Bio 1113 Exam 1

Characteristics of Life

1.) Composed of Cells

2.) Replication/Reproduction

3.) containing/processing/responding to information

4.) acquiring and using energy (thereby also producing waste)

5.) Evolution (genetics of species change between generation/common ancestry)

Why can’t things in science be proven?

Scientific knowledge always changing/expanding, New evidence always possible → re-evaluate, Better than “proven”: “highly supported by evidence”

Difference between hypothesis, theory, and law*

hypothesis-: tentative explanation of an observation, allows for falsifiable predictions

theory-are like hypotheses in that they must be testable and falsifiable, BUT highly supported by evidence so much less likely to be thrown out, also more broad in scope, they offer an explanation of the phenomenon being studied

law-just showing cause and effect relationships, usually in physics or chem, Distillation of repeated observations (often a mathematical relationship)

Scientific Method

involves a constant cycle of observation, hypothesis, prediction, testing, and making conclusions (though in practice, steps may be added, combined, or taken out of order)

Hypothesis

(usually in present tense) tentative explanation of an observation, must be testable and falsifiable

Prediction

A statement of what will happen if your hypothesis is correct in a specific circumstance

Outlines how to test hypothesis.

Generally in future tense and more specific

Needs at least two things: What is the scientist changing to understand its effects on the system (also called independent variable)? • What is the scientist measuring to see how the system responds to this change (also called dependent variable)?

What do scientific studies undergo before being published?

peer review

How to consider strength of a specific study?

Strong experimental design includes a control group to give something to compare against, as well as help control for confounding variables • Often this control group is given a placebo, which resembles the treatment

What is the best type if experiment?

one with a double-blind – neither the person administering the treatment nor the experimental subject know whether a placebo or actual treatment was given (eliminates possible psychological effects/bias and other confounding variables for both parties)

Confounding Variable*

factors that affect the dependent variable that were not controlled for, especially those that differ between experimental groups

Many elements of good study design involve eliminating confounding variables!

Experimental study vs observational study

Experimental-(manipulative), apply different treatments and measure results of manipulation

Observational-compare different groups, but researcher does not apply treatment

Results of experimental studies tend to be stronger/considered more reliable b/c observational is harder to isolate confounding variables & can get correlation but correlation does NOT equal causation

Might conducts observational study anyways because cheaper, faster, & ethical concerns

Sample Size & Stats

The more individuals measured in a study, the greater the confidence we have in the results • Statistics help us determine how confident we are that the results are meaningful/real

Few individuals in study could result in results coming from chance.

ex.) 7/10 is worse than 70/100

Atoms

smallest unit with the properties of a given element • Composed of protons (+), neutrons, and electrons (-) • If the number of protons ≠ number of electrons, the atom has a charge (and therefore, an ion)

Atoms can be connected by a variety of types of bonds

Chemical Bonds

can vary in how equally or not equally the atoms share electrons

• Nonpolar covalent bonds = equal sharing (neutral charge), Polar covalent bonds = unequal sharing (partial charge), Ionic bonds = complete transfer of electrons (full charge)

Electronegativity*

• Some elements are “pull” more on e- than others (more electronegative)

Biological molecules with mostly carbon and hydrogen are usually nonpolar

The more oxygens and nitrogens there are in a biological molecule, the more likely it is polar, especially in the region around those oxygens/nitrogens

Chemical bonds vary in strength

In biological systems (due to the polarity of water), covalent bonds tend to be the strongest, followed by ionic, and hydrogen bonds are very weak bonds

Hydrophillic*

(i.e. polar molecules and ions) dissolve easily in water

Hydrophobic*

(i.e. nonpolar molecules) do not dissolve easily in water, once in close proximity, interactions cause a weak attraction

Properties of water

Is Polar b/c:

• It forms hydrogen bonds with itself as well as other polar/charged molecules. Which then means that:

• It tends to cohere to other water molecules and adhere to surfaces & It has a high capacity to absorb heat

Hydrogen bonds

weak attractive force between oppositely charged regions of polar molecules that contain covalently bonded hydrogen • Much weaker than ionic or covalent • Allow for special properties of water that are vital to living things

cohesion

water molecules tend to stay together (water+water)

surface tension

cohesion of water molecules at the surface of water resists forces that increase surface area

adhesion

water molecules tend to also cling to some surfaces (water + other surface)

high specific heat

water resists changes in temperature (can absorb ↑ energy before it changes temperature)

organic molecules*

(carbon-based) molecules generally have a carbon “skeleton” that is modified by adding different functional groups • Carbon makes a versatile base for a skeleton because it generally forms four covalent bonds. For example, 4 single bonds, 2 double bonds, etc.

functional group*

frequently important to chemical behavior of a molecule and, thus, its function • For example, a polar functional group will make that molecule more hydrophilic

pH

measure of acidity (essentially, what the concentration of H+/hydrogen ions/protons is), scale is inverse and logarithmic

very acidic

low pH and more H+ ions

very basic (alkaline)

high pH and less H+ ions

where is energy for humans stored*

chemical bonds in food

How much energy is released depending on type of atoms and bonds*

nonpolar-longest, weakest bond, but store the most energy

polar-shorter, stronger bond

Macromolecule*

small unites called monomers and linked into larger complex structures called polymers

