Biology 122 Test 2

As replication completes...

(Replication goes from 5' to 3') -RNA primers are removed -DNA nucleotides fill the gaps -Ligase seals them into the backbone (covalent bonding) -Expansion of the replication bubble continues until replication is complete

Digestive enzymes --what keeps them from digesting their own body cells?

(enzymatic hydrolysis) -Hydrolyze large organic molecules into their component building blocks -->Amino cells cover the active site so the enzymes are made in an inactive form and secreted into digestive cavities where they are activated

Brush border enzymes

(intestinal) complete the job of pancreatic enzymes in breaking down food molecules -embedded in plasma membrane, they do the final job of digestion -Absorption happens primarily in the small intestine

Definitions: Insulation Conduction Radiation

- Lack of exchange due to layers of subcutaneous body fat -Exchanges by direct physical contact with a warmer or cooler object -Electromagnetic wave transfers between body and surroundings

Covalent bonds Hydrogen bonds

Covalent bonds - make up single nucleotide. Stronger bonds Hydrogen bonds - connect bases (weaker bonds than covalent)

Hemoglobin

- the molecule that transports oxygen in the blood. Efficiency of oxygen uptake in lungs and unloading at tissues (resting and exercising)

CirsprCas9

--Using biotechnology we can employ a similar system (CrisprCas9) to specifically modify a selected gene in the DNA It uses complementary base pairing between Cas9 sequence and edits the gene to which it attaches in the DNA Happens in nucleus

Which bases connect and what bonds are used?

-A and T -C and G hydrogen bonds connect bases

open circulatory system

-A circulatory system that allows the blood to flow out of the blood vessels and into various body cavities so that the cells are in direct contact with the blood -hemolymph? -Benefits: low energy cost. Can serve auxillary function

Alterations in Homeostasis Set points and normal ranges can change ...

-Age -Cyclic variation -Acclimatization

Double circuit circulation in reptiles

-Allow mixing, but has separation in the ventricle (not complete but better than amphibians) -has a mixed circuit that allows them to recirculate blood through systemic capillaries when no oxygen is gained from the pulmonary circuit 2 Atrium 1 Ventricle (separated)

Development involves...

-Cell division - multiplication (cleavage) -Cell differentiation - specialization (stem cells differentiating) -Morphogenesis - organization (3D organization) ex) stages of heart development

Endotherm and Ectotherm

-Endothermic animals generate heat by internal means ex. metabolism (mammals and most birds) -supports greater metabolic complexity -requires lots of ATP energy to sustain body temp under changing conditions -Ectothermic animals gain heat from external sources (most invertebrates, fish, amphibians, non-avian reptiles) -Restricts metabolic activity under cold conditions -Doesn't require production of nearly as much energy as endotherms do

Definitions: Convection Evaporation Blood Circulation

-Exchanges promoted by movement of the surrounding medium - Exchanges due to thermal energy-induced water loss to surroundings -Distribution of body heat throughout the body to reduce temperature variations between areas of high metabolism and those of lower metabolism OR to modify heat exchanges between the body and the environment.

Through the human genome project we learned ...

-Fewer human genes than expected -# of human genes - about the same as other organisms (even fruit flies and plants) -Human genes are very, very complex -Multiple levels of organization/regulation -Human gene sequences 99.9+% identical across the species -Sequences extremely similar to some other animal species

Overview of Human Genome Project

-Goal: to determine the entire sequence of the entire human genome -Timeline: 1984 (Preparation) -> 1990 (work began) -> 2003/06 (announced as complete in 2003, by 2006 it was actually complete) -Directors: Collins and Ventor - public funding -Involved public-private partnership at labs around the world -Cost less than expected (a billion dollars) -Finished sooner than expected

How is RNA different from DNA structurally?

-Ribose instead of deoxyribose -U instead of T base -Single stranded -DNA is larger than RNA

Histone modification

-adding chemical groups to histone tails alters the histone - DNA interaction Acetylation- looser structure ->allows transcription *can only be added to histones Methylation- tighter structure -> inhibits transcription *can be added to histones or DNA

Prokaryotes/Bacteria DNA

-circular chromosomes -genome is in 1 chromosome -genome is smaller -1 origin of replication

Components of circulatory system

-circulating fluid -network of interconnecting vessels -muscular pump (usually heart)

More complex organisms have...

