Bio 101 - Exam 1

Properties of Life

order, energy processing, regulation/homeostasis, response to the environment, reproduction, growth and development, evolutionary adaption

levels of bio organization

(least complex) molecule, organelle, cell, tissue, organ, organ system, organism, population, community, ecosystem, biosphere (most complex)

Animals

• eukaryotic

• multicell

• heterotroph

• lack cell wall

• body made up of cells organized into tissues

• motility

• specific developmental patterns/genes

Organic macromolecules

carbs, proteins, lipids, nucleic acids

Carbs (sugars)

Monomer

monosaccharide

Dimer

disaccharide - broken down for quick energy

Dehydration synthesis

monomer → dimer + H2O

many monosaccharides

polysaccharide - long string of glucose molecules

Starch

energy storage, in plants

Glycogen

energy storage, in animals

Cellulose

structural, in plant cell (cell walls made of this)

Chitin

structural, in cell walls of fungus

Oligosaccharide

a carb composed of a relatively small number of monosaccharide units

• used as identification tags

Proteins

Amino acid classification - ONLY LOOK AT R GROUP

water soluble, uncharged —> OH, SH, NH
water soluble, charged —> have - or +
uncharged —> no polar covalent bonds, all H or CH3

Primary protein structure

sequence of a chain of amino acids

Secondary protein structure

local folding of the polypeptide chain into helices or sheets

• interactions between non R groups

- Alpha helix

- Beta sheet

Tertiary protein structure

3D folding pattern of a protein due to side chain interactions

• globular proteins

• interactions between R groups

Quaternary protein structure

protein consisting of more than one amino acid chain

Chaperones

proteins that help other proteins fold

Enzymes

biological catalysts

Lipids

hydrophobic molecules

functions

• hormones

• energy source —> lots of covalent bonds

• major component of cell membranes

Sterols

Cholesterol

moves in blood as part of lipoprotein complex

• SO hydrophobic

LDL

carries cholesterol from liver to body cells

“bad” —> sticky and build up clots

HDL

picks up excess cholesterol from cells —> delivers to liver for disposal/recycling

“good” cholesterol

Fats and Oils = Triglycerides

• glycerol + 3 FA

• built by dehydration synthesis

Saturated FA

pack tightly, solid at room temp

high level LDL

animal fats

Unsaturated FA

loosely packed, liquid at room temp

bent

low LDL

high HDL

plant triglycerides = oils

Phospholipds

components of cell membranes

Membrane transport

Passive

• simple diffusion

• facilitated diffusion

• osmosis

Active

Vesicular (bulk)

Simple diffusion

high to low - down concentration gradient

no proteins

no energy

Facilitated diffusion

down direction

proteins needed to facilitate and aid diffusion

no energy needed

Channel proteins

pore-forming transmembrane proteins

many channels are gated

Carrier proteins

change shape during transport

GLUT1 and GLUT2

carrier proteins for glucose

1 —> metabolizing body cell, high concentration, glucose in cells used to make ATP

2 —> liver cell, low concentration

Osmosis

passive transport of water, direction down, proteins needed for rapid movement, no energy

Isotonic solution

[solute] inside cell = outside cell

Hypotonic solution

[solute] higher inside cell than outside cell

• water in

Hypertonic solution

[solute] higher outside cell than inside cell

• water out

Aquaporins

water channels that facilitate rapid water movement

Active transport

direction against concentration gradient, proteins needed, ATP needed

ex: NA+/K+ Pump

Vesicular transport

movement of substances into and out of the cell by vesicles

• endo and exo cystosis

Endocytosis

substance brought into cell

1. Phagocytosis

2. Pinocytosis

3. Receptor-mediated endocytosis

Exocytosis

substance released from cell

Functions of gut microbiome

harvesting energy from food, development, mental health, protection

Microbe gut-brain axis

the vagus nerve

• neuropod cells to stimulate vagus

short chain FA

• secreted by microbes —> blood vessels —> brain

serotonin

• stimulate cells in gut lining = hormones throughout body

immune system

• influence immune cells and inflammation

Antibiotics

use to kill or inhibit growth of bacteria

but not selective

Quorum sensing

system of stimulus and response correlated to population density

signal binds receptor → light gene turn on

Archaea found in diverse environments

halophiles - salt lovers

methanogens - methane producers

thermophiles - heat lovers

Nuclear lamina

Function

• shape of nucleus

• organizes chromatin = DNA

Structure

• lamin proteins (A, B)

