

translation The central dogma is generally how the flow of

information works in all organisms, except some viruses have RNA genomes and use reverse transcriptase to make DNA (e.g., HIV)

Section 17.1: DNA

DNA RNA Protein

DNA consists of two polydeoxynucleotide strands that wind around each other to form a right-handed double helix Each DNA nucleotide

monomer is composed of a nitrogenous base, a deoxyribose sugar, and phosphate

Figure 17.4 DNA Strand Structure

Section 17.1: DNA

Nucleotides are linked by 3′,5′-phosphodiester bonds These join the 3′-hydroxyl of

one nucleotide to the 5′-phosphate of another

Figure 17.4 DNA Strand Structure

Section 17.1: DNA

The antiparallel nature of the two strands allows hydrogen bonds to form between the nitrogenous bases

Two types of base pair (bp) in DNA: (1) adenine (purine) pairs with thymine (pyrimidine) and (2) the purine guanine pairs with the pyrimidine cytosine

Figure 17.5 DNA Structure

Section 17.1: DNA

The dimensions of crystalline B-DNA have been precisely measured:

1. One turn of the double helix spans 3.32 nm and consists of 10.3 base pairs

Figure 17.6 DNA Structure: GC Base Pair Dimensions

Section 17.1: DNA

2. Diameter of the double helix is 2.37 nm, only suitable for base pairing a purine with a pyrimidine3. The distance between adjacent base pairs is 0.29-0.30 nm

Figure 17.6 DNA Structure: AT Base Pair Dimensions

Section 17.1: DNA

DNA is a relatively stable molecule with several noncovalent interactions adding to its stability

1. Hydrophobic interactions—internal base clustering2. Hydrogen bonds—formation of preferred bonds: three between CG base pairs and two between AT base pairs3. Base stacking—bases are nearly planar and stacked, allowing for weak van der Waals forces between the rings4. Hydration—water interacts with the structure of DNA to stabilize structure5. Electrostatic interactions—destabilization by negatively charged phosphates of sugar-phosphate backbone are minimized by the shielding effect of water on Mg2+

Section 17.1: DNA

Mutation types—The most common are small single base changes, also called point mutations This results in transition or transversion

mutations Transition mutations, caused by deamination,

lead to purine for purine or pyrimidine for pyrimidine substitutions

Transversion mutations, caused by alkylating agents or ionizing radiation, occur when a purine is substituted for a pyrimidine or vice versa

Section 17.1: DNA

Point mutations that occur in a population with any frequency are referred to as single nucleotide polymorphisms (SNPs) Point mutations that occur within the coding

portion of a gene can be classified according to their impact on structure and/or function: Silent mutations have no discernable effect Missense mutations have an observable

effect Nonsense mutations changes a codon for an

amino acid to that of a premature stop codon

Section 17.1: DNA

Insertions and deletions, or indels, occur from one to thousands of bases Indels that occur within the coding region that are

not divisible by three cause a frameshift mutation

Genome rearrangements can cause disruptions in gene structure or regulation. Occur as a result of double strand breaks and can

lead to inversions, translocations, or duplications

Section 17.1: DNA

DNA Structure: The Genetic Material In the early decades of the twentieth century, life

scientists believed that of the two chromosome components (DNA and protein) that protein was most likely responsible for transmission of inherited traits The work of several scientists would lead to

another conclusion

Section 17.1: DNA

DNA Structure: Variations on a ThemeWatson and Crick’s discovery

is referred to as B-DNA (sodium salt)

Another form is the A-DNA, which forms when RNA/DNA duplexes form

Z-DNA (zigzag conformation) is left-handed DNA that can form as a result of torsion during transcription

Figure 17.12 A-DNA, B-DNA, and Z-DNA

Section 17.1: DNA

DNA can form other structures, including cruciforms, which are cross-like structures, probably a result of palindromes (inverted repeats)

Packaging large DNA molecules to fit inside a cell or nucleus requires a process termed supercoiling

Section 17.1: DNA

DNA Supercoiling Facilitates several

biological processes: packaging of DNA, replication, and transcription

Linear and circular DNA can be in a relaxed or supercoiled shape

Figure 17.13 Linear and Circular DNA and DNA Winding

Section 17.1: DNA

Chromosomes and ChromatinDNA is packaged into

chromosomes Prokaryotic and eukaryotic

chromosomes differ significantly

Prokaryotes—the E. coli chromosome is a circular DNA molecule that is extensively looped and coiled Supercoiled DNA

complexed with a protein core

Figure 17.17 The E. coli Chromosome Removed from a Cell

Section 17.1: DNA

Eukaryotes have extraordinarily large genomes when compared to prokaryotes Chromosome number and

length can vary by species Each eukaryotic chromosome

consists of a single, linear DNA molecule complexed with histone proteins to form nucleohistone Chromatin is the term used

to describe this complexFigure 17.18 Electron Micrograph of Chromatin

Section 17.1: DNA

Nucleosomes are formed by the binding of DNA and histone proteins Nucleosomes have a beaded

appearance when viewed by electron micrograph

Histone proteins have five major classes: H1, H2A, H2B, H3, and H4

A nucleosome is positively coiled DNA wrapped around a histone core (two copies each of H2A, H2B, H3, and H4)

Figure 17.18 Electron Micrograph of Chromatin

Section 17.1: DNA

Prokaryotic Genomes—Investigation of E. coli has revealed the following prokaryotic features:

1. Genome size—usually considerably less DNA and fewer genes (E. coli 4.6 megabases) than eukaryotic genomes2. Coding capacity—compact and continuous genes3. Gene expression—genes organized into operons

Prokaryotes often contain plasmids, which are usually small and circular DNA with additional genes (e.g., antibiotic resistance)

Section 17.1: DNA

Eukaryotic Genomes—Investigation has revealed the organization to be very complex

The following are unique eukaryotic genome features:

1. Genome size—eukaryotic genome size does not necessarily indicate complexity2. Coding capacity—enormous protein coding capacity, but the majority of DNA sequences do not have coding functions 3. Coding continuity—genes are interrupted by noncoding introns, which can be removed by splicing from the primary RNA transcript

Section 17.1: DNA

Existence of introns and exons allows eukaryotes to produce more than one polypeptide from each protein-coding gene

Alternative splicing allows for various combinations of exons to be joined to form different mRNAs

Intergenic sequences are those sequences that do not code for polypeptide primary sequence or RNAs

Section 17.1: DNA

Of the 3,200 Mb of the human genome, only 38% comprise genes and related sequence Only 4% codes for gene products Humans have about 23,000 protein coding

genesand several ncRNA genes

Section 17.1: DNA

25% of known protein-coding genes are related to DNA synthesis and repair

21% signal transduction 17% general biochemical

functions 38% other activities

Over 60% of the human genome is intergenic sequences

Figure 17.24 Human Protein-Coding Genes

Section 17.1: DNA

Two classes: tandem repeats and interspersed genome-wide repeats Tandem repeats (satellite DNA) are DNA

sequences in which multiple copies are arranged next to each other Certain tandem repeats play structural roles

like centromeres and telomeres Some are small, like microsatellites (1-4

bp) and minisatellites (10-100 bp) Used as markers in genetic disease,

forensic investigations, and kinship

Section 17.1: DNA

Interspersed genome-wide repeats are repetitive sequences scattered around the genome Often involve mobile genetic elements that can

duplicate and move around the genome Transposons and retrotransposones

LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements) are two types of transposons