-highly folded internal surfaces -extracellular body fluids for exchanging materials with the environment

Blood circulation - cross sectional area vs. velocity vs. pressure

-larger cross sectional area in arterioles than in aorta (big) -speed is inverse to cross sectional area (slow through capillaries) -pressure drops as you move away from the heart

Eukaryotic DNA

-linear chromosomes -more than 1 chromosome -genome is larger -many origins of replication per chromosome

Teeth, GI tract modifications for Carnivores

-long sharp, pointed canines and incisors to hold and tear apart the flesh of prey -molars are more jagged and smaller -an expandable stomach -small cecum -shorter large intestine

Double circuit circulation in amphibians

-loss of oxygen in the ventricle through mixing of oxygenated and deoxygenated blood 2 Atrium 1 Ventricle

Heart

-muscular pump -1 or 2 receiving chambers -Atria -receive blood from veins -1 or 2 standing chambers -ventricles

Talk about figure 18.8-3 (A eukaryotic gene and its transcript)

-proximal and distal control elements serve as binding sites for proteins called Transcription Factors

Teeth, GI tract modifications for Herbivores

-smaller, less pointed front teeth for cutting off bits of vegetation -molars are broad surfaces with ridges for grinding plant materials -longer GI tract -may have long cecum -much longer large intestine

Explain how an ectotherm could also be a homeotherm? Explain how an endotherm could also be a poikilotherm?

-there are organisms that live in surroundings where temp doesn't change, so they don't have to expend ATP -hibernation. reduce metabolic rate/body temp, bears have fat stores, make ATP at a lower rate

Plasmid

1 or few genes, small bits of DNA transmitted easily to other bacteria

elongation (translation)

1) A "next" tRNA binds to the adjacent codon, bringing the appropriate AA with it 2) The growing peptide chain is transferred to the new AA on the new tRNA 3) The 2 tRNAs shift over 1 position. The "empty" tRNA 4) A new tRNA for the next codon enters... this process requires energy (GTP)

Termination (translation)

1) A stop codon signals for the assembly to dissociate

3 steps of PCR (polymerase chain reaction)

1) Denaturation (heating) -dissolves the hydrogen bonds between the bases of the two complementary strands of the DNA double helix (______________________ ) so they will separate 2) Annealing (cooling) -allows short DNA "primer" sequences to bind to their complementary sequence on the two DNA strands (____________________________) 3) Extension -involves use of a special heat-resistant DNA polymerase (Taq) to polymerize a complementary strand on each parent strand from the 3' end of the primer. With repeated cycles the proportion of target DNA sequences in the mix is tremendously amplified .... From 2 in the 3rd cycle, 30 more cycles will produce more than 1 billion molecules that match the target sequence!

Cardiact Cycle

1) Diastole (Atrial and Ventricular) relaxed AV open, semilunar valves closed 2) Atrial systole (ventricular diastole) Semilunar valves open, AV valves closed 3) Ventricular systole, atrial diastole *left ventricle needs more pressure, so has more muscle *right ventricle needs less, or it would blow your lungs out

PCR

1) Identify the target sequence(s) eg- a single gene or set of STR's-that you want to amplify 2) Design primers that will initiate replication at each 3' end of the gene sequence 3) Use heat resistant DNA polymerase (Taq) 4) Combine DNA with primers, DNA pol, and free nucleotides in a thermocycler

Transcription

1) RNA polymerase binds to DNA at promoters start site 2) RNA pol unzips DNA around start site 3) RNA pol begins to assemble nucleotide sequence on the DNA template sequentially 4) RNA pol zips DNA back together behind it 5) TERMINATION: RNA pol and the new RNA transcript are released from DNA at termination site or after transcribing a termination sequence

Chambers of cow stomach

1) Rumen - many microorganisms begin digesting food 2) Reticulum - more microorganisms - regurgitation/ re-swallowing 3) Omasum 4) Abomasum

Herbivore types

1) Those with long cecum ex. Koala --> houses bacteria, and protists that help digest cellulose and other plant material (cellulose enzyme) 2) Those that have a crop ex. birds --> a muscular sac that helps mechanically digest food 3)Those that practice copraphagy ex. rabbits -->eat feces (2x thru digestive tract) 4) Ruminants ex. cows, deer --> have a 4 chambered stomach

Colon (large intestine)