Polymers can be built or split apart based on the subtraction or addition of water molecules

carbohydrates elements*

consist most often of C, H, and O, usually in the ratio of about 1 C to 2 H to 1 O (“ ose” suffix indicates carbohydrates)

carbohydrate function*

can store energy due to their large number of C-H and C-C nonpolar bonds, they are also relatively hydrophilic because of their polar C=O and –OH functional groups

The digestive system cannot absorb carbohydrates larger than a monosaccharide (larger molecules must be broken down before absorbed)

monosaccharides (especially glucose) are used in cellular respiration

monomer of carbs

monosaccharides:

glucose-main energy source in cellular respiration

Fructose: think high-fructose corn syrup

Galactose: found in dairy

can be linear or ring structure (mostly ring)

How do monosaccharides differ?

number of carbons • Even isomers may be different monosaccharides if the C=O (e.g. glucose vs fructose) is in a different spot or the –OH groups are oriented differently (e.g. glucose vs galactose)

How can the same monosaccharide (all C6H12O6) have different forms of the ring form?

alpha glucose-OH pointed down

beta glucose-OH pointed up

functionally different

disaccharides

carbohydrates that consist of two monosaccharides

•Sucrose: (table sugar) glucose + fructose

•Lactose: glucose + galactose (lactose intolerance – inability to break bond between glucose and galactose (enzyme)

maltose: glucose + glucose

how are monosaccharides bonded together

Monosaccharides may be covalently-bound together

condensation rxn or dehydration synthesis forms glycosidic linkages to form larger molecules, can be alpha or beta, and can happen anywhere -OH occurs

Polysaccharides are many monosaccharides covalently linked

polysaccharides*

consisting of many linked glucose molecules include starch, glycogen, and cellulose, all of which have the glucose arranged in different ways

starch

store energy in plants, long string of glucose molecules

glycogen

store energy in animals, Also long string of glucose

• Stored with lot of water – loss of “water weight”

both glycogen and starch

Both contain α-glucose, but differ in the amount of branching, making glycogen faster to digest.

cellulose*

plants use for structural support – cell wall

can’t be digested by humans because of the different arrangement of glucose molecules. This is caused due to the use of β-glucose in cellulose’s structure. Also, forms linear parallel strands linked by hydrogen bonds because of the different orientation of the glucose molecules

other structural polysaccharides

Chitin: important for insects and fungi

Peptidoglycan: bacterial cell walls

why do polysaccharides take longer for the human body to process

(because need to be broken down to be digested), leading to a longer, more persistent release of energy than do monosaccharides or disaccharides

other carb functions*

Besides energy storage and structure, carbohydrates also can be used in the making of other molecules and are important in cell-cell interactions/cell signaling

Make up parts of other molecules or are used as raw material to make other molecules • Also, important cell identity markers

carb nutrition facts

“dietary fiber”-mostly cellulose

“sugar”-monosaccharides & disaccharides

other polysaccharides-total carbs

monomer of proteins*

amino acids, linked together to create polypeptide chain

structure of amino acid

have a central carbon atom covalently bonded with an H, an amino (NH2), a carboxyl (C O O H), and an R group/side chain

The R group is what differentiates different amino acids and gives them different properties (acidic vs basic vs polar vs nonpolar, etc)

ionized vs non-ionized form of amino acids

ionized-charged H on amino group

non-ionized-H bonded to O on carboxyl group

how many amino acids are there

-20 directly from DNA

-additional 2 can be added during the process, only one of which used by humans

-100’s of others can be made through modification of these 22

how are peptide bonds formed

condensation reaction/dehydration synthesis, bond is stable & inflexible

protein: primary structure

a linear sequence of amino acids connected by covalent bonds (called peptide bonds) between a C of one amino acid and the N of the next

-Peptide bonds are strong and inflexible, so the flexibility in primary structure comes from other covalent bonds in the primary structure

flexibility (other than peptide bond), directionality, and R-group orientation

protein secondary structure

3-D shape due to hydrogen bonding between H of amino group and O of carboxyl group of nearby amino acids

alpha helix-bonds spread further apart

beta pleats-bond between only one amino acid

protein tertiary structure

3-D shape : due to interactions between R groups/side chains (H bonds, ionic, covalent, hydrophobic interactions/van der Waals, disulfide bonds) or between side chains and amino acid “backbone”

protein quatenary structure

more than one polypeptide

polypeptide vs oligopeptides

poly:> or = 50 AA

oligo:< 50 AA

protein structure & function*

amino acid sequence determines three-dimensional shape of proteins which determines protein function

