Science Focus (issue 022)

In Issue 018, we introduced you to the concept of transposable elements and its discoverer, Barbara McClintock. Maybe you find it crazy that our DNA can jump around the genome, creat ing new insertions. Sti l l, there are many more fascinating things about these elements. This article will take you through some of the most intriguing things about transposable elements and what they do other than jumping around. Classification and Origin Transposable elements (TEs) can be classified into two types based on their mechanism of insertion. Class 1 TEs are cal led retrotransposons. These elements jump around the genome by a copy-andpaste mechanism. The retrotransposons are fi rst transcribed into an RNA intermediate, then reverse transcribed into DNA. This process creates a DNA segment identical to the original retrotransposon. The DNA copy is then integrated into the genome to create a new inser tion. Class 2 TEs are DNA transposons that can be cut and pasted without amplification. A DNA transposon is excised from the original position and re-integrated into another part of the genome with the help of an enzyme called transposase. All TEs together make up around 50% of the human genome [1], although, throughout evolutionary, most have lost their ability to jump around. If you are familiar with the mechanism of viral infection, you may see some resemblance between these mechanisms. Indeed, retrotransposons and a particular type of virus, retrovirus, share many similarities, such as the ability to insert their DNA, synthesized from reverse transcription, into the host genome. In fact, endogenous retrovirus (ERV; not retrovirus but viral DNA in our genome) are a type of retrotransposon, which are the remnants of viral germ-line infections millions of years ago. The viral genome was integrated into our ancestors’ genome and passed on to future In Issue 018, we introduced 15 By Peace Foo 胡適之 benzoate was unsafe [4]. This motivated Henry Heinz and his company to search for a preservative-free ketchup [5, 6]. As other food scientists discovered [5], the key lay in the ripeness of the tomatoes used and the addition of more solutes. Ripe tomatoes contain more pectin and pectic acid, which are created by enzymatic reactions during the ripening process. Not only did the higher pectin content thicken the ketchup, the technique that Heinz adopted also cal led for the addition of more salt, sugar and vinegar [5], which did several things. The pectic acid and vinegar made ketchup more acidic. The addition of solutes like salt and sugar reduced the ability of water molecules to move, not just within ketchup, but also into microorganisms for the biological reactions necessary to support their growth [7]. Both effects inhibit microbial growth synergistically and prevent spoiling without resorting to preservatives. As a bonus, the riper tomatoes and added vinegar and sugar made ketchup both sweeter and sourer [8], giving it its distinct and much-loved flavor. It turns out additional tricks can be applied to the bottle for holding the ketchup, in order to facilitatea “smooth pour” [9]. But that will be the topic of another story. 茄汁是一種不太友善的醬汁。以下是你把茄汁從雪櫃取 出後發生的連環不幸事件:你嘗試倒出茄汁但不果,然後多 次猛力拍打瓶底,但茄汁依然無動於衷,只好苦等一會後再 來一次 — 啊 —!這次茄汁一下子從瓶裡射出,而你根本用 不著那麼多茄汁。茄汁是用途廣泛的調味料,適合配搭不同 食物,因此以上情境也許是茄汁愛好者習以為常的經驗。但 為甚麼這樣的事情會一再發生呢?為甚麼只有茄汁會出現 以上的情況? 作為有可變黏度流體的茄汁 我們想茄汁容易流動,但從雪櫃取出的茄汁卻是冰冷 的,決不是容易流動的。這時在物理學上它可以被形容為黏 滯(viscous),即不易流動 [1]。與其待它解凍,大多數人會 選擇用力敲打茄汁瓶的底部。根據牛頓黏滯定律,流 體的流動速度應與施加的力成正比,但茄汁有觸變性 (thixotropy)的特點 [2],意思是茄汁變稀或變得容 易流動的程度與施力是不成比例的,故此茄汁又被稱 為非牛頓流體 [3]。 為甚麼茄汁會有這樣的特性?由於分子間的吸引 力或有大型分子充當物理障礙阻礙分子流動 [1],黏 滯流體裡的分子不能自由流動。至於茄汁,它 95% 的 成分是由水和醋(乙酸)等等的小分子及鹽組成 [2], 但其觸變性正是由另外 5% 的成分所賦予的。 茄汁另外 5% 的成分是多種大型糖分子(多糖) [1],當中影響力最大的是果膠,它是番茄(及其他很 多蔬果和植物)裡具黏性的多糖,作用是把相鄰的細 胞壁連接起來 [1]。製作茄汁時把番茄皮和果肉攪碎 會把果膠釋放至番茄漿內 [3],果膠和其他纖維分子 會構成大型分子網絡結構,當中靠分子的電荷把分子 網絡拉住 [1]。這亦意味著包括水在內的小極性分子 並不能再自由流動,因為它們會被分子間作用力拉向 網絡 [1];當它們不能自由流動時,茄汁就會變得黏 滯。 你可能見過茄汁在放置一段長時間後表面會浮 現一層水;事實上,過多的水份最終可以離開分子 網絡,這過程稱為瀝取(leaching)[1]。此時你需 要搖勻茄汁,使分子再一次均勻分配而達至均勻化 (hom ge ized)。但記著,茄汁是非牛頓流體,當 你搖動茄汁瓶或猛敲瓶底時,施加的力會破壞維持分 子網絡的分子間引力,令茄汁中的水份以與所施的力 不相稱的速度飛快濺出! 到微生物學