1) Water absorption 2) Bacterial activity 3) Indigestible waste elimination

initiation of translation

1) a ribosome subunit binds mRNA at its start site 2) a tRNA with its correct anticodon will base pair with the start codon, bringing its AA with is (Met) the large ribosome subunit binds to the structure

Outcomes of the Human Genome Project

1. Technological Advances in gene sequencing -Shotgun sequencing developed during project -Next gen sequencing - no cloning steps involved (faster and cheaper) -A few hours entire genome -Cost- a few thousand dollars 2. Bioinformatics -HGP and other gene/protein sequencing has yielded an explosion of genetic data available for study -Computer data banks -Software Computational biologists develop/use software for answering questions based on large data sets

Artery and Veins components

3 layers of walls: connective tissue, smooth muscle, endothelium

closed circulatory system

A circulatory system in which the oxygen-carrying blood cells never leave the blood vessels -blood and interstitial fluid -Benefits: -highly effective delivery (increased pressure) -allows differential, regulated blood distribution

Epiglottis

A flap of tissue that seals off the windpipe and prevents food from entering.

Blood vessels

Arteries (many) Arterioles (small, tiny arteries) Capillaries (site for gas exchange) Venules (small veins) Veins Heart Arteries carry blood away from heart Vessels carry blood to the heart

Best definition of gene

A region of DNA that can be expressed to produce a final product, either: -a polypeptide (protein) -an RNA molecule

Definitions of a regulator and conformer

A regulator uses internal control mechanisms to moderate internal change in the face of external, environmental fluctuation ex) river otter temperature regulation A conformer allows its internal condition to vary with certain external changes ex) largemouth bass temp conformer

Talk about figure 18.10-1 (A model for the action of enhancers and transcription activators)

Activators are examples of SPECIFIC TRANSCRIPTION FACTORS -bind distal control elements upstream of the promoter -DNA bends to allow the specific transcription factors to interact with general transcription factors at the promoter - takes all of them for the RNA polymerase to bind! ---> RNA synthesis the whole structure is the transcription initiation complex

What are the four types of bases?

Adenine, Thymine, Guanine, Cytosine

Alternative splicing

Alternative splicing allows the same gene to be expressed in slightly different forms so they can work in slightly different ways

Physical Constraints on Animal Body Plan

An animal's shape, size, and environment affect what it can do •Different species may be adapted similarly to a similar environmental challenge. CONVERGENCE •Physical laws impose constraints on animal size and shape

restriction enzymes

Bacteria naturally produce these, to chop up foreign DNA that enters them (anti-virus protection) ex) Eco RI We harvest them to treat bacteria

Regulation of Gene Expression in bacteria

Bacteria often respond to environmental change by regulating transcription -cells/living organisms conserve energy and resources. produce only what they need -cells regulate enzyme production by: -feedback inhibition -gene regulation -prokaryotes control gene expression using operons

Nucleosomes

Bead-like structures formed by histones and DNA basic unit for DNA processing --a chromosome is about 50% DNA and 50% protein, which makes sure that the DNA is properly packaged, protected, and organized

Gas exchange for Fish

COUNTERCURRENT EXCHANGE -Water moves across gills at all times -Gills extract dissolved oxygen from water -Water comes in thru mouth, flows through gill plates in 1 direction (front to back), blood flows in opposite direction in capillary beds (back to front) -Partial pressure of O2 in H20 drops as its given off -Partial pressure of O2 in blood and H2O remain complementary so that it flows in one direction

Stomach

Chemical digestion of proteins - pepsin (protease) -->secreted as an inactive molecule activated within the stomach by HCl secreted by other stomach cells

Information molecules: DNA RNA Protein

DNA - long term information storage RNA - information transmission (doesn't last long) Protein - Information usage

Central Dogma of Molecular Biology

DNA -> RNA -> Protein tRNA rRNA other functional RNA

What makes up a nucleotide

Deoxyribose + Phosphate group + Nitrogenous base the sugar (deoxyribose) is in the middle! 1 less oxygen than ribose!

small intestine

Digestive organ where most chemical digestion and absorption of food takes place villi-increase surface area microvilli

Benefits of ectotherm/endotherms

Ectotherms tolerate greater internal temperature variation •Endotherms are active at a greater range of external temperatures• Endothermy is more energetically expensive than ectothermy

For a given variable...

