Biochemical Building Blocks

Biochemical Building Blocks
Section 2 Biochemical Building Blocks

Chapter 17 Nucleic Acids

Section 17.1: DNA Figure 17.2 Two Models of DNA Structure 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

Section 17.1: DNA Figure 17.2 Two Models of DNA Structure 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

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 DNA RNA Protein
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) DNA RNA Protein

Section 17.1: DNA 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 Figure 17.5 DNA Structure 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

The dimensions of crystalline B-DNA have been precisely measured:
Section 17.1: DNA Figure 17.6 DNA Structure: GC Base Pair Dimensions 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

Section 17.1: DNA Figure 17.6 DNA Structure: AT Base Pair Dimensions 2. Diameter of the double helix is 2.37 nm, only suitable for base pairing a purine with a pyrimidine 3. The distance between adjacent base pairs is nm

Section 17.1: DNA DNA is a relatively stable molecule with several noncovalent interactions adding to its stability 1. Hydrophobic interactions—internal base clustering 2. Hydrogen bonds—formation of preferred bonds: three between CG base pairs and two between AT base pairs 3. Base stacking—bases are nearly planar and stacked, allowing for weak van der Waals forces between the rings 4. Hydration—water interacts with the structure of DNA to stabilize structure 5. 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

DNA Structure: The Genetic Material
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

DNA Structure: Variations on a Theme
Section 17.1: DNA DNA Structure: Variations on a Theme Watson 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 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 Linear and Circular DNA and DNA Winding

Chromosomes and Chromatin
Section 17.1: DNA Chromosomes and Chromatin DNA 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 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 complex Figure 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 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 genomes 2. Coding capacity—compact and continuous genes 3. 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 complexity 2. 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 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 ( 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

Differences between DNA and RNA primary structure:
Section 17.2: RNA 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 deoxyribose 2. Uracil nucleotide instead of thymine Figure 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 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 Figure 17.26b Transfer RNA

Section 17.2: RNA Ribosomal RNA
Ribosomal 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 Figure rRNA Structure 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 Messenger RNA
Messenger 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 RNA
RNAs 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 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 17.3: Viruses 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 function Viruses can cause numerous different diseases, but have also been invaluable in the development of recombinant DNA technology Human papillomavirus can cause cervical cancer

Chapter 18 Genetic Information

Chapter 18: Overview Numerous contacts are involved including hydrophobic interactions, hydrogen bonding, and ionic bonds Between 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 Figure 18.2 DNA-Protein Interactions 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-helix 2. Helix-loop-helix 3. Leucine zipper 4. Zinc finger

Chapter 18: Overview 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

Variation may also be important for adaptability to environments
Section 18.1: Genetic Information: Replication, Repair, and Recombination All viable living organisms possess rapid and accurate DNA synthesis and effective DNA repair mechanisms Variation may also be important for adaptability to environments Variation is caused by genetic recombination and mutation

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

Figure 18.4 The Meselson-Stahl Experiment 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

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)

Figure 18.5 The DNA Polymerase Reaction 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

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
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 
Section 18.1: Genetic Information: Replication, Repair, and Recombination Figure 18.7 Cross Section of the b2-Clamp of DNA Polymerase III 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

There are four other DNA polymerases:
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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

Supercoiling control is accomplished by DNA topoisomerases
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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

Figure DNA Replication at a Replication Fork 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)

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

The replication fork moves forward as DnaB unwinds the helix
Section 18.1: Genetic Information: Replication, Repair, and Recombination Figure Replication Fork Formation 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)

For pol III to initiate DNA synthesis an RNA primer must be present
Section 18.1: Genetic Information: Replication, Repair, and Recombination Figure E. coli DNA Replication Model 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

Pol III synthesizes at the 3′ end of the primer
Section 18.1: Genetic Information: Replication, Repair, and Recombination Figure E. coli DNA Replication Model Pol III synthesizes at the 3′ end of the primer RNA primers are removed by pol I, which then synthesizes complementary DNA DNA ligase then joins Okazaki fragments Tandem operation of two pol III complexes requires the lagging strand be looped around the replisome

