Bio 1105 Final Exam VT

characteristics of living things

o All made of cells

o All store and process info

o Transformations of energy

o Systems grow and reproduce diversity

o Systems adapt and evolve

Hierarchical organization of living systems

Atom molecule macromolecule organelle cell tissue organ system organism population species community ecosystem biosphere

cohesion

polarity of water creates the attraction of H20 molec., creates surface tension

Macromolecules

carbs, nucleic acids, proteins, lipids

carbohydrates

energy and structural support, energy rich biofuels, surface signaling (ex. Sugars and starches)

Nucleic Acids

storage and expression of genetic info (ex. DNA, RNA, ATP, NAD+, NADP)

Proteins

enzymes and structural support (cell wall, membranes, amino acids)

Lipids

energy storage, membrane structure, signaling (ex. Phospholipid bilayer)

Macroelements

carbon, hydrogen, oxygen, phosphorus, potassium, iodine, nitrogen, sulfur, calcium, iron, maganesium

microelements

chlorine, manganese, copper, zinc

plasma membrane

regulates what comes in and out of the cell; cell to cell recognition

nucleus

instructions for protein synthesis and cell reproduction; contains genetic info

chromosomes

contain hereditary info used in the direct synthesis of proteins

nucleolus

synthesis of rRNA and ribosome assembly

ribosome

site of protein synthesis

ER

intercellular compartment forms transport vesicles; participates in lipid synthesis and synthesis of membrane secreted proteins

Golgi Apparatus

packages proteins for export from cell; forms secretory vesicles

Lysosomes

digest worn out organelles and cell debris; digest material taken up by endocytosis

microbodies

isolate particular chemical activities from the rest of the cell

mitochondria

"power plants" of the cell; sites of oxidative metabolism

chloroplast

sites of photsynthesis

flagella

motility or moving fluids over a surface, like a tail

cell wall

protection and support found around plant cells

endomembrane system

o Made up of nuclear envelope, plasma membrane, ER, Golgi Apparatus, lysosomes, and vacuole

o Functions:

♣ Synthesis of proteins and transports into membranes, organelles or out of cells

♣ Metabolism and movement of lipids

♣ Detoxification of poisons

phospholipids

fundamental structure of the membrane with polar hydrophilic heads and non polar hydrophobic tails

Fluid Mosaic Model

o Hydrogen bonding eater keeps membrane in bilayer configuration

o Phospholipids and unanchored proteins in membrane are loosely associated and can diffuse laterally

phagocytosis

o particle is engulfed, which folds around it and forms vesicle

pinocytosis

o fluid droplets are engulfed by membrane then forms vesicles

receptor mediated endocytosis

o triggered by a specific receptor forming clathrin coated vesicles

direct contact

o - cells communicate with cells nearby, recognized by its receptors

♣ Used a lot during cells development

paracrine signaling

o cell releases signal m0lecules that diffuses through the membrane of another cell (next door neighbors)

endocrine signaling

o signal molecule remains in extracellular membrane, may enter organism's circulatory system

♣ Hormones- long lived signaling cell, slow compared to other signaling

♣ Ex. Insulin moving

synaptic signaling

o in animals' nervous system provides rapid signaling to distant cells, neuron to neuron or neuron to target cell

♣ Neurotransmitters - released from long fiberous nerve cells

autocrine signaling

cells send signals to themselves that bind to specific receptors on own plasma

phosphorylation

o Chemical reaction resulted in the addition of a phosphate group to an organic molecule

G protein-coupled receptors

o Large family includes receptors for neurotransmitters, odors/tastes. Photons, endocrine hormones and growth factors

50% of know drugs target

gap junction

o provide passageways large enough to permit small substances such as glucose and amino acids to pass from one cell to the next

tight junction

along digestive tract; prevent leakage

catalysts

o influence chemical bonds to lower activation energy

o cannot violate the laws of thermodynamics

o don't alter the proportion of reactant turned into product

competitive inhibitors

competes with the substrate for the active site

noncompetitive inhibitors

bind to enzyme at the allosteric site causes a shape change that makes the substrate unable to bind substrate

Glycolysis

• first stage of cellular respiration

o Takes place in the cytoplasm

o Converts 1 glucose to 2 pyruvates

o 10 step biochemical pathway

o left with no carbons because they are being released as carbon dioxide

o Products:

♣ 2 ATP by substrate level phosphorylation

♣ 2 NADH

o 1st converted into two G3P molecules

♣ 1st 5 reactions

♣ activity requires energy input hydrolysis of 2 ATP molecules

o Each G3P molecule is converted into pyruvate

♣ Last 5 reactions

♣ G3P is oxidized: NAD+ NADH

♣ Pi is added to G3P and transferred to ADP 2 molecules of ATP at the end

Electron Transport Chain

A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.

aerobic respiration

Growing or metabolizing only in the presence of molecular oxygen

fermentation

The process by which cells break down molecules to release energy without using oxygen

Light Dependent Reactions

o Require light

o Occur in the thylakoid

o Capture energy from the sunlight

o Make ATP and reduce NADP+ to NADH

Light Independent Reactions

o Does not require light

o Occurs in the stroma

Use ATP and NADPH to synthesize organic molecules from CO2

chlorophyll a

♣ Main pigment in plants

♣ Absorbs violet-blue and red light

♣ Only pigment that can directly convert light energy into chemical energy

chlorophyll b

♣ Accessory pigment

♣ Absorbs blue and red-orange light

♣ Adds to rand of absorbed light

♣ Tissues will reflect green

carotenoids

♣ Accessory pigment

♣ Absorbs blue and blue-green light

♣ Adds to range of absorbed light

Calvin Cycle

Carbon fixation process in photosynthesis. Forms sugar and other organic compounds.