For a given variable, -An organism has a set point •Environmental fluctuation = stimulus •Detected by an internal sensor •Triggers a response -The response returns the variable to the set point negative and positive feedback loops

Gas exchange

Gas exchange is easy for small animals with a gastrovascular cavity or a flat body. -An internal system for fluid circulation between body surfaces and individual cells is necessary for most animals, ...because most do not have a flat body

Where does gas exchange occur? Pressure difference?

Gas exchange occurs in the capillaries because other blood vessels have too many layers and aren't permeable enough high pressure blood flow coming in capillaries (fluid moving out of capillary) Low pressure going out (fluid moving in capillary)

Animals are what kind of feeders

Heterotroph -Food provides nutritional needs -Chemical energy (breaking bonds releases ATP)(for ATP production) -Organic molecules (N and C in usable forms) -Essential nutrients (vitamins and minerals)

spiracles

external respiratory opening - air comes into tracheoles, distributed in air sacs

Thermoregulation

Is the process by which animals maintain an internal temperature within a tolerable range

When a cell no longer needs a given protein molecule... Figure 18.14 (regulation of gene expression by microRNAs)

It is... Labeled for destruction (Ubiquitin) Destructed in a proteasome (proteases detroy them in the proteasome) The amino acids products are then recycled Happens in cytosol??

If too much product is present the cell will stop its production but if there is too little the cell will make more?

Negative control (negative feedback)

Operon Operator

Operon - a cluster of functionally related genes under coordinated control. entire stretch of DNA including operator, promoter, and several related genes Operator - a regulatory switch of DNA usually positioned within the promoter

Figure 18.15 (condensation of chromatin at the centromere) look at figure in book

RNA not allowed to be processed, or it is degraded Some small functional RNA's (miRNA and siRNA) can selectively degrade mRNA molecules that the cell should not express

Processes for Balancing Heat Loss and Gain

Physiological processes: -Insulation -Circulation Physical processes: -Conduction -Convection -Radiation, -Evaporation Behavioral processes

gel electrophoresis

Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel DNA has a negative charge (phosphate groups) so it is attracted to the positive terminal of the electrophoresis system. The gel is porous - DNA fragments move at a speed proportional to their size (small=fast)

Mutualistic Adaptations

Prokaryotes and Eukaryotes in digestive tract regions -digest plant materials -produce vitamins and other nutrients -produce gas (methane, etc)

purines and pyrimidines

Purines (double ring): Adenine and guanine Pyrimidines (single ring): Cytosine and thymine (uracil in RNA)

Animals manage their internal environment by...

REGULATING or CONFORMING to the external environment

Product of regulatory gene that can bind to the on/off switch of an operon

Repressor

origin of replication

Site where the replication of a DNA molecule begins.

Distribution of Blood Flow

Sphincters -relaxed: blood flow throughout everything -contracted: not distributed fully -not exercising or eating

semiconservative replication

each new DNA molecule consists of one new strand and one old strand original strands of DNA separate and make new partners begins at a site called... the origin of replication

Figure 18.18 (determination and differentiation of muscle cells)

Transcription Factors: Master regulatory genes can oversee expression of tissue specific genes for the development of entire organs Products of master regulatory genes: Master transcription factors (trigger certain gene to be expressed) ex) myoD (master transcription factor)- (myo=muscle) oversees specialization of muscle the cell becomes a myoblast (swictches on myoD), which is determined to become a muscle cell when myoD is expressed by myoblast, myoD product switches on other transcription factors, which turn on muscle specific proteins ex) actin, myosin, etc. which allow muscle cell to contract When cells reach the end point of differentiation, the cell blocks cell-cycle proteins because no further division in necessary

Amino acid an E. coli can manufacture if it isn't supplied by the environment

Tryptophan

What is the product of a regulatory gene

a repressor (which has a specific shape that can change)

How do early cells, seemingly identical, know to differentiate along different paths? Figure 18.17 (Sources of developmental information for the early embryos)

a) Cytoplasmic determinants in the egg -cytoplasmic determinants are not evenly distributed in the cytosol, not random!! When cleavage divisions happens, the daughter cells will have different combinations of cytoplasmic determinants. The daughter cells are different in their potential. Takes you to a 2 cell stage b) Induction by nearby cells -as cells begin to start expressing proteins, there are signaling molecules whose job is to influence surrounding cells. By receiving signals from neighbor, those cells start to express genes accordingly.