Denature*

loss of 3-dimensional shape (& function), sometimes reversible

heat/chemical changes disrupts bonds/interactions

protein folding

protein shape is flexible, “active” vs “inactive” forms

prions

cause protein misfolding, but only in proteins with same AA sequence-self perpetuating & lead to nervous tissue damage

protein functions

structural

protection/defense

signaling/regulation

movement/contraction

transport

catalysis (enzymes)

enzymes*

proteins that speed up reactions & build/break down molecules

ends in -ase usually

An inability to break down or build a specific molecule can often be traced back to a missing or defective enzyme

active site

location of catalysis from substrate(s) to product(s), leads to specificity of enzyme, amino acids in active site very important ti function

essential amino acids

AAs that human bodies cannot produce, must be consumed in food

nucleic acids*

DNA and RNA, monomer-nucleotides

Nucleotides Formation

phosphate group, 5-carbon sugar, nitrogenous base

difference between RNA and DNA*

-The 5-carbon sugar differs between DNA (deoxyribose) and RNA (ribose) in that deoxyribose contains one less oxygen than ribose does

-The nitrogenous bases can be adenine, guanine, cytosine, thymine (just DNA), or uracil (just RNA)

A&T/U and C&G

-RNA is single stranded

activated nucleotide*

Nucleotides may be made more reactive by the addition of extra phosphate groups – “activated” nucleotides

ATP*

ATP: an activated nucleotide that is the most commonly-used direct source of energy for cells • Energy stored in glucose (and other macromolecules) is converted into energy stored in ATP before it can be used by cells

nucleotide bond

connected with phosphodiester linkages

directionality of nucleic acids*

There is a directionality to nucleic acid strands (5’ to 3’)

Nucleotides are always added to the 3’ end (the free –OH on the sugar molecule) rather than to the 5’ end (which contains an unlinked phosphate group) because the energy for the reaction comes from the bonds of activated nucleotides

what causes specific nucleotides to pair with each other

Pair up based on physical properties: size of nucleotide and number of hydrogen bonds formed when antiparallel

function of DNA*

stores genetic information

structure of DNA

Each DNA molecule is composed of two antiparallel strands twisted into a helix - the “backbone” of each strand of nucleotides is sugars and phosphates connected via covalent bonds; the two stands are connected by hydrogen bonds between bases

why is DNA stable

The structure is extremely stable, in part due to the way that the more hydrophobic parts of the structure are on the interior of the double helix and the charged phosphates group to the outside (among other features)

• H-bonds • Base stacking • Polar/Charged vs Nonpolar • Hydrophobic interactions • Very stable + forms own templates for replication: structure→function

RNA function*

one of the most important is that it is used as an intermediate between DNA and protein during protein synthesis

including acting as catalysts, like an enzyme

structure of RNA

Because of the –OH in the ribose structure, RNA is less stable than DNA

• RNA is usually single-stranded

• Creates a wider variety of shapes than DNA does – still uses base pairing between antiparallel nucleotides, but usually within the same strand

characteristic of Lipids*

not dissolving well in water-nonpolar (unlike other macromolecules, they don’t have monomers that characterize them)

fat

made through glycerol and fatty acid chain coming together through ester bond

3 main categories of lipids

triglycerides, steroids, and phospholipids

triglycerides*

(or “fat”): extremely non-polar lipids that are used as long-term energy storage (as opposed to shorter-term energy storage in the polysaccharide, glycogen).

structure of triglycerides

Nonpolar because they mostly are made of C and H in nonpolar covalent bonds. • This also makes it so that they store lots of energy because nonpolar covalent bonds, like C C and C-H generally store more energy than polar bonds, like C-O

• Triglycerides are made of a glycerol with three fatty acids.

saturated fatty acids

have no double bonds; usually solid at room temperature because the straight structure packs well; often found in animal-based foods

unsaturated fatty acid

have double bonds; usually liquid at room temperature because the double bonds form kinks; often found in vegetable oils and fish oils (some of these cannot be made by humans: “essential fatty acids”)

trans fatty acid

have double bonds, but are solid at room temperature because the double bond doesn’t form a kink; unnatural (found in highly-processed food) and hard to digest; indicated by “partially hydrogenated vegetable oil” labels

steroids

lipids formed by four linked carbon/hydrogen rings

The most common steroid is cholesterol, which is a component of cell membranes and is used to make steroid hormones

amphipathic*

molecules have polar/hydrophilic and non-polar/hydrophobic regions. They naturally form membranes because of this

• Cholesterol and phospholipids are amphipathic

phospholipids structure

a glycerol, two fatty acids, and head group that includes a phosphate

lipid bilayer*

selectively permeable – only let certain molecules cross

• Only small and non-polar molecules easily pass through the non-polar region of the bilayer

• Charged ions almost never get through, even if they are small, unless they can go through a protein channel

what affects permeability

membrane fluidity is affected by fatty acids – the more unsaturated fatty acids there are, the more permeable/fluid the membrane is

• Most phospholipids have at least one unsaturated fatty acid – this is part of why it is important to get sufficient essential fatty acids

• Temperature also affects permeability and membrane fluidity – increased temperature increases permeability/fluidity