Section 17.1: DNA

RNA is a versatile molecule, not only involved in protein synthesis, but plays structural and enzymatic roles as well

Differences between DNA and RNA primary structure:1. Ribose sugar instead of

deoxyribose2. Uracil nucleotide instead of

thymine

Figure 17.25 Secondary Structure of RNA

Section 17.2: RNA

3. RNA exists as a single strand that can form complex three- dimensional structures by base pairing with itself

4. Some RNA molecules have catalytic properties, or ribozymes (e.g., self-cleavages or cleave other RNA)

Figure 17.25 Secondary Structure of RNA

Section 17.2: RNA

Transfer RNA Transfer RNA (tRNA) molecules

transport amino acids to ribosomes for assembly (15% of cellular RNA) Average length: 75 bases

At least one tRNA for each amino acid

Structurally look like a warped cloverleaf due to extensive intrachain base pairing

Figure 17.26a Transfer RNA

Section 17.2: RNA

Amino acids are attached via specific aminoacyl-tRNA synthetases to the end opposite the three nucleotide anticodon Anticodon allows the tRNA

to recognize the correct mRNA codon and properly align its amino acid for protein synthesis

The tRNA loops help facilitate interactions with the correct aminoacyl-tRNA synthetases

Section 17.2: RNA

Figure 17.26b Transfer RNA

Ribosomal RNARibosomal RNA (rRNA) is the most abundant

RNA in living cells with a complex secondary structure

Components of ribosomes (eukaryotes and prokaryotes) Similar in shape and function, both have a small

and large subunit, but differ in size and chemical composition

Eukaryotic are larger (80S) with a 60S and 40S subunit, while prokaryotic are smaller (70S) with 50S and 30S subunits

Section 17.2: RNA

rRNA plays a role in scaffolding as well as enzymatic functions

Ribosomes also have proteins that interact with rRNA for structure and function

Section 17.2: RNA

Figure 17.27 rRNA Structure

Messenger RNAMessenger RNA (mRNA) is the carrier of

genetic information from DNA to protein synthesis (approximately 5% of total RNA)

mRNA varies considerably in size Prokaryotic and eukaryotic mRNA differ in

several respects Prokaryotes are polycistronic while eukaryotes

are usually monocistronic mRNAs are processed differently; eukaryotic

mRNA requires 5′ capping, 3′ tailing, and splicing

Section 17.2: RNA

Noncoding RNARNAs that do not directly code for polypeptides

are called noncoding RNAs (ncRNAs)Micro RNAs and small interfering RNAs are

among the shortest and involved in the RNA-induced silencing complex

Small Nucleolar RNAs (snoRNAs) facilitate chemical modifications to rRNA in the nucleolus

Section 17.2: RNA

Noncoding RNA Small interfering RNAs (siRNAs) are 21-23 nt

dsRNAs that play a crucial role in RNA interference (RNAi)

Small nuclear RNAs (snRNAs) combine with proteins to form small nuclear ribonucleoproteins (snRNPs) and are involved in splicing

Section 17.2: RNA

Viruses lack the properties that distinguish life from nonlife (e.g., no metabolism)

Once a virus has infected a cell, its nucleic acid can hijack the host’s nucleic acid and protein-synthesizing machinery The virus can then make copies of itself until it

ruptures the host cell or integrates into the host cell’s chromosome

Section 17.3: Viruses

A viral infection can provide biochemical insight, because it subverts the host cell’s functionViruses can cause numerous different diseases,

but have also been invaluable in the development of recombinant DNA technologyHuman papillomavirus can cause cervical

cancer

Section 17.3: Viruses

Chapter 18

Genetic Information

Numerous contacts are involved including hydrophobic interactions, hydrogen bonding, and ionic bondsBetween amino acid

residues and edges of bases within the major and minor grooves

Figure 18.1 Examples of Specific Amino Acid-Nucleotide Base Interactions during Protein-DNA Binding

Chapter 18: Overview

Three-dimensional structures of DNA-binding proteins have surprisingly similar structures

Most possess a twofold axis of symmetry and can be separated into families:

1. Helix-turn-helix2. Helix-loop-helix3. Leucine zipper4. Zinc finger

Figure 18.2 DNA-Protein Interactions


For example, many leucine zipper transcription factors form dimers as their leucine-containing a-helices associate via van der Waals forces

Figure 18.2 DNA-Protein Interactions


All viable living organisms possess rapid and accurate DNA synthesis and effective DNA repair mechanisms

Variation may also be important for adaptability to environmentsVariation is caused by genetic recombination and

mutation

Section 18.1: Genetic Information: Replication, Repair, and Recombination

DNA ReplicationDNA replication occurs before

cell division; the mechanism is similar in all living organisms After the two strands have

separated, each serves as a template for synthesis of a complementary strand

This process is referred to as semiconservative replication

Figure 18.3 Semiconservative DNA Replication


This was first demonstrated in 1958 in an experiment by Matthew Meselson and Franklin Stahl The experiment involved generating DNA with a

greater density by incorporating the heavy nitrogen isoptope 15N

Figure 18.4 The Meselson-Stahl Experiment


Most DNA replication takes place at replication factories, which are relatively stationary during the process

DNA Synthesis in Prokaryotes—DNA replication in E. coli consists of several basic steps: DNA unwinding requires helicases, which are

ATP-dependent enzymes that catalyze the unwinding of duplex DNA (e.g., DnaB in E. coli)


Primer synthesis is the formation of short RNA segments (primers) required for the initiation of DNA replication by primase (e.g., dnaG)

Figure 18.5 The DNA Polymerase Reaction


DNA synthesis is the synthesis of complementary DNA in a 5′3′ direction catalyzed by a large multienzyme complex referred to as DNA polymerase

Figure 18.5 The DNA Polymerase Reaction


DNA polymerase III (pol III) is the major DNA polymerase in prokaryotes

Catalyzes the nucleophilic attack of the 3′-hydroxyl group onto the a-phosphate

Figure 18.6 Mechanism of DNA Polymerases


Pol III holoenzyme is composed of at least 10 subunits

The core polymerase is formed of three subunits: a, e, and

The b-protein (sliding clamp) is two subunits and forms a donut-shaped ring around the template DNA


The g complex is composed of g, d, d, c, and Acts as the clamp-loader, loading b2-clamp

dimer b2-Clamp promotes processivity (prevents

dissociation of polymerase from the DNA template) The g-complex is ejected in an ATP-dependent

process and replication can proceed

Figure 18.7 Cross Section of the b2-Clamp of DNA Polymerase III


The DNA replicating machine (replisome) consists of two pol III holoenzymes, the primosome, and DNA unwinding proteins

There are four other DNA polymerases: DNA polymerase I is involved in RNA primer

removal and replacement with DNA DNA polymerase II, IV, and V are involved in

DNA repair translesion repair enzymes All three are part of the SOS response that

prevent cell death due to high levels of DNA damage


Joining DNA fragments—frequently during DNA synthesis, DNA segments must be joined together DNA ligase catalyzes the formation of the

phosphodiester bond between adjoining nucleotides

Supercoiling control is accomplished by DNA topoisomerases Relieve torque in the DNA, so the replication

process is not slowed


Type I topoisomerases produce transient single-strand breaks

Type II topoisomerases produce transient double-strand breaks DNA gyrase—a type II

topoisomerase in prokaryotes helps separate the replication products and create the negative (-) supercoils required for genome packaging