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

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

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 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 structure Figure The Eukaryotic Cell Cycle

Humans have 30,000 origins of replication
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 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 Formation of a Preinitiation Replication Complex

Cdc6 and Cdt1 bind ORC and recruit the MCM complex (helicase)
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 Eukaryotic Replication Fork Formation

Each strand is then stabilized by replication protein A (RPA)
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 Eukaryotic Replication Fork Formation

Replication occurs until replicons meet and fuse
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 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 Telomerase-Catalyzed Extension of a Chromosome

TEBPs bind GT-rich telomere sequences TRFs secure the 3′ overhang
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 Figure Telomerase-Catalyzed Extension of a Chromosome

Telomere shortening causes cell death
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 Figure Telomerase-Catalyzed Extension of a Chromosome

DNA Repair Mutations 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 generation Cells possess a great variety of DNA repair mechanisms

Direct Repairs A 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 Photoreactivation Repair of Thymine Dimers

Figure Base Excision Repair 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 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

Two types: global genomic repair and transcription coupled repair
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 Excision Repair of a Thymine Dimer in E. coli

Damage is recognized when RNA polymerase is stalled
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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

Recombination will be explained next
Section 18.1: Genetic Information: Replication, Repair, and Recombination 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 Recombination Recombination 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 wall 2. Transduction is when a bacteriophage inadvertently carries bacterial DNA to a recipient cell 3. 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 genomes Figure 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
Section 18.1: Genetic Information: Replication, Repair, and Recombination Figure 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

Section 18.2: Transcription
Figure DNA Coding Strand 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 Transcription Initiation in E. coli 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)

Two short consensus sequences at -10 (Pribnow box) and -35 are similar among many bacterial species Figure Typical E. coli Transcription Unit

Figure Intrinsic Termination 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

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 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 functions Regulatory 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 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 basepairs Typically occur within CpG islands and commonly found in vertebrates. CpGs are now believed to facilitate nucleosome destabilization

Figure The Eukaryotic RNAPII Core Promoter 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

Figure The Methylated Cap of Eukaryotic mRNA 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 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

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

Figure RNA Splicing 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

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 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

Section 18.3: Gene Expression
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

Figure The lac Operon in E. coli 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

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)

Figure 18.51a Riboswitches 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

Gene Expression in Eukaryotes Eukaryotic genomes have more intricate regulation of gene expression Gene expression is regulated at the following levels: genomic control, transcriptional control, RNA processing, RNA editing, RNA transport, and translational control

Figure Eukaryotic Gene Regulatory Proteins 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

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 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 Eukaryotic Gene Expression Triggered by Growth Factor Binding

Chapter 7 Carbohydrates

Carbohydrates are the most abundant biomolecule in nature
Chapter 7: Overview Carbohydrates are the most abundant biomolecule in nature Have 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

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

Monosaccharide Stereoisomers An 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

Figure 7.5 Formation of Hemiacetals and Hemiketals 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 7.6 Monosaccharide Structure 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 7.7 Haworth Structures of the Anomers of D-Glucose 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 7.8 Furan and Pyran 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 7.9 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

Figure 7.17 Formation of Acetals and Ketals 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 7.18 Methyl Glucoside Formation Naming of glycosides specifies the sugar component Acetals of glucose and fructose are glucoside and fructoside

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 lipids Catalyzed 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

Figure 7.21 a-D-glucopyranose Important Monosaccharides Glucose (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 7.22 b-D-fructofuranose 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 7.23 a-D-galactopyranose 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

Section 7.2: Disaccharides
Figure 7.27 Glycosidic Bonds Disaccharides Two 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))

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 Continued Sucrose 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

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 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

Homoglycans Have 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

Figure 7.33 Amylose 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

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

Figure 7.35 The Disaccharide Repeating Unit of Cellulose 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 7.36 Cellulose Microfibrils 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

