Decoding Life Test Cram

What is innate behavior?

behavior that is developmentally fixed such that all individuals in the population exhibit the same response to a stimulus

instinctive

What is a stimulus to innate behavior called?

releaser

Definition of Learned Behavior

behavior that is acquired, altered, or eliminated due to an animal’s experience

Types of Innate Behaviors

Fixed Action Patterns

Biological Clocks/Rhythms

Communication btwn animals

Movement

What are Fixed Action Patterns?

A sequence of behaviors that doesn’t change and once initiated by a sign stimulus or releaser, is always completed the same way.

The more prominent the stimulus, the greater the response.

What are Biological Clocks or Rhythms?

Environmental stimuli or internal (endogenous) stimuli trigger behaviors in animals

Circadian rhythms: daily (24 hr) cycles or biological clocks that influence behavior

Circannual rhythms influence yearly cycles of behavior like migration

Communication btwn animals

A stimulus (signal) transmitted from one animal to another will elicit a specific response. Typically, in the form of a chemical, tactile and visual stimuli

(can also be learned)

pheromones are a special case of communication

What are pheromones?

Chemical stimuli that are produced by one organism and, when released, have an effect on the behavior of other organisms of the same species

What are the two types of movement-based innate behaviors?

Kinesis and Taxis

What is kinesis?

a general change in activity or non-directional behavior by an animal in response to a stimulus. Fast movement usually indicates a search for a comfort zone, slow movement indicates it has found it.

What is taxis?

a directed movement by animals either towards or away from stimulus

positive → towards stimulus

negative → away from stimulus

What are the types of learned behaviors

1. Imprinting

2. Spatial learning

3. Associative Learning

4. Cognition

5. Social Learning

(some types of learning overlap with other behaviors)

What is imprinting?

innate behavior that will develop when an organism is exposed to a stimulus within a critical or sensitive period of time.

requires some level of genetic input/innate ability to imprint or be programmed to the stimulus

stimulus/response may be chemical OR visual. depends on the developmental stage of the animal

What is Spatial Learning

The establishment of a memory that reflects the organism’s environment by forming a cognitive map

i.e. ELEPHANTS

What is associative learning?

The learned ability to associate one environmental feature to another. A search image is often involved

search image → learned mental representation/focus

Special cases include:

1. Habituation

2. Classical Conditioning

3. Operant Conditioning

What is habituation?

loss of a response to unimportant stimuli

i.e. a carriage horse in NYC no longer responds with fear to noisy streets

What is classical conditioning?

responding to a new, substitute stimulus as if it were the original stimulus

i.e. Pavlov’s dogs salivate to the sound of a bell in anticipation of food to follow

What is operant conditioning?

Learning by trial and error

i.e. rats learn to run a maze after several tries

What is cognition?

Process of knowing that involves awareness, reasoning, recollection, and judgement

NOT LIMITED TO PRIMATES

Social learning

learning by observing other animals

Can natural selection act on behavior actions to increase the fitness of a species

TRUE

What are the types of social organization

1. Altruism/Kin Selection

2. Agonistic Behavior

3. Dominance Hierarchy

4. Territoriality

What is altruism/kin selection

behavior that reduces an animal’s individual fitness but increases the fitness of individuals in the immediate family or population

kin selection is the idea that altruistic behavior increases the survival of genes similar to those of the individual even if it doesn’t benefit/is detrimental to the individual

What is agonistic behavior?

type of behavior that involves a contest determining for example, which individual gets access to food or mates

usually more psychological than physical

ex. male giraffes use their broad necks to battle each other over mates

What is dominance hierarchy?

an organization of social animals

more dominant animals control less dominant individuals

reduces the amount/intensity of fighting

usually maintained by agonistic behaviors

i.e. lions fighting over a kill, female hyenas dominating reproduction in a pack

What is territoriality?

individuals establish choice living space, giving them access to critical resources, especially food and water

usually maintained by agonistic behaviors

What is optimal foraging?

maintaining high energy intake to expenditure ratio

(minimizes the energy costs of obtaining the food while maximizing the benefits of gaining the food energy

What is the purpose of a chi squared test?

determines whether data obtained experimentally provides a “good fit” to the expected data

is used to determine if any deviations from the expected results are due to random chance alone or to other circumstances

How to calculate chi squared?

How to understand/interpret chi-squared value (what does it mean with respect to the null hypothesis)

If the chi-squared value is larger than the table value → statistically significant → reject the null hypothesis

if the chi-squared value is smaller than the table value → not statistically significant → fail to reject the null hypothesis

Evolution of Life Worksheet Sequencing:

Order the following statements correctly

Flowchart of Metabolic Diversity

What are the four major types of organisms?