Figure 18.8 Replication of Prokaryotic DNA


In E. coli when the ATP/ADP ratio is high and there is enough DnaA, replication can begin at the initiation site (oriC)

Replication proceeds in both directions with each replication fork having helicases and a replisome

E. coli only has one origin of replication, making it a single replication unit (replicon) organism


Figure 18.9 DnaA Structure

DNA synthesis only occurs in the 5′3′ direction, so one strand is continuously synthesized (leading strand) while the other is not (lagging strand) The lagging strand is synthesized in short 5′3′

segments called Okazaki fragments (1,000–2,000 nucleotides)

Figure 18.10 DNA Replication at a Replication Fork


Replication begins when DnaA proteins bind to five to eight 9-bp sites within the oriC The oligomerization of DnaA results in a

nucleosome-like structure requiring ATP and histone-like protein (HU)

Causes three 13-bp repeats near the DnaA-DNA complex to open


DnaB complexed with DnaC enters the open oriC region; once DnaB is loaded, DnaC is released The replication fork moves forward as DnaB

unwinds the helix Topoisomerases relieve torque ahead of the

replisome Single strands are kept apart by numerous copies

of single-stranded DNA-binding protein (SSB)

Figure 18.11 Replication Fork Formation


For pol III to initiate DNA synthesis an RNA primer must be present On the leading strand, only a single primer is

required On the lagging strand, a primer is required for each

Okazaki fragment

Figure 18.12 E. coli DNA Replication Model


Pol III synthesizes at the 3′ end of the primerRNA primers are removed by pol I, which then

synthesizes complementary DNADNA ligase then joins Okazaki fragments

Tandem operation of two pol III complexes requires the lagging strand be looped around the replisome

Figure 18.12 E. coli DNA Replication Model


Despite the complexity and high processivity rate (1,000 base pairs per second per replication fork) of DNA replication in E. coli, it is amazingly accurate—one error per 109 or 1010 base pairs This is due to the precise nature of the copying

process (complementary), proofreading mechanism of DNA pol I and III, and postreplication repair mechanisms


Replication ends when the replication forks meet at the other side of the circular chromosome at the termination site (ter region) The DNA-binding protein tus binds to the ter

causing replication arrest

Figure 18.13 Role of Tus in DNA Replication Termination in E. coli


DNA Synthesis in Eukaryotes has a great deal in common with prokaryotes; they also have significant differences DNA Polymerase There are 15

eukaryotic DNA polymerases Three (a, d, and e) are

involved in nuclear DNA replication

Pol g replicates and repairs mitochondrial DNA

Polymerases b, z and function in nuclear DNA repair

Figure 18.14 The Eukaryotic Cell Cycle


Timing of replication—eukaryotic replication is limited to a very specific phase of the cell cycle (S phase)

Replication rate is slower in eukaryotes (50 bp per second per replication fork) due to complex chromatin structureFigure 18.14 The

Eukaryotic Cell Cycle


Replicons—eukaryotes have multiple replicons (about every 40 kb) to compress the replication of their large genomes into short periods Humans have 30,000 origins

of replication Okazaki fragments are from

100 to 200 nucleotides long

Figure 18.15 Multiple-Replicon Model of Eukaryotic Chromosomal DNA Replication


The Eukaryotic Replication Process—In higher eukaryotes, replication begins with the assembly of the preinitiation replication complex (preRC) Process begins in early G1 when

cdk and cyclin levels are low, limiting DNA replication to once per cell cycle

preRC assembly begins when the origin replication complex (ORC) binds to the origin

Figure 18.16 Formation of a Preinitiation Replication Complex


Cdc6 and Cdt1 bind ORC and recruit the MCM complex (helicase)

Conversion of the preRC to an active initiation complex requires the addition of pol a/primase, pol e, and accessory proteins

Cell cycle regulating kinases then phosphorylate and activate preRC components

The proteins that bind ORC and complete preRC structure are the replication licensing factors (RLFs)

Figure 18.17 Eukaryotic Replication Fork Formation


When the initiation complex is active, newly phosphorylated MCM separates the DNA strands Each strand is then stabilized

by replication protein A (RPA)

Pol a/Primase extends each primer by a short segment of DNA, then polymerase d and e continue the process

Replication factor C (RFC), a clamp loader, controls the attachment of polymerase d


Figure 18.17 Eukaryotic Replication Fork Formation

After binding ATP, RFC binds PCNA, a processivity factor

RFC/PCNA complex converts DNA polymerase d and e into processive enzymes RFC/PCNA complex loads either

polymerase, triggering ATP hydrolysis

Replication occurs until replicons meet and fuse

Figure 18.18 Replication Protein A Structure


When the replication machinery reaches the 3′ end of the lagging strand, there is insufficient space for a new RNA primer This leaves the end of the chromosome without

its complementary base pairs Chromosomes with 3′-ssDNA overhangs are very

susceptible to nuclease digestion Eukaryotes compensate with telomerase, a

ribonucleoprotein with reverse transcriptase ability


Telomerase has an RNA base sequence complementary to the TG-rich sequence of telomeres Telomerase uses this

sequence to synthesize a single-stranded DNA to extend the 3′ strand of the telomere

Afterward the normal replication machinery synthesizes a primer and Okazaki fragment

Figure 18.19 Telomerase-Catalyzed Extension of a Chromosome


The chromosome ends are then sequestered and stabilized by telomere end-binding proteins (TEBPs) and telomere repeat-binding factors (TRFs) TEBPs bind GT-rich

telomere sequences TRFs secure the 3′

overhang Telomerase is normally only

active in germ cells



During normal human aging, the telomeres of somatic cells shorten over time Once telomeres are

reduced to a critical length, chromosome replication cannot occur

Telomere shortening causes cell death

90% of all cancers have hyperactive telomerase



DNA RepairMutations are caused by metabolic activities or

environmental exposures on DNA The natural rate of mutation is about 1.0

mutation per 100,000 genes per generationCells possess a great variety of DNA repair

mechanisms


Direct RepairsA few types of DNA damage

can be repaired without the removal of nucleotides Breaks in the

phosphodiester linkages can be repaired by DNA ligase

In photoreactivation repair, pyrimidine dimers are restored to their original monomeric structure using a photoreactivating enzyme and visible light

Figure 18.20 Photoreactivation Repair of Thymine Dimers


The resulting apurinic or apyrimidinic sites are resolved through the action of nucleases that remove the residue, DNA polymerase (pol I in bacteria; DNA polymerase b in mammals), and DNA ligase

Figure 18.21 Base Excision Repair


Single Strand Repairs use the complementary, undamaged strand as a template Base excision repair is a mechanism that removes

and then replaces individual nucleotides whose bases have undergone damage

A DNA glycosylase cleaves the N-glycosidic linkage between the damaged base and the deoxyribose

Figure 18.21 Base Excision Repair


In nucleotide excision repair, bulky (2-30 nt) lesions are removed and the resulting gap is filled