Heteroglycans High-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

Heteroglycans 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 Proteoglycans Distinguished 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

Glycoproteins Commonly 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 weight Glycoprotein 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

Lectins Continued Biological processes include binding to microorganisms, binding to toxins, and involved in leukocyte rolling Figure 7.40 Role of Oligosaccharides in Biological Recognition

The Glycome Total set of sugars and glycans in a cell or organism is the glycome Constantly in flux depending on the cell’s response to environment There is no template for glycan biosynthesis; it is done in a stepwise process Glycoforms can result based upon slight variations in glycan composition of each glycoprotein

Chapter 11 Lipids and Membranes

Section 11.1: Lipid Classes
Figure 11.1 Fatty Acid Structure Fatty Acids Monocarboxylic 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

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

Figure 11.3 Space-Filling and Conformational Models 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

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

Figure 11.4a Eicosanoids Eicosanoids A 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 11.4b 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

Figure 11.4c Eicosanoids 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 11.5 Triacylglycerol Triacylglycerols Triacylglycerols are esters of glycerol with three fatty acids Neutral fats because they have no charge Contain fatty acids of varying lengths and can be a mixture of saturated and unsaturated

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

Figure 11.5 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 space 2. More reduced and thus can release more electrons per molecule when oxidized

Figure 11.8 The Wax Ester Melissyl Cerotate Wax Esters Waxes are complex mixtures of nonpolar lipids Protective coatings on the leaves, stems, and fruits of plants and on the skin and fur of animals Wax 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 11.9 Phospholipid Molecules in Aqueous Solution Phospholipids Amphipathic 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

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 GPI Anchor

Figure Phospholipases Phospholipases Hydrolyze ester bonds in glycerophospholipid molecules Three major functions: membrane remodeling, signal transduction, and digestion Membrane remodeling—removal of fatty acids to adjust the ratio of saturated to unsaturated or repair a damaged fatty acid

Phospholipases Continued Signal 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 damage Bacterial a-toxin and necrosis from snake venom (PLA2)

Figure Sphingolipid Components Sphingolipids Important components of animal and plant membranes Sphingosine (long-chain amino alcohol) and ceramide in animal cells

Sphingomyelin is found in most cell membranes, but is most abundant in the myelin sheath of nerve cells Figure Space-Filling and Conformational Models of Sphingolmyelin

Figure 11.14a Selected Glycolipids 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 11.14b 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 Isoprene Isoprenoids Vast array of biomolecules containing repeating five-carbon structural units, or isoprene units Isoprenoids consist of terpenes and steroids Terpenes are classified by the number of isoprene units they have Monoterpenes (used in perfumes), sesquiterpines (e.g., citronella), tetraterpenes (e.g., carotenoids)

Figure Vitamin K, a Mixed Terpenoid 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 Prenylated Proteins 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 Structure of Cholesterol 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

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 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 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

Section 11.2: 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 Figure Lateral Diffusion in Biological 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

Section 11.2: 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 Diagrammatic View of a Lipid Bilayer

Section 11.2: Membranes 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

Section 11.2: Membranes Figure Integral and Peripheral Membrane Proteins Membrane Proteins—most functions associated with the membrane require membrane proteins Classified by their relationship with the membrane: peripheral or integral

Section 11.2: Membranes 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 Red Blood Cell Integral Membrane Proteins

Section 11.2: Membranes Figure Lipid Rafts 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

Section 11.2: Membranes Figure The Lipid Raft Environment 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

Section 11.2: Membranes Membrane Function
Figure Transport across Membranes Membrane Function There are a vast array of membrane functions, including transport of polar and charged substances and the relay of signals

Section 11.2: 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

Section 11.2: Membranes Figure Transport across Membranes 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

Section 11.2: 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

Section 11.2: Membranes Figure The Na+-K+ ATPase and Glucose Transport 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

Section 11.2: Membranes Figure 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

Section 11.2: Membranes 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

Biochemical Building Blocks

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