DNA pol III

synthesizes fragment, main replicating enzyme

DNA pol II

DNA repairing enzyme

DNA pol I

replaces RNA with DNA

Transcription

o When DNA is read and a complementary strand of RNA is formed

o Occurs in the nucleus of eukaryotes

G1 phase

primary growth phase (longest of the phases)

S phase

replication of DNA is signaled

G2 phase

more growth and prep for mitosis

M phase

nuclear and cytoplasmic division

prophase

♣ bipolar spindle assembles, chromosomes condense, nuclear envelope breaks down

prometaphase

chromosomes attach to microtubules at the kinetochores, chromosomes move to the equator of the cell

metaphase

♣ all chromosomes are aligned at the equator , called the metaphase plate, chromosomes are attached to opposite poles and are under tension

anaphase

sister chromatids separate, chromosomes move to plates, poles further separate

telophase

- chromosomes decondense, nuclear envelope begins to reform

cytokinesis

♣ Animal cells- cleavage furrow forms to divide the cells

♣ Plants- cell plate forms to divide the cells

G1/S Check point

♣ Growth factors, nutritional state of the cell , size of the cell

♣ Cell will either keep on growing or divide

G2/M Checkpoint

♣ Replication completed, DNA integrity

P53 protein comes into play

Spindle Checkpoint

♣ Chromosomes attached at metaphase plate

♣ Nondisjunction can occur if they are not properly attached

cyclins

proteins that intimate mitosis

proto-oncogenes

o only one chromosome in the pair is mutated

♣ Normal genes that become oncogenes when mutated

♣ Oncogenes may be overexpressed or stuck in the "on" state

Gain-of-function mutation: only one needs to be mutated

dosage compensation

o Ensures equal expression genes from the sex chromosomes even though females have two X chromosomes and males only have 1

nondisjunction

o Failure of homologues or sister chromatids to separate properly during meiosis

Leads to aneuploidy

aneuploidy

loss or gain of a chromosome

restriction endonuclease

o Breaks the double helix of DNA at specific sequence, in bacteria these enzymes protect the organisms from viruses

o Specific enzyme can only cut a specific section

o Generates ends of unpaired bases (sticky ends), useful for pair recombinant DNA

Polymerase Chain Reactions

o Denaturation, annealing of primers, DNA synthesis

o Uses heat cycles and DNA polymerase to replicate a segment of DNA many times

o DNA polymerase is the only enzyme used in cellular DNA replication that is required to perform PCR

o Mimics DNA replication

vector

o DNA molecule into which the DNA sequence of interest can be inserted

♣ Must:

• Have ability to be replicated by the host's cellular machinery

• Have selectable marker gene

• Have a way to insert the DNA of interest

cDNA (complementary DNA)

o made using reverse transcriptase, an enzyme isolated from retroviruses that converts RNA into DNA

o a way to examine alternative splicing in different tissues

genetic map

• provide relative locations of genes

o determined by recombination frequency

o first knowledge of genome came from construction of genetic maps

physical map

shows actual location of landmarks

restriction map

common type of physical map

♣ DNA cut with Restriction enzymes and the banding [attern is analyzed to generate map

♣ Distance on this type of map can be measured in base pairs (bp) or kilobases

clone-by-clone sequencing

Overlapping regions between bacterial artificial chromosomes

shotgun sequencing

o DNA is randomly cut into smaller fragments, cloned, the sequenced

o Occurs a lot faster

cleavages

o the first cell divisions in early embryos

♣ Occur rapidly

♣ No G1 or G2 phase

♣ No cell growth

Single cell multicellular organism

cell differentiation

o Changes in gene expression that ultimately result in cell specialization

♣ Progressive restriction of the number o fates that the wells with in a lineage can adopt occurs over multiple divisions

totipotent

- form all tissues of an organism plus extraembryonic tissues (ex. Zygote)

pluripotent

form all tissues of an organism but extraembryonic (ex. Embryonic stem cells from blastocysts)

multipotent

♣ can only form certain cell type (ex. Adult stem cells)

unipotent

♣ can only form one cell type

• Spermatogonia- sperm stem cells can only become sperm

morphogenesis

o Development of organisms body form

o Achieved through the following mechanisms:

Cell growth, division, migration, changes in cell shape , and programmed cell death (apoptosis)

meristems

clusters of cells responsible for producing new cells at the ends of plants

c. elegans

about as primitive an organism that exists which nonetheless shares many of the essential biological characteristics that are central problems of human biology

nuclear reprograming

o Resets a differentiated call to an undifferentiated stem cell shape

reproductive cloning

o nucleus of differentiated cell is put into a denucleated egg

therapeutic cloning

o nucleus of differentiated cell is put into the egg of a human

♣ The embryonic stem cells are harvested and cultured

apoptosis

o Programmed cell death

The cell breaks into several apoptic bodies ; the organelles are still functional and are recycled or metabolized by other cells

Hox genes

Class of homeotic genes. Changes in these genes can have a profound impact on morphology.

population

A group of individuals that belong to the same species and live in the same area

evolution

change in the population of organisms over a long period of time through shifts in allele frequencies

genetic variation

Differences among individuals in the composition of their genes or other DNA segments in a population

molecular hybridization

is tagged singled strands that are used to determined where wanted colonies are growing