Two types: global genomic repair and transcription coupled repair

The excision enzymes of this process seem to recognize the distortion rather than the base sequence

Figure 18.22 Excision Repair of a Thymine Dimer in E. coli


Transcription coupled repair occurs only on a strand being actively transcribed Damage is recognized when RNA polymerase is

stalled Mfd is a transcription-repair coupling factor that

displaces the polymerase and recruits UvrA2B to initiate damage removal


Mismatch repair is a single-strand repair mechanism that corrects helix distorting base mispairings resulting from proofreading errors or replication slippage A key feature is the capacity to distinguish

between old and newly synthesized strands For a finite amount of time each daughter strand

is hemimethylated, i.e., it consists of one methylated and one nonmethylated strand


Double-strand breaks (DSBs) are especially dangerous for cells because they can result in a lethal breakdown of chromosomes Caused by radiation, ROS, DNA damaging agents,

or as result of replication errors DSBs are repaired by two mechanisms: non-

homologous end joining (NHEJ) and homologous recombination NHEJ is error prone because there is no

requirement for sequence homology Recombination will be explained next


DNA RecombinationRecombination is the rearrangement of DNA

sequences by exchanging segments from different molecules

Genetic recombination is a principle source of the variations that make evolution possible

Two types of recombination: General recombination occurs between

homologous DNA molecules (most common during meiosis)

Site-specific recombination—the exchange of sequences only requires short regions of DNA homology (e.g., transposition)


Bacterial Recombination is involved in several forms of intermicrobial DNA transfer:

1. Transformation is the process of naked DNA molecules entering the cell through small holes in the cell wall2. Transduction is when a bacteriophage inadvertently carries bacterial DNA to a recipient cell3. Conjugation is an unconventional sexual mating that involves passing DNA from a donor cell through a sex pilus to a recipient cell


Eukaryotic Recombination occurs during the first phase of meiosis to ensure accurate homologous chromosome pairing and crossing over It is similar to prokaryotic recombination but has a

larger number of proteins because of the more complex genomes

Rad52 is believed to be the initial sensor of DSBs Rad51, BRCA1, and BRCA2 are involved in DSB

repair


Site Specific Recombination and Transposition—This process relies on short segments of homologous DNA called attachment (att) sites or insertional (IS) elements

Recombination at these sites can lead to insertions, deletions, inversions, and translocations

Integration of bacteriophage l DNA into the E. coli chromosome requires homologous att sites in the phage and bacterial genomesFigure 18.27 Insertion of the

Bacteriophage l Genome into the E. coli Chromosome


Barbara McClintock, a geneticist working with Indian Corn (maize), found that mobile genetic elements were responsible for variation in corn kernel color (1940s)

In 1967, transposable elements were confirmed and Dr. McClintock received the Nobel Prize in physiology and medicine


The IS elements of simple prokaryotic transposons consist of a transposase gene flanked by short inverted terminal repeats More complex bacterial transposons (composite

transposons) will have specific genes (e.g., antibiotic resistance) between simple IS elements

Insertion of the Tn3 transposon into bacterial DNA involves the duplication of the target site

Two mechanisms of transposition have been observed: replicative and nonreplicative


Figure 18.28 Bacterial Insertion Elements


Replicative transposition involves the transfer of one strand of the donor DNA to the target position, followed by replication and site-specific recombination

Figure 18.29a Replicative Transposition


Transcription is a complex process involving a variety of enzymes and associated proteins

RNA polymerase is the enzyme that catalyzes the addition of ribonucleotides in a 5′3′ direction The template strand (-) of DNA is antiparallel

to the new RNA strand The noncoding strand (+) has the same base

sequence as the RNA, except the transcript has uracil for thymine

Figure 18.31 DNA Coding Strand

Section 18.2: Transcription

Transcription consists of three stages: initiation, elongation, and termination Initiation involves the binding of RNA polymerase

to the promoter (regulatory sequence upstream of a gene)

Figure 18.33 Transcription Initiation in E. coli


Two short consensus sequences at -10 (Pribnow box) and -35 are similar among many bacterial species

Figure 18.34 Typical E. coli Transcription Unit


Two types of transcription termination in bacteria: intrinsic termination and rho-dependent termination

In intrinsic termination, RNA synthesis is terminated by the transcription of an inverted repeat sequence The inverted repeat forms a stable hairpin that

causes the RNA polymerase to slow or stop RNA transcript is released due to weak base-pair

interactions

Figure 18.36 Intrinsic Termination


In rho-dependent termination, RNA synthesis is terminated with the aid of the ATP-dependent helicase rho factor Rho binds to a specific

recognition sequence on the nascent RNA chain, upstream from the termination site

Unwinds the RNA-DNA helix to release the transcript

Figure 18.37 Rho-Dependent Termination


Transcription in Eukaryotes Similar to prokaryotic transcription in several

aspects Polymerases are similar in structure and function Initiation factors are distantly related, but perform

similar functionsRegulatory mechanisms differ significantly in both

organisms One major difference is the limited access to DNA

of the transcription machinery


Chromatin is usually at least partially condensed

For transcription to occur, DNA most be sufficiently accessible for RNA polymerase

Histone tails of nucleosomes are modified by histone acetyl transferases (HATs) to allow access

Histone-DNA contacts are weakened by chromatin remodeling complexes, SWI,SNF, and NURF

Figure 18.39 Chromatin Remodeling


Eukaryotic promoters- Promoter sequences in eukaryotic DNA are larger, more complex, and variable than in prokaryotes Each consists of a core promoter which can be

focused or dispersed Focused contain the transcription start site (TSS)

and core promoter elements (CPE) The most studied CPE is the consensus sequence

called the TATA box (25–30 bp upstream)


TATA-binding protein (TBP) a subunit of the transcription factor TFIID binds the TATA box and is the first step of RNA polymerase assembly

Other core elements include the Inr (initiator), BRE (B recognition element), and DPE (downstream promoter element)

Dispersed genes often have multiple TSSs which are distributed over a broad region of 50-100 basepairs Typically occur within CpG islands and

commonly found in vertebrates. CpGs are now believed to facilitate

nucleosome destabilization


Proximal promoter elements are transcription factor binding sites within 250 bp of the TSS

The frequency of transcription initiation is often affected by upstream sites such as the CAAT box and GC box Can also be affected by enhancers that may

be thousands of base pairs upstream

Section 18.2: TranscriptionFigure 18.40 The Eukaryotic RNAPII

Core Promoter

RNA Processing- mRNA is the product of extensive posttranscriptional processing Pre-mRNAs become associated with about 20 different types

of nuclear proteins in ribonucleoprotein particles (hnRNP) Shortly after transcription begins, capping occurs at the 5′

end

Figure 18.46 The Methylated Cap of Eukaryotic mRNA


The cap structure consists of a 7-methylguanosine linked to the mRNA through a triphosphate linkage

Synthesized when the transcript is about 30 nt long The 5′ cap serves to protect the 5′ end from

exonucleases and promotes translation

Figure 18.46 The Methylated Cap of Eukaryotic mRNA


One of the more remarkable features of eukaryotic RNA processing is the removal of introns from an RNA transcript (RNA splicing) Introns are cut out of the primary transcript and

exons are linked together to form a functional product

The number of introns and exons is highly variable among different genes and species

