Introduc)on  to  the  Science  of  Living  Organisms  Biology  11  

 

•  If  you  missed  Wednesday’s  first  class  you  can  find  slides  and  the  syllabus  on  bcourses:  h"ps://bcourses.berkeley.edu/courses/1195924  

•  There  are  some  example  exam  ques)ons  posted  at  the  end  of  the  slides  

Overview    

• What  defines  living  organisms?  

• What  is  the  chemical  basis  of  life?  

What  defines  living  organisms?  

1. Organisms  are  made  of  cells  2. Organisms  are  made  of  the  same  subset  of  molecules:  – Proteins  – Carbohydrates  – Lipids    – Nucleic  acids  

What  defines  living  organisms?  

1.  Organisms  are  made  of  cells  2.  Organisms  are  made  of  the  same  subset  of  

molecules  3.  Organisms  reproduce  by  passing  along  DNA.  DNA  

guides  development  –  DNA  –  deoxyribonucleic  acid  -­‐  is  the  signature  molecule  of  life  

and  inheritance.    

What  defines  living  organisms?  

1.  Organisms  are  made  of  cells  2.  Organisms  are  made  of  the  same  subset  of  

molecules  3.  Organisms  reproduce  by  passing  along  DNA.  DNA  

guides  development  4.  Organisms  obtain  and  convert  energy  from  their  

surroundings.  Cells  use  energy  for  repair,  maintenance,  growth,  and  reproduc)on.    

Energy  input  (mainly  sunlight)  

PRODUCERS  plants  and  other  self-­‐feeding  organisms  that  make  their  own  food  

CONSUMERS  animals,  most  fungi,  many  pro)sts  and  bacteria  that  cannot  make  their  own  food  

Energy  output  (mainly  metabolic  heat)  

Nutrient  cycling    

What  defines  living  organisms?  

1.  Organisms  are  made  of  cells  2.  Organisms  are  made  of  the  same  subset  of  molecules  3.  Organisms  reproduce  by  passing  along  DNA.  DNA  guides  

development  4.  Organisms  obtain  and  convert  energy  from  their  

surroundings.  Cells  use  energy  for  repair,  maintenance,  growth,  and  reproduc)on.    

5.  Organisms  sense  and  respond  to  changes  in  their  internal  and  external  environment  in  controlled  ways  to  maintain  homeostasis  

 

Sensing  and  responding  

•  Includes:  – ATrac)on  – Avoidance  – Escape  – Expression  of  protec)ve  proteins  – Changes  in  physiology  

Homeostasis  example  –  blood  glucose  

Marieb    &  Hoehn  ,  (2005),  Human  Anatomy  &  Physiology  

HOMEOSTASIS, EXAMPLE: BLOOD GLUCOSE

Glucose

Insulin released

Glucose uptake

Glucose

What  defines  living  organisms?  1.  Organisms  are  made  of  cells  2.  Organisms  are  made  of  the  same  subset  of  molecules  3.  Organisms  reproduce  by  passing  along  DNA.  DNA  guides  

development  4.  Organisms  obtain  and  convert  energy  from  their  

surroundings.  Cells  use  energy  for  repair,  maintenance,  growth,  and  reproduc)on.    

5.  Organisms  sense  and  respond  to  changes  in  their  internal  and  external  environment  in  controlled  ways  to  maintain  homeostasis  

6.  Organisms  evolve.  Their  DNA  changes  from  genera)on  to  genera)on  

Evolu)on  

•  Gene)cally  based  change  in  a  line  of  descent  over  )me  

•  Popula)on  changes,  not  individuals  •  The  basis  for  evolu)on  is  varia)on  in  traits  – Muta)ons  – Heritable  changes  in  DNA  

•  What  becomes  of  individuals  with  different  traits  is  determined  by  selec)on  

Ar)ficial  Selec)on  

Natural  Selec)on  

•  The  outcome  of  differences  in  survival  and  reproduc)on  among  individuals  that  vary  in  their  heritable  traits  

•  This  process  helps  explain  evolu)on  –  changes  in  a  line  of  descent  over  genera)ons  

THE  CHEMICAL  BASIS  OF  LIFE  

Basic  building  blocks  

•  Atom  –  smallest  unit  of  an  element  that  s)ll  retains  the  elements  proper)es  (conduc)vity,  reac)vity,  etc)  

•  Element  –  a  pure  chemical  substance  made  up  of  one  atom  

Using  chemistry  in  archeology  

•  Assumed  that  manure  wasn’t  used  at  fer)lizer  un)l  the  )mes  of  Romans  

•  Recent  research  shows  that  manure  was  used  during  the  Neolithic  

•  How  did  researchers  figure  this  out?  

