Bio units 1-3

Limitations of DNA Polymerase

1. they cannot unwind double-stranded DNA

2. they cannot start a chain, they can only add a nucleotide to an existing nucleotide strand

3. they can only add nucleotides to 3’ ends (5’ → 3’ synthesis)

4. they cannot link existing DNA chains to eachother

crossing over

because they have similar DNA sequences, homologous chromosomes exchange part of their DNA during Meiosis 1

chiasma = site of crossing over

This process also serves as a checkpoint to make sure each chromosome is paired up before chromosomes divide , this creates recombinant chromosomes

independent assortment

each chromosome pair splits during meiosis 1 randomly and independently

meiosis

creates haploid gametes from diploid cells

creates 4 daughter cells with half as many chromosomes as the parent cell

cell respiration equation

32ADP+ 32P → 32ATP

Microtubules (MT)

hollow tubes assembled of tubulin

dynamic - grow and shrink with the addition or removal of different proteins

functions: maintain cell shape and movement of chromosomes during cell division, form mitotic spindle

tight junction

liquid seal

transmembrane proteins pull cell membranes together, often making a water-tight barrier between cells

desmosome

rivet

transmembrane proteins anchor cells together

microfilaments

solid rods, actin (protein) polymers, form linear and branched structures

dynamic - grow and shrink with the addition or removal of different proteins

functions: maintain cell shape and movement

• skeleton, muscle

• amoeboid movement

membrane functions

transport of molecules in and out of cell

catalysis - membrane bound enzymes

signaling

cell adhesion

positive control

receives a treatment or test with a known result

negative control

a group in an experiment that does not receive any type of treatment and, therefore, should not show any change during the experiment

Dependent vs independent variable

An independent variable is the factor manipulated to observe its effect, whereas a dependent variable is the outcome or response that is measured

ionic bonds

creates ions (charged atoms), attraction between oppositely charged ions

covalent

electrons shared,

non polar = equally charged

polar = creates partial charges and not equally shared

hydrogen bonds

attraction between partially charged atoms created by polar covalent bonds, no electrons shared or transferred, transient/temporary, positive atom around H, usually with O or N

Van der Waals interactions

asymmetrical electron distribution, temporary “patches” of positive and negative charge, causes atoms to “stick” to each other - weakest interaction

cohesion

creates surface tension, making it difficult to break surface of water

Acidity

acid <7 increases H+

basic >7 decreases H+

buffer maintains H+

hydroxyl groups

make functional groups hydrophilic

sugar humans can’t digest

cellulose

globular proteins

soluble (dissolved in body fluids), carry out tasks

fibrous proteins

not soluble, job is generally structural

protein structure

alpha carbon backbone R group, amino acid and carboxyl group, side chains (R group) determines amino acid properties

why do proteins fold

chemical interactions between different amino acids

cofactors

non-peptide helpers in proteins, provide chemical qualities unavailable from amino acids

affinity

strength of protein ligand interaction

amphipathic

has hydrophobic and hydrophilic regions

passive transport proteins

allow hydrophilic ions and molecules to travel down concentration gradient (facilitated diffusion)

active transport proteins

use energy to move against concentration gradient

what molecules can pass through membrane

small, hydrophobic molecules

lysosome

digests objects brought into the cell by endocytosis

SER

contains enzymes for destroying toxins, where phospholipids are made

peroxisome

manages hydrogen peroxide levels in cells, regulates fat metabolism

RER

covered with ribosomes, site of protein synthesis

golgi apparatus

sorts, modifies, and ships proteins outside of cell

vesicle

small sack surrounded by membrane used to move things between organelles

cytoskeleton + its functions

dynamic work of fibrous proteins throughout cytoplasm

functions: provide cell with shape and rigidity and help attach cell to other cells and surroundings, movement of vesicles, organelles, chromosomes during mitosis

kinetics

speed of chemical reactions, determined by the instability of the transition state between the reactants and products

enzymes

reduce activation energy to speed up chemical reactions by stabilizing transition state, usually not permanently altered and can be used again

point of saturation

increasing substrate concentration does not affect reaction rate

anabolic

metabolic reaction that joins molecules together and uses energy

catabolic

breaks down larger molecules and consumes energy

competitive modulators

similar shape to substrate, compete for active site, overcome by high substrate concentration

allosteric noncompetitive modulators

bind away from active site, alter protein shape, can increase or decrease enzyme activity depending on how it changes enzyme shape, unaffected by substrate concentration

negative feedback

products of a reaction or pathway inhibit an enzyme in the pathway, reducing production of the product

positive feedback

products of a reaction or pathway activate an enzyme in the pathway, increasing production of the product