RNA splicing takes place in a 4.8-megadalton RNA-protein complex called the spliceosome

Splicing occurs at certain conserved sequences


In eukaryotic nuclear pre-mRNA transcripts, there are two intron types: GU-AG and AU-AC

In GU-AG introns, 5′-GU-3′ and 5′-AG-3′ are the first and last dinucleotides of the intron, respectively

The splice event occurs in two reactions:1. A 2′-OH of an adenosine nucleotide within the intron attacks a phosphate in the 5′ splice site, forming a lariat

Figure 18.47 RNA Splicing


2. The lariat is cleaved and the two exons joined when the 3′-OH of the upstream exon attacks a phosphate adjacent to the lariat 5′ splice site is the

donor site and the 3′ splice site is the acceptor site

Four active spliceosomes form with each pre-mRNA to form a supraspliceosome

Figure 18.47 RNA Splicing


An exon junction complex (EJC) binds to each splice site 20 nt unpstream of the exon-exon junction

EJCs play a role in nonsense-mediated decay protecting against premature stop codons Result from splicing errors, random mutations

or rearrangements Four active spliceosomes form with the majority

of mammalian pre-mRNAs to form a supraspliceosome


The precise and timely regulation of gene expression is required for handling changing environments, cell differentiation, and intercellular cooperation

Constitutive genes are routinely transcribed because they code for gene products required for normal cell function

Other genes are inducible or repressible, depending on the cellular state

Section 18.3: Gene Expression

Gene Expression in Prokaryotes The highly regulated metabolism of prokaryotes

such as E. coli allows these organisms to manage limited resources and to respond to a changing environment

Control of inducible genes is often affected by the groups of linked structural and regulatory genes called operons

Figure 18.49 The lac Operon in E. coli


Riboswitches are metabolite-sensing domains in the 5-untranslated regions of mRNAs (mostly bacteria) Riboswitches monitor cellular metabolite

concentrations Genes containing riboswitches typically code for

proteins that are involved in the synthesis of molecules that are expensive to produce, such as TPP (thiamine pyrophosphate) or FMN (flavin mononucleotide)

Composed of two structural elements: an aptamer (binds metabolite) and expression platform (expression regulator)


When the aptamer binds the metabolite, it undergoes a structural change that alters the structure of the expression platform

For example, when TPP binds its aptamer, the riboswitch is converted from a structure that has an open translation initiation site to one with the start site sequestered in a hairpin loop, blocking translation

Figure 18.51a Riboswitches


Gene Expression in Eukaryotes Eukaryotic genomes have more intricate

regulation of gene expressionGene expression is regulated at the following

levels: genomic control, transcriptional control, RNA processing, RNA editing, RNA transport, and translational control


Genomic Control—Two major influences on transcription initiation: chromatin structure and transcription factor-regulated RNA polymerase complex formation A significant amount of regulation occurs through

transcription initiation control The particular set of proteins that assembles on a

regulatory DNA sequence is a result of the DNA structure, gene regulatory proteins present, and their affinity for one another

Figure 18.52 Eukaryotic Gene Regulatory Proteins


RNA processing—Among the most important types of RNA processing is alternative splicing The joining of different

combinations of exons to form cell-specific proteins

Figure 18.53 RNA Processing


In general, mRNAs with longer poly(A) tails are more stable, increasing their opportunities for translation

The site of polyadenylation can alter an mRNA’s structural and functional properties There are two forms of IgM: membrane bound

and secreted The plasma membrane bound form produced

during early B-lymphocyte differentiation has two extra exons because the polyadenylation sequence is further downstream


After transcription, base changes are effected by means of RNA editing Alterations in mRNA base sequence can have

several consequences: RNA stability, translation initiation, alteration of splice sites, and amino acid sequence changes

Posttranscriptional Gene Silencing—A form of postranscriptional gene regulation involves microRNAs (miRNAs) miRNAs inhibit translation by binding to

complementary sequences in the 3′-UTR of target mRNAs


Translational Control—Covalent modification of several translation factors has been shown to alter translation rate in response to various stimuli For example, when cellular iron is low, a

repressor protein binds mRNAs coding for the iron storage protein ferritin

Signal Transduction and Gene Expression—Cells can alter gene expression patterns in response to signals from their environment This is often initiated by binding of a ligand to a

receptor that then initiates a signal transduction cascade


The best understood signal transduction examples are for cell proliferation, because of the tremendous amount of research done to understand cancer

This includes two complicating features of intracellular signal molecules: Each type of signal may activate one or more

pathways Signal transduction pathways may result in the

same or overlapping responses


Growth factor effects are believed to include gene expression, which specifically overcomes inhibitions at cell-cycle checkpoints—especially the G1 checkpoint

Induce two classes of genes at the end of their signal transduction cascades Early response genes are rapidly activated

(within 15 minutes) and are often transcription factors Includes the protooncogenes jun, fos, and myc


Delayed response genes are induced by the activities of the transcription factors and proteins produced during the early response phase Can include Cdks and

cyclins

Figure 18.56 Eukaryotic Gene Expression Triggered by Growth Factor Binding


Chapter 7

Carbohydrates

Carbohydrates are the most abundant biomolecule in natureHave a wide variety of cellular functions: energy,

structure, communication, and precursors for other biomolecules

They are a direct link between solar energy and chemical bond energy

Chapter 7: Overview

Section 7.1: Monosaccharides

Monosaccharides, or simple sugars, are polyhydroxy aldehydes or ketones Sugars with an aldehyde functional group are aldoses

Sugars with an ketone functional group are ketoses

Figure 7.1 General Formulas for the Aldose and Ketose Forms of Monosaccharides

Section 7.1: MonosaccharidesMonosaccharide

StereoisomersAn increase in the number of

chiral carbons increases the number of possible optical isomers

2n where n is the number of chiral carbons

Almost all naturally occurring monosaccharides are the D form All can be considered to be

derived from D-glyceraldehyde or nonchiral dihydroxyacetone

Figure 7.3 The D Family of Aldoses


Cyclic Structure of Monosaccharides Sugars with four or more carbons exist primarily

in cyclic forms Ring formation occurs because aldehyde and

ketone groups react reversibly with hydroxyl groups in an aqueous solution to form hemiacetals and hemiketals

Figure 7.5 Formation of Hemiacetals and Hemiketals


The two possible diastereomers that form because of cyclization are called anomers

Hydroxyl group on hemiacetal occurs on carbon 1 and can be in the up position (above ring) or down position (below ring) In the D-sugar form, because the anomeric carbon

is chiral, two stereoisomers of the aldose can form the a-anomer or b-anomer

Figure 7.6 Monosaccharide Structure


Haworth Structures—these structures more accurately depict bond angle and length in ring structures than the original Fischer structures In the D-sugar form, when the anomer hydroxyl is

up it gives a b-anomeric form (left in Fischer projection) while down gives the a-anomeric form (right)

Figure 7.7 Haworth Structures of the Anomers of D-Glucose


Five-membered rings are called furanoses and six-membered rings are pyranoses

Cyclic form of fructose is fructofuranose, while glucose in the pyranose form is glucopyranose