• lamin-associated proteins

Nuclear envelope

2 membranes, still phospholipid bilayer —> sterols and proteins

Chromatin

DNA & associated proteins

Nucleolus

ribosomes parts made here

Endomembrane system

regulates protein traffic and lipid synthesis

• smooth ER

• rough ER

• nuclear envelope

• golgi apparatus

• transport vesicles

• lysosome

• plasma membrane

Smooth ER

no ribosomes

lipid production

Rough ER

ribosomes

protein production

Lysosomes

digestive compartments, recycling centers of cell

• contain hydrolytic enzymes

• pH = 5

  • how = protein pumps in lysosomal membrane

  • why = optimal pH for hydrolytic enzymes - ideal for folding

Lipid transfer proteins - LTPs

how lipids get from smooth ER to other membranes, slower process

box like vs bridge like

Cytoskeleton

microfilament

• long, thin, rod-like proteins

• actin subunits → fold into glob and dynamic

• cell division

microtubule

• dynamic, added/removed for length - LEGO

• tubulin subunits → spiral add-on

• chromosome movement, vesicle transport (through endomem sys)

intermediate filament

• not dynamic, no add on/off

• no subunit

• nuclear lamina → structural support of nucleus

Motor protein

converts energy of ATP into motion

Peroxisomes

Oxidation - breakdown of molecules

Mitochondria and chloroplasts

energy conversions

food energy → ATP vs solar energy → chemical energy

Endosymbiosis theory

one organism lives inside another —> happy and health

mitochondria and choloplast example

DNA

nucleic acid molecule that contains instructions (genes)

Chromosome

DNA molecule with part or all of the genetic material of an organism

Chromatin

chromosome + proteins that form the chromosomes found in eukaryotic nuclei

• histones = main type of protein - package massive amounts of DNA into genome

Genome

complete set of DNA in an organism

Gene

segment of DNA that contains info to make an RNA

Prokaryotes - DNA

single, circular chromosome in nucleoid region

Eukaryotic - DNA

chromosomes are long and linear, multiple of them

• 46 CHROMOSOMES

Helicase

unwinds double helix at replication fork

moves into

breaks H+ bonds → allows single strand template to be available

Single strand binding proteins

stabilize replication bubble, keep single strands from re-pairing

Topoidomerase

relieves twisting (supercoiling) ahead of helicase

allows helicase to keep moving

DNA pol 1

removes RNA primers and fills in gap with DNA nucleotides

• no 3’ OH available

DNA ligase

makes phosphodiester bond to connect DNA fragments

Okazaki fragments

lagging strand

Telomeres

region of repetitive DNA sequences at the end of a chromosome

• TTAGGG

-how eukaryotes cope with end-replication issue

Hayflick limit

40 cell divisions → cell death

happens in somatic (non reproductive) cells

Embryo and Stem cells

contain telomerase

• enzyme that can “fill in the gap” → chromosome maintain length upon each cell division

• long are better

DNA repair

1. DNA pol has proofreading function

   1. 3’ → 5’ exonuclease activity

2. Mismatch repair system

   1. remove/replace incorrectly paired nts resulting from replication errors

      1. (mistakes missed by DNA pol)

   2. - endonuclease cuts out mismatch

   3. DNA pol fills in correct nts

   4. DNA ligase makes last phosphodiester bond

3. Excision repair

   1. long after replication complete

      1. endonuclease cuts DNA

      2. DNA pol fills in gap

      3. Ligase connect pieces
         
         

Chromosome packaging

nucleosome consists of a cluster of 8 histone proteins around which DNA is wrapped 2x

• metaphase chromosome (tightest level)

  • ONLY at beginning of cell division

Flow of genetic information in cells

DNA —transcription—> mRNA —translation—> protein —> trait

RNA polymerase

makes RNA from a DNA template

binds to promoter region of gene to initiate transcription

Eukaryotes modify mRNA after transcription

addition of 5’ cap and Poly-A-tail

Intron removal

RNA splicing

• necessary for movement of RNA from nucleus to cytosol

Translation

production of protein from an mRNA

mRNA

messenger

provides codons

• 3 letter “word” in mRNA specifies which amino acid is put into protein

tRNA

transfer

connection between mRNA and protein

anticodon will bind with complementary codon in mRNA

Translation initiation

1. mRna binds to small ribosomal subunit

   1. start codon in P site, 5’ cap helps with correct placement

2. anticodon of first tRNA binds to start codon

3. large subunit binds

Translation elongation

1. codon recognition

2. peptide bond formation

3. translocation

4. exit

Translation termination

1. stop codon enters A site

2. release factor binds A site

3. complex falls apart

   1. polypeptide released → folds → targeted to correct cellular location

Mutation

change in an organism’s DNA

Point mutation

in DNA, a single nt base is changed, inserted or deleted

Substituion

replacement of one pair of nts with another

• missense

• nonsense

• silent

Missense

different amino acid is encoded

• conservative - new amino acid is similar to original → okay

• non-conservative - new aminon acid is different than orginal → bad

Nonsense

puts in a stop codon

consequence - truncated protein = bad

Silent

no change in amino acid

Insertion, deletion

addition or loss of nt pairs