{"id":220136,"date":"2025-05-27T15:06:26","date_gmt":"2025-05-27T15:06:26","guid":{"rendered":"https:\/\/learnexams.com\/blog\/?p=220136"},"modified":"2025-05-27T15:06:28","modified_gmt":"2025-05-27T15:06:28","slug":"make-sure-you-clearly-indicate-all-charges","status":"publish","type":"post","link":"https:\/\/www.learnexams.com\/blog\/2025\/05\/27\/make-sure-you-clearly-indicate-all-charges\/","title":{"rendered":"Make sure you clearly indicate all charges."},"content":{"rendered":"\n

Draw the structure of histidine at pH 4 and at pH 8. Make sure you clearly indicate all charges.<\/p>\n\n\n\n

Briefly describe the nature of the H-bonds that stabilize parallel and antiparallel b-sheets. How do the H-bonds in these two types of secondary structure differ? You can draw simple diagrams if you wish, but there is no need for detailed structures.<\/p>\n\n\n\n

The Correct Answer and Explanation is:<\/mark><\/strong><\/p>\n\n\n\n

a) Structure of Histidine at pH 4 and pH 8<\/strong><\/h3>\n\n\n\n

Histidine has three ionizable groups:<\/p>\n\n\n\n

    \n
  • \u03b1-amino group (pKa \u2248 9.2)<\/li>\n\n\n\n
  • \u03b1-carboxyl group (pKa \u2248 2.0)<\/li>\n\n\n\n
  • Imidazole side chain (pKa \u2248 6.0)<\/li>\n<\/ul>\n\n\n\n

    At pH 4<\/strong> (below pKa of imidazole):<\/h4>\n\n\n\n
      \n
    • The carboxyl group<\/strong> is deprotonated<\/strong> (\u2013COO\u207b)<\/li>\n\n\n\n
    • The amino group<\/strong> is protonated<\/strong> (\u2013NH\u2083\u207a)<\/li>\n\n\n\n
    • The imidazole side chain<\/strong> is protonated<\/strong> (positively charged)<\/li>\n<\/ul>\n\n\n\n