Figure 7.8 Furan and Pyran

Figure 7.9 Fischer and Haworth Representations of D-Fructose


Reaction of Monosaccharides The carbonyl and hydroxyl groups can undergo

several chemical reactions Most important include oxidation, reduction,

isomerization, esterification, glycoside formation, and glycosylation reactions


Glycoside Formation—hemiacetals and hemiketals react with alcohols to form the corresponding acetal and ketal When the cyclic hemiacetal or hemiketal form of

the monosaccharide reacts with an alcohol, the new linkage is a glycosidic linkage and the compound a glycoside

Figure 7.17 Formation of Acetals and Ketals


Naming of glycosides specifies the sugar component Acetals of glucose and fructose are glucoside

and fructoside

Figure 7.18 Methyl Glucoside Formation


If an acetal linkage is formed between the hemiacetal hydroxyl of one monosaccharide and the hydroxyl of another, this forms a disaccharide

In polysaccharides, large numbers of monosaccharides are linked together through acetal linkages


Glycosylation Reactions attach sugars or glycans (sugar polymers) to proteins or lipidsCatalyzed by glycosyl transferases, glycosidic

bonds are formed between anomeric carbons in certain glycans and oxygen or nitrogen of other types of molecules, resulting in N- or O-glycosidic bonds


Glycation is the reaction of reducing sugars with nucleophilic nitrogen atoms in a nonenzymatic reaction

Most researched example of the glycation reaction is the nonenzymatic glycation of protein (Maillard reaction)

The Schiff base that forms rearranges to a stable ketoamine, called the Amadori product

Can further react to form advanced glycation end products (AGEs) Promote inflammatory processes and involved in

age-related diseases


Figure 7.20 The Maillard Reaction


Important MonosaccharidesGlucose (D-Glucose) —originally called

dextrose, it is found in large quantities throughout the natural world The primary fuel for living cells Preferred energy source for brain cells and cells

without mitochondria (erythrocytes)

Figure 7.21 a-D-glucopyranose


Fructose (D-Fructose) is often referred to as fruit sugar, because of its high content in fruit On a per-gram basis, it is twice as sweet as sucrose;

therefore, it is often used as a sweetening agent in processed food

Figure 7.22 b-D-fructofuranose


Galactose is necessary to synthesize a variety of important biomolecules Important biomolecules include lactose, glycolipids,

phospholipids, proetoglycan, and glycoproteins Galactosemia is a genetic disorder resulting from

a missing enzyme in galactose metabolism

Figure 7.23 a-D-galactopyranose

Section 7.2: Disaccharides

DisaccharidesTwo monosaccharides linked by a glycosidic bond Linkages are named by a- or b-conformation and

by which carbons are connected (e.g., a(1,4) or b(1,4))

Figure 7.27 Glycosidic Bonds


Disaccharides Continued Lactose (milk sugar) is the

disaccharide found in milk One molecule of galactose linked

to one molecule of glucose (b(1,4) linkage)

It is common to have a deficiency in the enzyme that breaks down lactose (lactase)

Lactose is a reducing sugar

Figure 7.28 a- and b-lactose


Disaccharides ContinuedSucrose is common table sugar

(cane or beet sugar) produced in the leaves and stems of plants One molecule of glucose linked

to one molecule of fructose, linked by an a,b(1,2) glycosidic bond Glycosidic bond occurs

between both anomeric carbons

Sucrose is a nonreducing sugar

Figure 7.31 Sucrose

Section 7.3: Polysaccharides

Polysaccharides (glycans) are composed of large numbers of monosaccharides connected by glycosidic linkages Smaller glycans made of 10 to 15 monomers

called oligosaccharides, most often attached to polypeptides as glycoproteins

Two broad classes: N- and O-linked oligosaccharides


O-Glycosidic linkages attach glycans to the side chain hydroxyl of serine or threonine residues or the hydroxyl oxygens of membrane lipids

Figure 7.32 Oligosaccharides Linked to Polypeptides

N-linked oligosaccharides are attached to polypeptides by an N-glycosidic bond with the side chain amide nitrogen from the amino acid asparagine Three major

types of asparagine-linked oligosaccharides: high mannose, hybrid, and complex


HomoglycansHave one type of monosaccharide and are found

in starch, glycogen, cellulose, and chitin (glucose monomer)

Starch and glycogen are energy storage molecules while chitin and cellulose are structural

Chitin is part of the cell wall of fungi and arthropod exoskeleton

Cellulose is the primary component of plant cell walls

No fixed molecular weight, because the size is a reflection of the metabolic state of the cell producing them


Starch—the energy reservoir of plant cells and a significant source of carbohydrate in the human diet Two polysaccharides occur together in starch:

amylose and amylopectin Amylose is composed of long, unbranched chains

of D-glucose with a(1,4) linkages between them

Figure 7.33 Amylose


Amylose typically contains thousands of glucose monomers and a molecular weight from 150,000 to 600,000 Da

The other form is amylopectin, which is a branched polymer containing both a(1,6) and a(1,4) linkages Branch points occur every 20 to 25 residues

Figure 7.33 Amylose


Glycogen is the carbohydrate storage molecule in vertebrates found in greatest abundance in the liver and muscle cells Up to 8–10% of the wet weight of liver cells and 2–

3% in muscle cells Similar in structure to amylopectin, with more

branch points More compact and easily mobilized than other

polysaccharides


Figure 7.34 (a) Amylopectin and (b) Glycogen


Cellulose is a polymer of D-glucopyranosides linked by b(1,4) glycosidic bonds

It is the most important structural polysaccharide of plants (most abundant organic substance on earth)

Figure 7.35 The Disaccharide Repeating Unit of Cellulose


Pairs of unbranched cellulose molecules (12,000 glucose units each) are held together by hydrogen bonding to form sheetlike strips, or microfibrils Each microfibril bundle is tough and inflexible with

a tensile strength comparable to that of steel wire Important for dietary fiber, wood, paper, and

textiles

Figure 7.36 Cellulose Microfibrils


HeteroglycansHigh-molecular-weight carbohydrate polymers

that contain more than one type of monosaccharide

Major types: N- and O-linked glycosaminoglycans (glycans), glycosaminoglycans, glycan components of glycolipids, and GPI (glycosylphosphatidylinositol) anchors GPI anchors and glycolipids will be discussed in

Chapter 11

Section 7.3: PolysaccharidesHeteroglycans Continued

N- and O-Glycans—many proteins have N- and O-linked oligosacchaarides N-linked (N-glycans) are linked via a b-glycosidic

bond O-linked (O-glycans) have a disaccharide core of

galactosyl-b-(1,3)-N-acetylgalactosamine linked via an a-glycosidic bond to the hydroxyl of serine or threonine residues

Glycosaminoglycans (GAGs) are linear polymers with disaccharide repeating units Five classes: hyaluronic acid, chondroitin sulfate,

dermatan sulfate, heparin and heparin sulfate, and keratin sulfate

Varying uses based on repeating unit

Section 7.4: Glycoconjugates

Glycoconjugates result from carbohydrates being linked to proteins and lipids

ProteoglycansDistinguished from other

glycoproteins by their high carbohydrate content (about 95%)

Occur on cell surfaces or are secreted to the extracellular matrix

Figure 7.38 Proteoglycan Aggregate From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press


GlycoproteinsCommonly defined as proteins that are covalently

linked to carbohydrates through N- and O-linkages Several addition reactions in the lumen of the

endoplasmic reticulum and Golgi complex are responsible for final N-linked oligosaccharide structure