   

How  do  we  describe  elements?  

n=1

n=2

Valence electrons

ATOMS (EXAMPLE, CARBON)

the smallest unit that retain the properties of an element

C 6 12

atomic number = No. of protons

mass number =protons+neutrons

Hydrogen (H)

Carbon  

Periodic  Table  Columns  represent  atoms  with  the  same  number  of  valence  electrons  

Isotopes  •  Atoms  of  an  element  always  have  the  same  number  of  protons  (i.e.  the  same  atomic  number)  

•  Atoms  of  an  element  that  differ  in  the  number  of  neutrons  are  called  isotopes  (i.e.  different  atomic  mass)  

•  Isotopes  of  an  element  have  similar  reac)vity  because  the  number  of  valence  electrons  is  similar  

•  The  difference  in  mass  between  two  isotopes  of  an  element  leads  to  varia)on  in  chemical  processes  that  break  and  form  bonds      

Bogaard A et al. PNAS 2013;110:12589-12594

Nitrogen  isotopes  in  manure  Think  of  this  as  the  ra)o  of  heavy  15N  to  light  14N  found  in  different  crops  

FerQlizer  method  

Isotopes  in  ancient  seeds  

•  Analyzed  seeds  from  harvested  crops  preserved  in  Neolithic  houses  

•  Found  that  the  nitrogen  isotope  values  were  similar  to  high  levels  of  manure  applica)on    

•  Changes  how  we  view  Neolithic  society  – Slash  and  burn  à  long-­‐term  investment  in  land  – Nomadic  à  )es  to  land  – Could  have  led  to  territoriality  over  good  land  

 

Methods) (18) and can be used in conjunction with crop !15Nvalues to assess growing conditions and management practices,such as irrigation.Herein we present unique evidence for crop growing con-

ditions and farming practices based on carbon and nitrogenstable isotope determinations of 124 bulk crop samples (totaling>2,500 individual cereal grains or pulse seeds) from 13 Neolithicsites across Europe (Figs. 2 and 3), interpreted in the light ofherbivore forage !15N values estimated from stable isotopicanalysis of associated (domestic and wild) herbivore bone col-lagen, modern isotopic comparanda (12, 13, 16–18), experi-mental work on the effects of charring (19, 20), and associatedarable weed assemblages (4, 5, 21, 22). The sites mostly date tothe earlier Neolithic in their respective regions (Table 1) andwere selected on the basis of richness in well-preserved charredcrop material (Fig. 3); together, these sites provide a rough“transect” from southeast to northwest Europe (Fig. 2).

Results and DiscussionFig. 4 shows !13C and !15N values of cereals and pulses fromfour sites, and Table 2 summarizes results from all sites (forindividual sample results, see Table S2). Unsurprisingly, a broadclimatic trend in humidity is apparent if wheat or barley !13Cvalues at sites in or near the Mediterranean zone are comparedwith those in temperate zones (Fig. 2): thus, !13C values of wheat