Photoautotrophs: plants, cyanobacteria, protists (algae, euglena)

Chemoautotrophs: Archaea (vent bacteria), extremophiles

Photoheterotrophs: nitrogen-fixing bacteria (use light for energy but CO₂ is not source of carbon for them)

Chemoheterotrophs: humans, animals, fungi, some protists

What are ribozymes and what was significant about their discovery?

RNA that can catalyze its own reactions, such as replication. An RNA polymer could have self-polymerized, and then acted as its own enzyme and a template for replication of a complementary RNA.

Ribozymes provide evidence that RNA was the first genetic material

Test? — self catalyzes the formation of peptide bonds btwn amino acids

ex. ribonucleic proteins, ribosomes, telomerase

Fill out the chart correctly

What was the Griffith Experiment? (Describe procedure and why was it significant?)

Procedure:

• Experiment was performed on pneumococcus bacteria (supposed test question)

• There were rough and smooth forms of the bacteria (rough = no virus, smooth = virus)

  • remember “feet up feet down” assay (quantitative way to measure the lethality of the bacterium)

• Griffith injected the mice with different variations of the bacteria

  • rough strain (nv) → mouse lives

  • smooth strain(v) → mouse dies

  • heat-killed smooth strain → mouse lives

  • rough strain + head-kill smooth strain → mouse dies???

    • Transformation must have occurred somehow

Significance:

• IDENTIFIED A TRANSFORMING FACTOR

  • still didn’t know what it was (many thought proteins, didn’t know it was DNA yet)

What was the Avery, Macleod, McCarty Experiment? (Describe procedure and why was it significant?)

Procedure:

• used proteases, RNAses, DNAses (enzymes that destroy, proteins, RNA, DNA)

  • added to bacteria to inactivate the respective component

  • checked what happened when inactivated strains were mixed with live (unmodified strains) to see if some sort of modification happened

Significance:

• Built on Griffith’s methodology

• DNA IS THE TRANSFORMING FACTOR!!!

What was the Hershey Chase Experiment? (Describe procedure and significance)

Procedure:

• Remember that protein (amino acids) contain sulfur but not phosphorus. DNA contains phosphorus but not sulfur

• Radioactively labeled samples of phages were prepared

  • 1. DNA is labeled with ³²P

  • 2. Protein is labeled with ³⁵S

• Bacterial cells were precipitated from solution in centrifuge (blender)

  • ³⁵S was found in the supernatant (liquid) → phage protein could not have entered cells

  • ³²P was found within the bacteria cell → phage DNA DID enter cells

    • new viruses isolated from the bacterial cell centrifugation contained the radioactive ³²P (marker for DNA)

Significance:

• Answered the question of what component of chromosomes contains hereditary info—DNA or proteins

  • established DNA as genetic material

• Viral hereditary material must enter the cell in order to code for production of new viral particles → DNA entered cell → DNA must be hereditary material

What is Chargaff’s Rule?

his experiments showed that %C = %G and %A = %T

this info was shared with Watson and Crick which helped them create their double helix model

Why were Rosalind Franklin and Maurice Wilkins significant?

They performed x-ray crystallography on DNA molecule

• DNA was crystallized

• crystallized structure hit with X-rays, which diffracted in a regular pattern

• pattern was visualized on a photographic plate

• PHOTO 51 was the photo that proved double helix

Wilkins was the guy that snitched about Franklin’s data to Watson and Crick which she wanted to confirm before sharing

Who were James Watson and Francis Crick?

• double helix model

• explained how genetic material could be replicated and passed onto daughter cells

• also explained how DNA could be used as a template for transcription of RNA

What was the Messelson-Stahl Experiment? (Describe procedure and significance)

Procedure:

• E coli is grown in ¹⁵N (heavy isotope)

• Switched to ¹⁴N (lighter) after one/two replication cycles

• take samples of DNA

• mix with cesium chloride and separate the heavy and light DNA with centrifugation

Significance:

• parent DNA is all heavy

• 1st gen: all DNA is intermediate → only disproves conservative model

• 2nd gen: half intermediate, half light → disproves dispersive model (otherwise there shouldn’t be any 14-14 DNA)

What is Recombinant DNA technology?

• combining DNA from 2 different sources such as bacteria + humans

• possible due to the universality of the genetic code

  • ex. gene cloning

Explain how cloning a gene works

1. Insert non-bacterial gene into bacteria

2. when bacterial chromosome replicates, inserted gene is also replicated and passed to daughter cells

3. huge numbers of bacteria can be easily + quickly grown, producing millions of copies of the desired gene to be studied

What are vectors?

vehicles for transferring DNA from one location to another

• plasmids: small, circular pieces of double-stranded DNA that can replicate independently of a cell’s main chromosomal DNA (primarily in bacteria)

• virus/phage

Why can’t bacteria express human gene?