O-glycan synthesis occurs later, probably initiating in the Golgi complex

Carbohydrate could be 1%–85% of total weightGlycoprotein Functions occur in cells as soluble

and membrane-bound forms and are nearly ubiquitous in living organisms Vertebrate animals are particularly rich in

glycoproteins


Figure 7.39 The Glycocalyx

Section 7.5: The Sugar Code

Living organisms require large coding capacities for information transfer Profound complexity of functioning systems To succeed as a coding mechanism, a class of

molecules must have a large capacity for variation

Glycosylation is the most important posttranslational modification in terms of coding capacity

More possibilities with hexasaccharides than hexapeptides


In addition to their immense combinatorial possibilities they are also relatively inflexible, which makes them perfect for precise ligand binding

Lectins Lectins, or carbohydrate-binding proteins, are

involved in translating the sugar code Bind specifically to carbohydrates via hydrogen

bonding, van der Waals forces, and hydrophobic interactions


Figure 7.40 Role of Oligosaccharides in Biological Recognition

Lectins ContinuedBiological processes

include binding to microorganisms, binding to toxins, and involved in leukocyte rolling


The Glycome Total set of sugars and glycans in a cell or

organism is the glycomeConstantly in flux depending on the cell’s

response to environment There is no template for glycan biosynthesis; it is

done in a stepwise processGlycoforms can result based upon slight

variations in glycan composition of each glycoprotein

Chapter 11

Lipids and Membranes

Fatty AcidsMonocarboxylic acids that typically contain

hydrocarbon chains of variable lengths (12 to 20 or more carbons)

Numbered from the carboxylate end, and the a-carbon is adjacent to the carboxylate group

Terminal methyl carbon is denoted the omega (w) carbon

Important in triacylglycerols and phospholipids

Figure 11.1 Fatty Acid Structure

Section 11.1: Lipid Classes

Most naturally occurring fatty acids have an even number of carbons in an unbranched chain

Fatty acids that contain only single carbon-carbon bonds are saturated

Fatty acids that contain one or more double bonds are unsaturated Can occur in two isomeric forms: cis

(like groups on the same side) and trans (like groups are on opposite sides)

Figure 11.2 Isomeric Forms of Unsaturated Molecules


The double bonds in most naturally occurring fatty acids are cis and cause a kink in the fatty acid chain

Unsaturated fatty acids are liquid at room temperature; saturated fatty acids are usually solid Monounsaturated fatty acids have one double

bond while polyunsaturated fats have two or more

Figure 11.3 Space-Filling and Conformational Models


Plants and bacteria can synthesize all fatty acids they require from acetyl-CoA

Animals acquire most of theirs from dietary sources Nonessential fatty acids can be synthesized

while essential fatty acids must be acquired from the diet

Omega-3 fatty acids (i.e., a-linolenic acid and its derivatives) may promote cardiovascular health

Certain fatty acids attach to proteins called acylated proteins; the groups (acyl groups) help facilitate interactions with the environment Myristoylation and palmitoylation


EicosanoidsA diverse group of powerful, hormone-like

(generally autocrine) molecules produced in most mammalian tissues

Include prostaglandins, thromboxanes, and leukotrienes Mediate a wide variety of physiological processes:

smooth muscle contraction, inflammation, pain perception, and blood flow regulation

Figure 11.4a Eicosanoids


Eicosonoids are often derived from arachidonic acid or eicosapentaenoic acid (EPA)

Prostaglandins contain a cyclopentane ring and hydroxyl groups at C-11 and C-15 Prostaglandins are involved in inflammation,

digestion, and reproduction

Figure 11.4a Eicosanoids


Figure 11.4b Eicosanoids


Thromboxanes differ structurally from other eicosanoids in that they have a cyclic ether Synthesized by polymorphonuclear lymphocytes Involved in platelet aggregation and

vasoconstriction following tissue injury

Leukotrienes were named from their discovery in white blood cells and triene group in their structure LTC4, LTD4, and LTE4 have been identified as

components of slow-reacting substance of anaphylaxis

Other effects of leukotrienes: blood vessel fluid leakage, white blood cell chemoattractant, vasoconstriction, edema, and bronchoconstriction

Figure 11.4c Eicosanoids


Triacylglycerols Triacylglycerols are esters of glycerol with three

fatty acidsNeutral fats because they have no chargeContain fatty acids of varying lengths and can be

a mixture of saturated and unsaturated

Figure 11.5 Triacylglycerol


Depending on fatty acid composition, can be termed fats or oils Fats are solid at room

temperature and have a high saturated fatty acid composition

Oils are liquid at room temperature and have a high unsaturated fatty acid composition

Figure 11.6 Space-Filling and Conformational Models of a Triacylglycerol


Roles in animals: energy storage (also in plants), insulation at low temperatures, and water repellent for some animals’ feathers and fur Better storage form of energy for two reasons:

1. Hydrophobic and coalesce into droplets; store an equivalent amount of energy in about one-eighth the space2. More reduced and thus can release more electrons per molecule when oxidized

Figure 11.5 Triacylglycerol


Wax EstersWaxes are complex mixtures of nonpolar lipids Protective coatings on the leaves, stems, and

fruits of plants and on the skin and fur of animalsWax esters composed of long-chain fatty acids

and long-chain alcohols are prominent constituents of most waxes Examples include carnuba (melissyl cerotate) and

beeswax

Figure 11.8 The Wax Ester Melissyl Cerotate


PhospholipidsAmphipathic with a polar head group (phosphate

and other polar or charged groups) and hydrophobic fatty acids

Act in membrane formation, emulsification, and as a surfactant

Spontaneously rearrange into ordered structures when suspended in water

Figure 11.9 Phospholipid Molecules in Aqueous Solution


Two types of phospholipids: phosphoglycerides and sphingomyelins Sphingomyelins contain sphingosine instead of

glycerol (also classified as sphingolipids) Phosphoglycerides contain a glycerol, fatty

acids, phosphate, and an alcohol Simplest phosphoglyceride is phosphatidic acid

composed of glycerol-3-phosphate and two fatty acids

Phosphatidylcholine (lecithin) is an example of alcohol esterified to the phosphate group as choline


Another phosphoglyceride, phosphatidylinositol, is an important structural component of glycosyl phosphatidylinositol (GPI) anchors GPI anchors attach

certain proteins to the membrane surface

Proteins are attached via an amide linkage

Figure 11.10 GPI Anchor


PhospholipasesHydrolyze ester bonds in glycerophospholipid

molecules Three major functions: membrane remodeling,

signal transduction, and digestionMembrane remodeling—removal of fatty

acids to adjust the ratio of saturated to unsaturated or repair a damaged fatty acid

Figure 11.11 Phospholipases


Phospholipases ContinuedSignal Transduction—phospholipid

hydrolysis initiates the signal transduction by numerous hormones

Digestion—pancreatic phospholipases degrade dietary phospholipids in the small intestine

Toxic Phospholipases—various organisms use membrane-degrading phospholipases as a means of inflicting damageBacterial a-toxin and necrosis from snake

venom (PLA2)