Euchromatin Heterochromatin

accessible for transcription very tighly compacted and inaccessible

What kind of chemical bond links the three components of a nucleotide, and in what configuration?

covalent bonds they make up a sugar-phosphate backbone with the base pointing inward P-S-P-S-P-S-P-S 5' end - beginning 3' end - ending

Enzymatic hydrolysis

digestive enzymes chemically break down complex food molecule into simpler ones using water

Fluid feeder

ex) Mosquito Gains nutrients by extracting bodily fluids from its hosts

Substrate feeder

ex) caterpillar Feeds on the leaves on which it lives

suspension feeders (filter feeders)

ex) humpback whale -feeds on small organisms suspended in water

Bulk feeder

ex) rock python Eats relatively large amounts in a single meal but eats somewhat infrequently humans are bulk feeders!!

Double circuit circulation in mammals and birds

full separation 2 Atrium 2 Ventricle

Definitions: genome chromosome gene pool gene genotype phenotype DNA RNA Alleles

genome-full set of DNA/genes in an individual chromosome-pairs of segments of DNA. Humans have 23 pairs. Sets of genes gene pool-set of genes in a population. All potential genes of a population gene-a complex sequence of nucleotides. base pairing. codes for DNA genotype phenotype-physical trait that is expressed for a particular gene DNA- molecule that makes up genes. Deoxyribose sugar. nucleic acid. double strand RNA-single strand. ribonucleic acid Alleles-AA (homozygous dominant) Aa (heterozygous) aa (homozygous recessive)

Definitions: helicase primase DNA polymerase Topoisomerase Ligase

helicase- unzips/separates the two strands of double-helix DNA primase-lays down a short RNA nucleotide sequence on the DNA to initiate replication DNA polymerase-reads" the template DNA strand, assembles a daughter strand on it Topoisomerase-prevents DNA kinking as strands are being separated for replication Ligase- forms covalent bonds between backbone sugars and phosphates

An example of an inducible operon is the...?

lac Operon

pancreatic enzymes

lipase protease amylase nuclease -break down food molecules almost completely

Figure 18.11 Cell type-specific transcription

liver cells express albumin but don't express crystalline lens cells of the eye express crystalline but don't express albumin

Telomeres

long, noncoding (nonsense) sequences at the end of chromosomes. Protects the DNA strands. They get shorter over time

Eukaryotic regulation of gene expression

look in notes!!

lAC operon

look in notes!!

Single Circuit circulation

look on notes?

Promoter

makes RNA polymerase

Mouth

mechanical digestion-->teeth/tongue chemical digestion-->salivary amylase (breaks down complex carbs)

Why do hearts have valves?

needed to make 1 way flow

Homeostasis is maintained by...

negative feedback (returns variable to normal range or set point) •Buildup of the end product shuts the system off •Positive feedback loops also occur in animals, but usually not for homeostasis

Part of a promoter, a switch that allows or blocks expression of operon genes?

operator

Recombinant plasmid

plasmid that has had a particular gene inserted into it using restriction enzymes cloning vectors - modifies DNA sequences within unique DNA segment, make multiple copies of DNA/RNA of specific sequence, store DNA in construct expression vectors - synthesizes protein coded by cloned DNA sequence

DNA recombination (Gene Cloning) for bacterial cell

plasmids are expressed under special circumstances, they can be passed directly from 1 bacteria to another. This is why antibiotic resistance spreads quickly Restriction enzymes?

Are operons found in prokaryotes or eukaryotes?

prokaryotes

STR's

short tandem repeats of noncoding DNA within spaces between genes

Histones

small proteins form a cluster of 8, loops of DNA form around them made of positively charged amino acids, attracted to DNA Histone + linker DNA = nucleosome

Obtaining oxygen from air

tracheoles and lungs

intracellular digestion extracellular digestion

type of digestion in which food is digested inside specialized cells that pass nutrients to other cells by diffusion Digestion that takes place outside of the cell.

poikilotherm and homeotherm

•A poikilotherm can survive relatively wide fluctuations in body temperature •A homeotherm requires body temp to remain close to a specific set point Not to be confused with ectothermy and endothermy!-Some endotherms "hibernate" (torpor)-Some ectotherms have very stable external environments

Homeostasis

•Organisms use homeostasis to maintain a "steady state" or internal balance regardless of external environment •In humans, body temperature, blood pH, and glucose concentration are each maintained at a constant level