lnLroducuon Lo Lhe Sclence of

Llvlng Crganlsms
8lology 11

lf you mlssed Wednesday's rsL class you can
nd slldes and Lhe syllabus on bcourses:
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2234356
1here are some example exam quesuons
posLed aL Lhe end of Lhe slldes
Cvervlew
WhaL denes llvlng organlsms?
WhaL ls Lhe chemlcal basls of
llfe?
WhaL denes llvlng organlsms?
1. Crganlsms are made of cells
2. Crganlsms are made of Lhe same subseL
of molecules:
roLelns
CarbohydraLes
Llplds
nuclelc aclds
WhaL denes llvlng organlsms?
1. Crganlsms are made of cells
2. Crganlsms are made of Lhe same subseL of
molecules
3. Crganlsms reproduce by passlng along unA. unA
guldes developmenL
unA - deoxyrlbonuclelc acld - ls Lhe slgnaLure molecule of llfe
and lnherlLance.
WhaL denes llvlng organlsms?
1. Crganlsms are made of cells
2. Crganlsms are made of Lhe same subseL of
molecules
3. Crganlsms reproduce by passlng along unA. unA
guldes developmenL
4. Crganlsms obLaln and converL energy from Lhelr
surroundlngs. Cells use energy for repalr,
malnLenance, growLh, and reproducuon.
89,+:0 ;9#*< =>?;9/0 $*9/;:!<@
ABCDEF8BG
planLs and oLher self-feedlng organlsms
LhaL make Lhelr own food
FCHGEI8BG
anlmals, mosL fungl, many prousLs and
bacLerla LhaL cannoL make Lhelr own food
89,+:0 )*<#*< =>?;9/0 >,<?')/;( !,?<@
H*<+;,9< (0(/;9:

WhaL denes llvlng organlsms?
1. Crganlsms are made of cells
2. Crganlsms are made of Lhe same subseL of molecules
3. Crganlsms reproduce by passlng along unA. unA guldes
developmenL
4. Crganlsms obLaln and converL energy from Lhelr
surroundlngs. Cells use energy for repalr, malnLenance,
growLh, and reproducuon.
3. Crganlsms sense and respond Lo changes ln Lhelr
lnLernal and exLernal envlronmenL ln conLrolled ways Lo
malnLaln homeosLasls

Senslng and respondlng
lncludes:
Auracuon
Avoldance
Lscape
Lxpresslon of proLecuve proLelns
Changes ln physlology
PomeosLasls example - blood glucose
Marleb & Poehn ,
(2003), Puman
AnaLomy & hyslology
HOMEOSTASIS, EXAMPLE: BLOOD GLUCOSE
Glucose
Insulin released
Glucose uptake
Glucose
WhaL denes llvlng organlsms?
1. Crganlsms are made of cells
2. Crganlsms are made of Lhe same subseL of molecules
3. Crganlsms reproduce by passlng along unA. unA guldes
developmenL
4. Crganlsms obLaln and converL energy from Lhelr
surroundlngs. Cells use energy for repalr, malnLenance,
growLh, and reproducuon.
3. Crganlsms sense and respond Lo changes ln Lhelr
lnLernal and exLernal envlronmenL ln conLrolled ways Lo
malnLaln homeosLasls
6. Crganlsms evolve. 1helr unA changes from generauon
Lo generauon
Lvoluuon
Ceneucally based change ln a llne of descenL
over ume
opulauon changes, noL lndlvlduals
1he basls for evoluuon ls varlauon ln LralLs
MuLauons
PerlLable changes ln unA
WhaL becomes of lndlvlduals wlLh dlerenL
LralLs ls deLermlned by selecuon
Aruclal Selecuon
naLural Selecuon
1he ouLcome of dlerences ln survlval and
reproducuon among lndlvlduals LhaL vary ln
Lhelr herlLable LralLs
1hls process helps explaln evoluuon - changes
ln a llne of descenL over generauons
JK8 FK8ILFMN OMGLG CP NLP8
8aslc bulldlng blocks
ALom - smallesL unlL of an elemenL LhaL sull
reLalns Lhe elemenLs properues (conducuvlLy,
reacuvlLy, eLc)
LlemenL - a pure chemlcal subsLance made up
of one aLom
uslng chemlsLry ln archeology
Assumed LhaL manure
wasn'L used aL ferullzer
unul Lhe umes of
8omans
8ecenL research shows
LhaL manure was used
durlng Lhe neollLhlc
Pow dld researchers
gure Lhls ouL?


