8: Peptide Bonds, Polypeptides and Proteins
- Page ID
- 181729
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 8.0: Introduction
- This page covers the significance of proteins, detailing their synthesis from amino acids via peptide bonds and their roles in biological systems. It references historical contributions by Mulder and Berzelius, discusses gene-encoded polypeptide chains, and emphasizes the influence of amino acid side chains on protein structure and function. The text concludes by contrasting polypeptides with nucleic acids and exploring the evolutionary implications of shared amino acids.
- 8.1: Specifying a polypeptide’s sequence
- This page explains how DNA encodes polypeptide synthesis through transcription and translation processes. It highlights the role of codons in determining amino acid sequences and introduces the genetic code, which features start and stop codons. The content lays the foundation for understanding protein synthesis across different organisms like bacteria, archaea, and eukaryotes.
- 8.2: The origin of the genetic code
- This page discusses the uncertain origins of the genetic code, highlighting theories such as the frozen accident model related to LUCA and evolutionary bottlenecks. It suggests that early life may have consisted of various proto-organisms using different codes, with the current common code representing one lineage's survival.
- 8.3: Protein synthesis- transcription (DNA to RNA)
- This page explains polypeptide synthesis from DNA, emphasizing transcription initiation through specific DNA region recognition by transcription factors. These factors regulate RNA polymerase activity, influencing gene expression complexity. The role of multiple transcription factors in regulating gene groups according to environmental changes is discussed, along with the mechanisms of transcription factor action and RNA synthesis.
- 8.4: Protein synthesis- translation (RNA to polypeptide)
- This page explains the translation process, where ribosomes and tRNAs synthesize polypeptides from mRNA. Ribosomes consist of rRNAs and proteins, forming small and large subunits that enable polypeptide production. tRNAs, carrying amino acids, match codons on mRNA through their anticodon loops and are activated by distinct amino acyl tRNA synthetases. The differences in ribosomes across organisms reveal their evolutionary importance and implications for antibiotic function.
- 8.5: The translation (polypeptide synthesis) cycle
- This page covers protein synthesis, focusing on the regulated steps in mRNA-directed polypeptide synthesis (translation). It explains the roles of cellular components, the significance of the start codon, ribosomes, and differences in eukaryotic and prokaryotic translation. Additionally, it discusses how mRNA stability and degradation affect polypeptide levels, providing a foundation for further exploration of translation processes.
- 8.6: Effects of point mutations on polypeptides and proteins
- This page explores the influence of mutations on gene expression, detailing regulatory, coding, and non-coding regions. It categorizes mutations into synonymous, mis-sense, and non-sense types, discussing their effects on polypeptide function. It emphasizes codon bias in translation efficiency, spliceosome involvement in splicing mechanisms, and the complexities of eukaryotic genomes via alternative splicing.
- 8.7: Getting more complex- gene regulation in eukaryotes
- This page contrasts gene expression and polypeptide synthesis in prokaryotes and eukaryotes, highlighting the nucleus's role and mRNA processing. Eukaryotic mRNAs are modified before translation, with nuclear pores regulating transport. Nonsense-mediated decay (NMD) degrades faulty mRNA to protect against mutations, while starvation responses can lead to translation termination, reflecting a trade-off between individual survival and community needs.
- 8.8: Turning polypeptides into proteins
- This page addresses the complexities of protein synthesis and structure beyond the one gene-one protein model, emphasizing the importance of proper polypeptide folding into various structures influenced by environmental factors and molecular interactions. It discusses the role of hydrophobic interactions, peptide bonds, and chaperones in this process, highlighting how errors during translation can impact protein functionality.
- 8.9: Regulating protein activity, concentrations, and stability (half-life)
- This page discusses protein interactions and their regulation, focusing on enzymes that lower activation energy to enhance reaction rates. It emphasizes the importance of controlling protein synthesis, degradation, and activity to adapt to environmental changes. Protein degradation, facilitated by proteases, is vital for regulating protein levels and is a stochastic process fueled by ATP hydrolysis.
- 8.10: Allosteric and post-translational regulation
- This page discusses allosteric regulation, a process where regulatory molecules reversibly bind to proteins, modifying their structure and function. It contrasts this with competitive and non-competitive inhibition, which involve different binding methods. The page also highlights post-translational modifications, like phosphorylation and glycosylation, which involve covalent changes that influence protein activity and interactions.
- 8.11: Diseases of folding and misfolding
- This page discusses the differences between functional and mis-folded proteins, specifically in relation to prion diseases like Kuru, scrapie, and variant Creutzfeldt-Jakob disease. It covers the prion protein's role, genetic factors, neuronal damage, and key concepts such as iatrogenic transmission and resistance of PrP aggregates to proteolysis. The section emphasizes the historical context of prion diseases and includes reflective questions on associated biochemical processes.
- 8.12: Molecular machines
- This page highlights Drew Berry's video "Molecular Machines," which explores the complex dynamics of molecular biology within cells. It illustrates how molecules function like machines to carry out vital processes such as replication, transcription, and translation. The video emphasizes the beauty and complexity of these interactions, using animations to aid understanding of molecular activity and cellular mechanisms essential for sustaining life.