No promoter for human gene (can be solved by adding a promoter)

Bacteria have no introns + no spliceosome (solved by making cDNA from mature mRNA of human gene & inserting that into the plasmid)

What are restriction enzymes?

called endonucleases because they cut somewhere within the DNA molecule

originally isolated from bacteria - in nature bacteria use them as a protective mechanism to degrade invading foreign DNA such as viral DNA

enzymes recognize short stretches of bases called recognition sequences (4-6 bases in length) which are scattered throughout the genome

DNA cuts at a specific place called a restriction site

cuts sometimes produce staggered (overlapping ends) known as sticky ends

different restriction enzymes recognize and cut different DNA sequences

cuts generate restriction fragments

bacteria protect their own DNA (chromosomal and plasmid) at restriction sites that are reorganized by their own enzymes.

addition of methyl groups helps to inhibit the enzyme from digesting bacterial DNA

Explain how restriction enzymes can be used to generate a recombinant molecule (“gene splicing”)

Making the recombinant plasmid:

1. same restriction enzyme to cut both the human gene and plasmid and generate sticky ends

2. mix fragments from both sources together to allow cDNA regions (sticky ends) to combine

3. By chance, some plasmid DNA will combine with human gene DNA to produce a recombinant molecule → not every plasmid will contain gene of interest

4. sticky ends are joined together by ligase

Transformation

1. allow plasmids to enter bacterial cells. the uptake of DNA (transformation) usually requires treating the cell with chemical/heat to make membrane more permeable

Reporter genes

• Identify the bacteria that took up a plasmid

• identify the bacteria carrying plasmids containing gene of interest

How do we identify the bacteria that took up a plasmid that has the gene of interest?

Plasmids are engineered to contain antibiotic resistance genes → serve as reporter genes (to select bacteria that have taken up a plasmid containing gene of interest)

think pGLO

What are the applications of recombinant DNA technology?

1. Production of pharmaceutical products (ex. insulin, GH, etc.)

2. Agriculture (producing better crops and animals)

   • transgenic organism (genetically engineered plants + animals)

     1. disease resistance gene from one plant to another

     2. splice GH genes into livestock to increase muscle mass

3. Environmental

   • engineering bacteria to clean up oil spills or metabolize toxic waste

4. Vaccines

Explain how Electrophoresis and DNA fingerprinting works

• DNA fingerprinting identifies individuals by analyzing unique patterns within their DNA (tandem repeats)

• Electrophoresis is what separates fragments of DNA by size

• When comparing different people’s DNA, each person will produce different restriction fragment banding pattern because of polymorphic nature (differing like content) of DNA regions)

  • these small differences are sometimes called SNPs

  • most polymorphisms are found in non-coding regions

This is RFLP

Describe the steps of RFLP (Restriction Fragment Length Polymorphism)

• Digest (cut) large DNA molecules w/ restriction enzyme into fragments

• samples containing fragments are loaded into wells cut into a gel

• Electric current in the gel draws DNA fragments (negative chage) to the positive pole

• As fragments migrate they are primarily separated by size due to pores int the gel

  • shorter fragments move further b/c they can travel more easily through pores

• bands of DNA are not visible until they are stained with a dye or identified by a radioactive probe/enzyme-linked tag (Southern blotting??)

Note: PCR is used with RFLP today

Describe PCR-RFLP

• PCR Amplification

  • specific region of DNA is copied using PCR (millions of copies

• Restriction Enzyme Digestion

  • amplified DNA fragments are treated w/ specific restriction enzyme that cuts the DNA at a specific sequence

  • the SNP being studied within the sequence is located within or alters the restriction site

• Gel Electrophoresis

  • digested RNA fragments are run on an agarose gel (separated by size + stained/visualized)

• Analysis:

  • compare banding pattern w/ known reference patterns

    • if the polymorphism is present, restriction enzyme will cut the DNA differently to produce a new fragment pattern compared to DNA without the polymorphism

What is PCR and how does it work?

• PCR is used to make millions of copies of a specific piece of DNA so it can be studied

• What you need

  • DNA sample - contains target sequence you want to copy

  • deoxynucleotide triphosphates (dNTPs) - building blocks of DNA

  • taq polymerase - the heat resistant enzyme that builds DNA

  • two primers - they attach to the end of the target sequence

• Procedure

  • mix everything in a tube

  • heat → dna strands separate (denature)

  • cool → primers bind to target sequence (anneal)

  • extend → taq poly adds nucleotides to build new DNA (extend)

  • repeat

    • Note: done in a thermocycler to automatically control temp

What are variable number tandem repeats

regions in the genome (introns or intergenic regions) where a short DNA sequence is repeated back to back

the # of these repeated units varies greatly among individuals → good genetic markers for identification and research

DNA sequencing

I don’t even know if we needa know this but here’s the diagram