      Histidine structure at pH 4:<\/strong><\/p>\n\n\n\n

            NH3\u207a\n       |\nH\u2082N\u2013CH\u2013COO\u207b\n       |\n     CH\u2082\n       |\n    C\u2083H\u2083N\u2082H\u207a  (protonated imidazole, positively charged)\n<\/code><\/pre>\n\n\n\n
      Net charge:<\/strong> +1<\/strong><\/p>\n\n\n\n
      At pH 8<\/strong> (above pKa of imidazole, below amino group pKa):<\/h4>\n\n\n\n
        \n
      • The carboxyl group<\/strong> is deprotonated<\/strong> (\u2013COO\u207b)<\/li>\n\n\n\n
      • The amino group<\/strong> is protonated<\/strong> (\u2013NH\u2083\u207a)<\/li>\n\n\n\n
      • The imidazole side chain<\/strong> is neutral<\/strong> (not protonated)<\/li>\n<\/ul>\n\n\n\n
        Histidine structure at pH 8:<\/strong><\/p>\n\n\n\n
              NH3\u207a\n       |\nH\u2082N\u2013CH\u2013COO\u207b\n       |\n     CH\u2082\n       |\n    C\u2083H\u2083N\u2082   (neutral imidazole ring)\n<\/code><\/pre>\n\n\n\n
        Net charge:<\/strong> 0<\/strong><\/p>\n\n\n\n
        \n\n\n\n
        b) Hydrogen Bonds in Parallel vs Antiparallel \u03b2-Sheets<\/strong><\/h3>\n\n\n\n
        Parallel \u03b2-Sheets:<\/h4>\n\n\n\n
          \n
        • Adjacent \u03b2-strands run in the same direction<\/strong> (N \u2192 C).<\/li>\n\n\n\n
        • Hydrogen bonds between strands are angled<\/strong> and slightly weaker<\/strong> due to non-linear alignment.<\/li>\n\n\n\n
        • Each amino acid forms hydrogen bonds with two different residues<\/strong> on the opposite strand.<\/li>\n<\/ul>\n\n\n\n
          Antiparallel \u03b2-Sheets:<\/h4>\n\n\n\n
            \n
          • Adjacent \u03b2-strands run in opposite directions<\/strong>.<\/li>\n\n\n\n
          • Hydrogen bonds are linear<\/strong>, making them stronger and more stable<\/strong>.<\/li>\n\n\n\n
          • Each amino acid typically forms hydrogen bonds with one directly opposite residue<\/strong>.<\/li>\n<\/ul>\n\n\n\n
            \n\n\n\n
            Diagram (simplified):<\/h3>\n\n\n\n
            Parallel:<\/h4>\n\n\n\n
            Strand A \u2192   N \u2014 C \u2014 N \u2014 C \u2014 N \u2014 C\nStrand B \u2192   N \u2014 C \u2014 N \u2014 C \u2014 N \u2014 C\n       H-bonds angled\n<\/code><\/pre>\n\n\n\n
            Antiparallel:<\/h4>\n\n\n\n
            Strand A \u2192   N \u2014 C \u2014 N \u2014 C \u2014 N \u2014 C\nStrand B \u2190   C \u2014 N \u2014 C \u2014 N \u2014 C \u2014 N\n       H-bonds straight\n<\/code><\/pre>\n\n\n\n
            \n\n\n\n
            Explanation<\/h3>\n\n\n\n
            In proteins, \u03b2-sheets are stabilized by hydrogen bonds between backbone amide groups of \u03b2-strands. These \u03b2-strands can be arranged either in parallel<\/strong> or antiparallel<\/strong> orientations.<\/p>\n\n\n\n
            In parallel \u03b2-sheets<\/strong>, the adjacent strands run in the same direction<\/strong> (from the N-terminus to the C-terminus). Due to this alignment, the hydrogen bonds between the carbonyl oxygen (C=O) of one strand and the amide hydrogen (N\u2013H) of the adjacent strand are slightly bent<\/strong>. These bent hydrogen bonds are less optimal and thus weaker<\/strong> compared to those in antiparallel sheets. Additionally, in parallel \u03b2-sheets, a single residue in one strand typically forms hydrogen bonds with two different residues<\/strong> on the adjacent strand, contributing to the complexity and slightly reduced stability.<\/p>\n\n\n\n
            In contrast, antiparallel \u03b2-sheets<\/strong> have strands running in opposite directions<\/strong>. This orientation allows the hydrogen bonds to form linearly<\/strong>, which is energetically more favorable. As a result, the hydrogen bonds in antiparallel \u03b2-sheets are stronger and more stable<\/strong>. Here, each amino acid forms a hydrogen bond with a single amino acid directly across from it, leading to a more regular and stable structure.<\/p>\n\n\n\n
            Because of the difference in hydrogen bonding geometry, antiparallel \u03b2-sheets are generally more stable<\/strong> and are more commonly found in proteins. However, both types are important for protein structure and can coexist in the same protein. The nature of hydrogen bonding significantly influences the mechanical and structural properties of proteins.<\/p>\n\n\n\n
            \"\"<\/figure>\n","protected":false},"excerpt":{"rendered":"
            Draw the structure of histidine at pH 4 and at pH 8. Make sure you clearly indicate all charges. Briefly describe the nature of the H-bonds that stabilize parallel and antiparallel b-sheets. How do the H-bonds in these two types of secondary structure differ? You can draw simple diagrams if you wish, but there is […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"categories":[25],"tags":[],"class_list":["post-220136","post","type-post","status-publish","format-standard","hentry","category-exams-certification"],"_links":{"self":[{"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/posts\/220136","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/comments?post=220136"}],"version-history":[{"count":0,"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/posts\/220136\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/media?parent=220136"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/categories?post=220136"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.learnexams.com\/blog\/wp-json\/wp\/v2\/tags?post=220136"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}