Pow do we descrlbe elemenLs?
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
erlodlc 1able
Columns represenL aLoms wlLh Lhe same number of valence elecLrons
lsoLopes
ALoms of an elemenL always have Lhe same number of
proLons (l.e. Lhe same aLomlc number)
ALoms of an elemenL LhaL dler ln Lhe number of
neuLrons are called ;$)<)#,$ (l.e. dlerenL aLomlc mass)
lsoLopes of an elemenL have slmllar reacuvlLy because
Lhe number of valence elecLrons ls slmllar
1he dlerence ln mass beLween Lwo lsoLopes of an
elemenL leads Lo varlauon ln chemlcal processes LhaL
break and form bonds
Bogaard A et al. PNAS
2013;110:12589-12594
nlLrogen lsoLopes ln manure
1hlnk of Lhls
as Lhe rauo of
heavy
13
n Lo
llghL
14
n
found ln
dlerenL
crops
P,+Q/;R,+ >,<!)1
lsoLopes ln anclenL seeds
Analyzed seeds from harvesLed crops
preserved ln neollLhlc houses
lound LhaL Lhe nlLrogen lsoLope values were
slmllar Lo hlgh levels of manure appllcauon
Changes how we vlew neollLhlc socleLy
Slash and burn ! long-Lerm lnvesLmenL ln land
nomadlc ! ues Lo land
Could have led Lo LerrlLorlallLy over good land

Methods) (18) and can be used in conjunction with crop
15
N
values 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 nitrogen
stable isotope determinations of 124 bulk crop samples (totaling
>2,500 individual cereal grains or pulse seeds) from 13 Neolithic
sites across Europe (Figs. 2 and 3), interpreted in the light of
herbivore forage
15
N values estimated from stable isotopic
analysis of associated (domestic and wild) herbivore bone col-
lagen, modern isotopic comparanda (12, 13, 1618), experi-
mental work on the effects of charring (19, 20), and associated
arable weed assemblages (4, 5, 21, 22). The sites mostly date to
the earlier Neolithic in their respective regions (Table 1) and
were selected on the basis of richness in well-preserved charred
crop material (Fig. 3); together, these sites provide a rough
transect from southeast to northwest Europe (Fig. 2).
Results and Discussion
Fig. 4 shows
13
C and
15
N values of cereals and pulses from
four sites, and Table 2 summarizes results from all sites (for
individual sample results, see Table S2). Unsurprisingly, a broad
climatic trend in humidity is apparent if wheat or barley
13
C
values at sites in or near the Mediterranean zone are compared
with those in temperate zones (Fig. 2): thus,
13
C values of wheat
(or barley) from sites in Greece and Bulgaria are lower than
those from Germany and Denmark (Fig. 4 and Table 2). Ex-
tensive isotope investigations of cereals and pulses from modern
experimental stations and farm studies across Europe, however,
have shown that crop
15
N values reect management practices
rather than broad climatic trends (13). For six of the sites in
Table 2, herbivore forage
15
N values have been estimated from
the
15
N determinations of associated bone collagen of large
herbivores by subtracting 4 as an average of the 35 range
associated with the trophic shift (15). At these sites, cereal grain