Sphingolipids Important components of animal and plant

membranes Sphingosine (long-chain amino alcohol) and

ceramide in animal cells

Figure 11.12 Sphingolipid Components


Sphingomyelin is found in most cell membranes, but is most abundant in the myelin sheath of nerve cells

Figure 11.13 Space-Filling and Conformational Models of Sphingolmyelin


The ceramides are also precursors of glycolipids A monosaccharide, disacchaaride, or

oligosaccharide attached to a ceramide through an O-glycosidic bond

Most important classes are cerebrosides, sulfatides, and gangliosides (may bind bacteria and their toxins)

Figure 11.14a Selected Glycolipids


Cerebrosides have a monosaccharide for their head group Galactocerebroside is found in brain cell

membranes Sulfatides are negatively charged at physiological

pH Gangliosides possess oligosaccharide groups;

occur in most animal tissues and GM2 is involved in Tay-Sachs disease

Figure 11.14b Selected Glycolipids


IsoprenoidsVast array of biomolecules containing repeating

five-carbon structural units, or isoprene units Isoprenoids consist of terpenes and steroidsTerpenes are classified by the number of

isoprene units they have Monoterpenes (used in perfumes), sesquiterpines

(e.g., citronella), tetraterpenes (e.g., carotenoids)

Figure 11.15 Isoprene


Carotenoids are the orange pigments found in plants

Mixed terpenoids consist of a nonterpene group attached to the isoprenoid group (prenyl groups) Include vitamin K and vitamin E

Figure 11.16 Vitamin K, a Mixed Terpenoid


A variety of proteins are covalently attached to prenyl groups (prenylation): farnesyl and geranylgeranyl groups Unknown function, but may be involved in cell

growth

Figure 11.17 Prenylated Proteins


Steroids are derivatives of triterpenes with four fused rings (e.g., cholesterol) Found in all eukaryotes and some bacteria Differentiated by double-bond placement and

various substituents

Figure 11.18 Structure of Cholesterol


Cholesterol is an important molecule in animal cells that is classified as a sterol, because C-3 is oxidized to a hydroxyl group Essential in animal membranes; a precursor of

all steroid hormones, vitamin D, and bile salts Usually stored in cells as a fatty acid ester

The term steroid is commonly used to describe all derivatives of the steroid ring structure


Figure 11.19 Animal Steroids


Lipoproteins Term most often applied to a

group of molecular complexes found in the blood plasma of mammals

Transport lipid molecules through the bloodstream from organ to organ

Protein components (apolipoproteins) for lipoproteins are synthesized in the liver or intestine

Figure 11.21 Plasma Lipoproteins


Lipoproteins are classified according to their density: Chylomicrons are large lipoproteins of extremely

low density that transport triacylglycerol and cholesteryl esters (synthesized in the intestines)

Very low density lipoproteins (VLDL) are synthesized in the liver and transport lipids to the tissues

Low density lipoproteins (LDL) are principle transporters of cholesterol and cholesteryl esters to tissues

High density lipoprotein (HDL) is a protein-rich particle produced in the liver and intestine that seems to be a scavenger of excess cholesterol from membranes


A membrane is a noncovalent heteropolymer of lipid bilayer and associated proteins (fluid mosaic model)

Membrane Structure Proportions of lipid, protein, and carbohydrate vary

considerably among cell types and organelles

Section 11.2: Membranes

Membrane lipids: phospholipids form bimolecular layers at relatively low concentrations; this is the basis of membrane structure Membrane lipids are largely responsible for many

membrane properties Membrane fluidity refers to the viscosity of the

lipid bilayer Rapid lateral movement is apparently responsible

for normal membrane function

Figure 11.25 Lateral Diffusion in Biological Membranes


The movement of molecules from one side of a membrane to the other requires a flipase

Membrane fluidity largely depends on the percentage of unsaturated fatty acids and cholesterol Cholesterol contributes

to stability with its rigid ring system and fluidity with its flexible hydrocarbon tail

Figure 11.24 Diagrammatic View of a Lipid Bilayer


Selective permeability is provided by the hydrophobic chains of the lipid bilayer, which is impermeable to most all molecules (except small nonpolar molecules) Membrane proteins help regulate the

movement of ionic and polar substances Small nonpolar substances may diffuse down

their concentration gradient Self-sealing is a result of the lateral flow of lipid

molecules after a small disruption Asymmetry of biological membranes is necessary

for their function The lipid composition on each side of the

membrane is different


Membrane Proteins—most functions associated with the membrane require membrane proteins

Classified by their relationship with the membrane: peripheral or integral

Figure 11.26 Integral and Peripheral Membrane Proteins


Integral proteins embed in or pass through the membrane Red blood cell anion

exchanger Peripheral proteins are

bound to the membrane primarily through noncovalent interactions

Can be linked covalently through myristic, palmitic, or prenyl groups GPI anchors link a wide

variety of proteins to the membrane

Figure 11.27 Red Blood Cell Integral Membrane Proteins


Membrane Microdomains—lipids and proteins in membranes are not uniformly distributed Specialized microdomains like “lipid rafts” can be

found in the external leaflet of the plasma membrane

Figure 11.28 Lipid Rafts


Lipid rafts often include cholesterol, sphingolipids, and certain proteins

Lipid molecules are more ordered (less fluid) than non- raft regions Lipid rafts have been implicated in a number of

processes: exocytosis, endocytosis, and signal transduction

Figure 11.29 The Lipid Raft Environment


Membrane Function There are a vast array of membrane functions,

including transport of polar and charged substances and the relay of signals

Figure 11.30 Transport across Membranes


Membrane Transport—the mechanisms are vital to living organisms

Ions and molecules constantly move across the plasma membrane and membranes of organelles Important for nutrient intake, waste excretion,

and the regulation of ion concentration Biological transport mechanisms are classified

according to whether they require energy


In passive transport, there is no energy input, while in active transport, energy is required Passive is exemplified by simple diffusion and

facilitated diffusion (with the concentration gradient)

Active transport uses energy to transport molecules against a concentration gradient

Figure 11.30 Transport across Membranes


Simple diffusion involves the propulsion of each solute by random molecular motion from an area of high concentration to an area of low concentration Diffusion of gases O2 and CO2 across

membranes is proportional to their concentration gradients

Does not require a protein channel Facilitated diffusion uses channel proteins to

move large or charged molecules down their concentration gradient Examples include chemically gated Na+ channel

and voltage-gated K+ channel


Active transport has two forms: primary and secondary In primary active transport, transmembrane

ATP-hydrolyzing enzymes provide the energy to drive the transport of ions or molecules Na+-K+ ATPase

Figure 11.31 The Na+-K+ ATPase and Glucose Transport


In secondary active transport, concentration gradients formed by primary active transport are used to move other substances across the membrane Na+-K+ ATPase pump in the kidney drives the

movement of D-glucose against its concentration gradient

Figure 11.31 The Na+-K+ ATPase and Glucose Transport


Membrane Receptors provide mechanisms by which cells monitor and respond to changes in their environment

Chemical signals bind to membrane receptors in multicellular organisms for intracellular communication

Other receptors are involved in cell-cell recognition

Binding of ligand to membrane receptor causes a conformational change and programmed response


Section 2 Biochemical Building Blocks. Chapter 17 Nucleic Acids.

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Transcript of Section 2 Biochemical Building Blocks. Chapter 17 Nucleic Acids.