equilibrium

(death), state of maximum stability, achieved in isolated systems, avoided in open systems

energy coupling

an exergonic reaction to an endergonic reaction

photosynthesis

captures light energy, stores in stable forms, (light → carbohydrates)

cellular respiration

converts energy from stable to versatile forms (carbohydrates → ATP)

substrate level phosphorlyation

phosphate transferred directly from substrate to ADP

phosphofructokinase

catalyzes first step that irreversibly commits substrate to glycolysis, stimulated by AMP (from ADP)

anaerobic respiration

cell respiration without oxygen

carbon in photosynthesis comes from

the air

endosymbiosis

one organism living inside another, mitochondrion, photosynthetic chloroplast

evidence: double-membrane, own DNA, ribosomes and proteins, autonomous growth/replication, energy production

chloroplasts

site of photosynthesis, 3 membrane-bound compartments: intermembrane space, stroma, thylakoid space

transpiration

evaporative loss of water through stroma

3 methods of cell signaling

contact dependent, local chemicals (paracrine) - receptors on cells, long distance signaling

gap junction

protein channels that connect adjacent cells, small molecules can pass directly from cell-to-cell, good for fast, unregulated comminication

receptor

protein that recognizes a specific signaling molecule and sends some signal within cell to change behavior

long distance communication

endocrine: chemical - hormones travel through blood

nervous: electrical + chemical - action potentials (electrical nerve impulses) and neurotransmitters (signaling molecules)

hydrophobic signals

membrane permeable (direct diffusion), cytoplasmic or nuclear receptors, often directly regulate DNA

hydrophilic signals

membrane impermeable, membrane receptors signal ‘transduced’ into cell, ex. proteins

agonist

mimics signaling molecule, activates receptor/pathway

antagonist

blocks receptor, inhibits receptor/pathway

signal transduction

internal amplification, enzyme-mediated - phosphorylation cascade, one enzyme activates the next, small molecule mediated

second messenger: signaling molecule that is created and has effects inside of cell

first messenger

extracellular signaling molecule

second messenger

activated intracellular molecules, ions, often produced by enzymes activated by receptor

chromosome

one continuous DNA molecule

chromatin

DNA molecule wrapped around protein (histones)

centromere

site (specific DNA sequence) where proteins bind to help divide chromosomes during cell division, creates cinched “waist”

genome

entirety of an organisms hereditary information

chromosome in prokaryotes

singular circular chromosome

chromosomes in eukaryotes

multiple linear chromosomes

DNA replication

whole genome is duplicated so each daughter cell gets complete genome

sister chromatids

joined identical copies of original chromosome, created by DNA replication

mitosis

separation of sister chromatids and distribution to daughter cells

mitotic spindle

microtubules which pull the sister chromatids apart during mitosis, spindle extends from centrosomes

kinetochore microtubules

connect to proteins at centromere, position chromosomes in center of cell, and then pull apart

polar (nonkinetochore) microtubules

overlap, motors push rod-like MTs apart to elongate the cell

cytokinesis

separation of the cytoplasm at the end of mitosis

animal = cleavage furrow

plant = cell plate

cyclin proteins

level fluctuates “cycles”, synthesis/degradation regulated by signals and negative feedback, multiple cyclins act at different points in cycle

cyclin-dependent kinases (CDKs)

constant level, activity depends on cyclins, cyclin-CDK complex controls cell cycle progression, S Phase Cyclin-CDK activates DNA replication

oncogenes

stimulate cell division

tumor surpressors

code for proteins that inhibit division, or prevent cancers in other ways, ex. p53 and p21

terminally differentiated

body cells in their final form which do not divide, ex. muscle, skin, brain, and immune cells

stem cell

unspecialized cell that produces new cells that can specialize

embryonic stem cells

come from embryos and need to be able to make the whole body or any part of it (totipotent and pluripotent)

adult stem cells

found in specific parts of body and only replace specific set of cells in adults (unipotent, multipotent, or pluripotent)

how does cancer harm the body?

cancer cells take up spaces and resources

causes of cancer

mutations, radiation, carcinogens:cancer causing substances, viral oncogenes, immunodeficiency

DNA repair

enzymes fix mutations to slow cancer process

allele

a specific version of a gene, different alleles for the same gene result in slightly different versions of the protein

humans have

23 homologous pairs of chromosomes

homologous chromosomes

have the same genes but are not identical and may not have the same alleles

diploid

cells with 2 copies of each chromosome

haploid

cells with 1 copy of each chromosome, ex. gametes

n

number of unique chromosomes an organism has, humans n=23, haploids have “n” chromosomes, diploids have “2n” chromosomes

genotype

the collection of alleles an individual has for a specific trait