15
N values tend to be considerably higher than those inferred
for forage. Although variation in
15
N values among cereal
components may contribute to this contrast (cereal grain is ca.
2.5 higher in
15
N 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 an
approximation of the local
15
N value of nonarable vegetation.
Contrasts in cereal and forage
15
N values suggest that arable
soil N was relatively enriched in
15
N. Weed evidence available at
a number of sites indicates that cultivation plots were long
established, with soils tending to be intensively disturbed and
productive (4, 5, 21, 22). Although these conditions exclude
some potential causes of
15
N-enrichment, such as wetland de-
nitrication, salinity, and recent clearance (32, 33), they consti-
tute a plausible context for manuring.
Cereal grain
15
N values at most sites are consistent with
signicant rates of manure application (Figs. 1 and 4, and Table 2).
There is also considerable diversity in cereal
15
N values at some
sites. Local variation in manuring rates was observed in stable
isotope studies of present-day traditional farming regimes in
Asturias, Spain, and the Sighisoara region of western Romania
(13). Variation is likely where manure is concentrated at specic
locations in the landscape because it is heavy to transport and
so tends to be used in close proximity to pens, byres, and so forth
(9, 34). Low cereal
15
N values (<3) indicative of long-term
unmanured cultivation occur alongside high values at some sites
(Fig. 4 AC, and Table 2), and are dominant among the emmer
wheat samples from Sarup, Denmark (Fig. 4D). Herbivore for-
age
15
N values from all sites (ca. 13) (Table 2) fall within
the range of unmanured cereals (Fig. 1).
Estimated forage
15
N values are often similar to those of
pulses. As expected (13), pulses tend to exhibit lower
15
N values
than 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 in
a study of present-day broad bean gardens in Evvia, Greece
(13), increases pulse
15
N values considerably above 0. The
archaeobotanical pulse
15
N values thus point to intensive ma-
nuring, variously comparable to, or higher than, the rates applied
to associated cereals. Furthermore, high pulse
13
C 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 supplementary
irrigation.
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
15
N values in modern bulk cereal samples (wheats and
barleys) grown under different rates of manuring at long-term agricultural
experiments: Rothamsted, United Kingdom, Askov, Denmark, and Bad
Lauchstdt, Germany (13). Dashed horizontal lines represent thresholds of
low (i.e., residual from previous land use history only), medium, and high
manuring 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.
hup://www.sclencedally.com/releases/
2013/07/130716134740.hLm
WhaL deLermlnes whlch aLoms wlll
lnLeracL?
1he number of valence elecLrons
All aLoms wanL Lo be compleLed
Polds 2 e
-
Polds 8 e
-
Molecules
I)/,(*/, - when aL leasL Lwo aLoms are
bound LogeLher
Lxamples: naCl, C
2
L)9$ - aLoms or molecules LhaL are charged
(l.e. + or -) due Lo Lhe loss or galn of an
elecLron or elecLrons
Lxample: k
+
, CP
-
Molecular bonds
L)9;( ')91$ - Lwo lons LhaL are held
held LogeLher by opposlLe charges
+ and - charges auracL
Lxample: na
+
+ Cl
-
= naCl
Molecular bonds
F)S?/,9< ')91$ - elecLrons are shared
beLween aLoms
Lxample: P
2
hup://www.youLube.com/waLch?
v=ku2Czwx1qhc
CovalenL bonds - polar or nonpolar
H)9#)/?+ ()S?/,9< ')91$ - aLoms exerL Lhe
same pull on Lhe elecLrons

A)/?+ ()S?/,9< ')91$ - aLoms exerL unequal
pulls on Lhe elecLrons glvlng rlse Lo parual
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 (O
2
)
O=O
water (H
2
O)
HOH
+ +
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 (O
2
)
O=O
water (H
2
O)
HOH
+ +
Molecular bonds
K01+):,9 ')91$ - weak lnLeracuon beLween
a sllghLly negauve aLom and a sllghLly posluve
hydrogen aLom
Pydrogen bonds are weak buL can sLablllze a
sLrucLure

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.
12
C and
14
C.) 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 !
15
N 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