(or barley) from sites in Greece and Bulgaria are lower thanthose from Germany and Denmark (Fig. 4 and Table 2). Ex-tensive isotope investigations of cereals and pulses from modernexperimental stations and farm studies across Europe, however,have shown that crop !15N values re!ect management practicesrather than broad climatic trends (13). For six of the sites inTable 2, herbivore forage !15N values have been estimated fromthe !15N determinations of associated bone collagen of largeherbivores by subtracting 4‰ as an average of the 3–5‰ rangeassociated with the trophic shift (15). At these sites, cereal grain!15N values tend to be considerably higher than those inferredfor forage. Although variation in !15N values among cerealcomponents may contribute to this contrast (cereal grain is ca.2.5‰ higher in !15N than associated rachis) (12, 13), even do-mestic herbivores receiving supplementary cereal fodder con-sumed a range of taxa and plant matter from various habitats (8)and, hence, inferred forage stable isotope values provide anapproximation of the local !15N value of nonarable vegetation.Contrasts in cereal and forage !15N values suggest that arablesoil N was relatively enriched in 15N. Weed evidence available ata number of sites indicates that cultivation plots were longestablished, with soils tending to be intensively disturbed andproductive (4, 5, 21, 22). Although these conditions excludesome potential causes of 15N-enrichment, such as wetland de-nitri"cation, salinity, and recent clearance (32, 33), they consti-tute a plausible context for manuring.Cereal grain !15N values at most sites are consistent with

signi"cant rates of manure application (Figs. 1 and 4, and Table 2).There is also considerable diversity in cereal !15N values at somesites. Local variation in manuring rates was observed in stableisotope studies of present-day traditional farming regimes inAsturias, Spain, and the Sighisoara region of western Romania(13). Variation is likely where manure is concentrated at speci"clocations in the landscape because it is heavy to transport andso tends to be used in close proximity to pens, byres, and so forth(9, 34). Low cereal !15N values (<3‰) indicative of long-termunmanured cultivation occur alongside high values at some sites(Fig. 4 A–C, and Table 2), and are dominant among the emmerwheat samples from Sarup, Denmark (Fig. 4D). Herbivore for-age !15N values from all sites (ca. 1–3‰) (Table 2) fall withinthe range of unmanured cereals (Fig. 1).Estimated forage !15N values are often similar to those of

pulses. As expected (13), pulses tend to exhibit lower !15N valuesthan associated cereals (Fig. 4 A and B, and Table 2). Only ex-tremely intensive manuring (>35 tons/ha over a prolonged pe-riod, resulting in the formation of “dung-soil”), as observed ina study of present-day broad bean gardens in Evvia, Greece(13), increases pulse !15N values considerably above 0‰. Thearchaeobotanical pulse !15N values thus point to intensive ma-nuring, variously comparable to, or higher than, the rates appliedto associated cereals. Furthermore, high pulse !13C values rel-ative to wheat at sites in Greece and Bulgaria (Fig. 4 A and B,and Table 2) indicate a higher water status and suggest prefer-ential use of well-watered soils for pulses or supplementaryirrigation.Overall, the crop nitrogen isotope compositions indicate that

early farmers in Europe made strategic use of manure as a re-source that was limited both by the scale of herding and by the

Fig. 1. Ranges of !15N values in modern bulk cereal samples (wheats andbarleys) grown under different rates of manuring at long-term agriculturalexperiments: Rothamsted, United Kingdom, Askov, Denmark, and BadLauchstädt, Germany (13). Dashed horizontal lines represent thresholds oflow (i.e., residual from previous land use history only), medium, and highmanuring rates.

Fig. 2. Map showing the archaeological sites. Fig. 3. Neolithic hulled barley grain from Koufovouno.

12590 | www.pnas.org/cgi/doi/10.1073/pnas.1305918110 Bogaard et al.

hTp://www.sciencedaily.com/releases/2013/07/130716134740.htm  

What  determines  which  atoms  will  interact?  

•  The  number  of  valence  electrons  •  All  atoms  want  to  be  completed  

Holds  2  e-­‐  

Holds  8  e-­‐  

Molecules  

•  Molecule  -­‐  when  at  least  two  atoms  are  bound  together  – Examples:  NaCl,    O2  

•  Ions  –  atoms  or  molecules  that  are  charged  (i.e.  +  or  -­‐)  due  to  the  loss  or  gain  of  an  electron  or  electrons    – Example:  K+,  OH-­‐  

Molecular  bonds  

•  Ionic  bonds  –  two  ions  that  are  held  held  together  by  opposite  charges  •  +  and  –  charges  aTract  •  Example:  Na+  +  Cl-­‐  =  NaCl  

Molecular  bonds  

•  Covalent  bonds  –  electrons  are  shared  between  atoms  

•  Example:  H2  

hTp://www.youtube.com/watch?v=Ku2CzwxTqhc  

Covalent  bonds  –  polar  or  nonpolar  

•  Nonpolar  covalent  bonds  –  atoms  exert  the  same  pull  on  the  electrons  

 •  Polar  covalent  bonds  –  atoms  exert  unequal  pulls  on  the  electrons  giving  rise  to  par)al  charge  

COVALENT BONDS (POLAR OR NONPOLAR)

Nonpolar covalent bond – atoms exert the same pull on the electrons

Polar covalent bond – atoms exert unequal pulls on the electrons giving rise to partial charge

molecular oxygen (O2)

O=O

water (H2O)

H—O—H

+ +

COVALENT BONDS (POLAR OR NONPOLAR)

Nonpolar covalent bond – atoms exert the same pull on the electrons

Polar covalent bond – atoms exert unequal pulls on the electrons giving rise to partial charge

molecular oxygen (O2)

O=O

water (H2O)

H—O—H

+ +

Molecular  bonds  

•  Hydrogen  bonds  –  weak  interac)on  between  a  slightly  nega)ve  atom  and  a  slightly  posi)ve  hydrogen  atom  – Hydrogen  bonds  are  weak  but  can  stabilize  a  structure  

 

Hydrogen bond – weak

attraction between a

slightly negative atom

and a slightly positive

hydrogen atom

MOLECULAR BONDS

H H

O

Hydrogen bonds can link

chains

+

Partial charges!

Lecture 2

Outline:

1. What defines living organisms? a. Made of cells b. Similar molecules c. Reproduce with DNA d. Convert energy e. Sense and respond to environment. Maintain homeostasis. f. Evolve

2. What is the chemical basis of life? a. Using isotopes and elements in archeology – an example b. Atom c. Elements d. Isotopes e. Valence electrons f. Molecular bonds (some of this will be covered in lecture 3)

i. Ionic bonds ii. Covalent bonds

iii. Polarity iv. Hydrogen bonds

Sample Exam Questions:

1. All atoms of an element have the same number of: a. ions b. protons only c. neutrons only d. electrons. e. protons and neutrons

2. An atom of sodium has an atomic number of 11 and a mass of 23. How many neutrons does it have? a. 11 b. 12 c. 23 d. 34 e. 35

3. Carbon has several isotopes (e.g. 12C and 14C.) These isotopes differ in the number of: a. electrons only b. neutrons only c. protons only d. electrons and protons e. protons and neutrons

4. Which of the following is (are) classified as true chemical bonds? a. hydrogen only b. ionic only c. covalent only d. both ionic and covalent e. hydrogen, ionic and covalent

5. About 12 to 24 hours after the last meal, a person's blood sugar level normally varies from 60 to 90 mg per 100 ml of blood, although it may rise to 130 mg per 100 ml after meals high in carbohydrates. That the blood sugar level is maintained within a fairly narrow range, despite uneven intake of sugar, is due to the bodily process called: a. adaptation b. homeostasis c. inheritance d. metabolism e. development

6. Grass growing in a field is eaten by a deer. Later on, the deer dies and its body is decomposed, in part, by bacteria. Which organism(s) are consumers? a. grass only b. deer only c. bacteria only d. grass and bacteria e. deer and bacteria

7. As energy is transferred among organisms, some escapes from the environment as energy. a. electrical b. heat c. light d. mechanical e. nuclear

Thought Questions:

1. Draw a shell model of an uncharged nitrogen atom (nitrogen has 7 protons). 2. Explain why atoms such as helium, neon, and argon do not react with other atoms. 3. What are some examples of things that might happen to an ecosystem if all of the

consumers were removed? 4. One of the causes of diabetes is inadequate insulin production. How would this

effect blood sugar homeostasis? 5. Name the independent, dependent, control and experimental variables in the graph

of slide 21 that depicts δ15N vs. fertilizer method. 6. Explain how Na+ forms from Na and Cl- forms from Cl.

Sample Exam Question Answers:

1. B 2. B 3. B 4. D 5. B 6. E 7. B