Bio Final-all units

Controlled experiment

where experimental group is compared to control group

field study

one study done out and about, not in a lab

retrospective study

researchers may interview people, use medical records, or examine death certificates so they can identify factors that led to that outcome

prospective study

researchers enter the picture at the beginning of the study, enrolling participants(cohort) then collecting data for a period of time.

statistical analyses

assess how likely it is the results are due to random chance'

p-value

*  Indicates a statistically significant difference with other bars

Is correlation the same as causation

no, it is not. A low p-value can indicate correlation but not causation

Covalent bonds

type of strong chemical bond where two atoms share one/more pairs of valence electrons

electronegativity

measure of atoms attraction for shared electrons

nonpolar covalent bond

electrons are shared equally between 2 atoms of similar electronegativity

polar covalent bonds

atoms differ in electronegativity. Shared electrons are pulled closer to the more electronegative atom making it slightly negative and the other atom slightly positive

hydrogen bonds

weak chemical bond formed when a slightly positive hydrogen of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule   

polar molecules

molecule containing polar covalent bond and having an uneq1ual distribution of charges in different regions of the molecule

cohesion

water and water

adhesion 

attraction between two different molecules

heat temperature

thermal energy in transfer from one body of atter to another

protein

functional biological molecule consisting of one or more polypeptide folded into a specific 3D structure has its own specific shape

denaturation

where a protein unravels, can be because of pH, salt, or heat

amino acids

organic molecule containing a carboxyl group and an amino group; monomer of proteins

R- group

variable chemical group with one or more carbon atoms with various functional groups attached

hydrophobic

r groups nonpolar '“waterfearing”

hydrophilic

r groups polar and possibly charged “water loving”

peptide bond

covalent bond between 2 amino acid units in a polypeptide, formed by a dehydration reaction

polypeptide

a polymer of amino acids linked by peptide bonds

DNA

deoxyribonucleic acid, double helix, consist of nucleotide monomers with deoxyribose sugar and the nitrogenous bases adenine, guanine, thymine, and cytosine; can replicate

nucleic acids

polymer consisting of many nucleotides; blueprint for proteins DNA+RNA

RNA

ribonucleic acid type of nucleic acid with a ribose sugar and the nitrogenous bases A, C, G, and uracil, single stranded, protein synthesis, gene regulation

nucleotides

building block of nucleic acids, 5 carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups

gene expression 

genetic information flows from genes to proteins, the flow of genetic information from the genotype to the phenotypes

competitive inhibitor

if it fits, it sits

Reversible competitive inhibitor

can interact and detach as much as they want

irreversible enzyme competitive inhibitor

gets attached by covalent bond and never detatches

competitive reversible inhibitor

attaches at active site and blocks the substrate

noncompetitive reversible inhibitor

changes the shape of the active site reducing the ability to bind

energy transformation process

involves multiple reactions

increases efficiency of energy release

one single reaction uses big activation energy where as multiple smaller reactions is smaller activation energy but same energy released

provides more points of control

ATP

adenosine triphosphate, main energy currency in cells

ADP+Pi vs ATP free energy

ADP+Pi has lower free energy than ATP

Electron carriers

shuttles, molecules that allow transfer of electrons between other molecules

Oxidized

lost electrons, NAD+, ready to accept electrons

reduced

has electrons, NADPH, has electrons

glucose is the only energy source for WHAT

red blood cells

if enough O2 is present

glucose can be broken down to make the most amount of ATP

Phosphorylation

cells use released energy to power endergonic reactions by transferring the phosphate group to other molecules. Energizes the molecules and enables cellular work

chemical- driving synthesis of molecules

Transport- moving substances across a membrane

Mechanical- enabling movement

Photosynthesis

occurs in chloroplasts of plants, Alge, and some prokaryotes. Stores energy in chemical bonds of sugars. Source of O2 and food for most ecosystems

CO2+H2O+Sunlight → Organic molecules (glucose)+ O2

Cellular respiration

occurs in mitochondria of almost all eukaryotes (animals, plants, fungi, protists). Releases energy stored in food to power cellular work. ATP is the energy currency produced.

Glucose(breaks down organic molecular using)+O2 → CO2+H2O+ATP

exergonic reaction: releases O2

energy flows

one-way flow from the sun → photosynthesis → cellular respiration → heat

matter flows

recycled between processes (CO2+H2O < - > Sugars+O2)

Breathing

exchange of gases taking in O2 releasing CO2

Cellular respiration uses O2

to breakdown food molecules and produce ATP

Both cellular respiration and Breathing

O2 from breathing enters lungs → bloodstream → muscle cells

in muscle cells O2 used in cellular respiration to make ATP

Gas exchange summary

O2 inhaled → used in cells → becomes H2O

CO2 exhaled → comes from glucose, not the inhaled O2

BMR

basal metabolic rate 1,300-1,800kcal/day for basic life functioning

NAD+ 

electron carriers → accepts electrons → becomes NADH

Electron transport chain

• NADH delivers electrons to ETC (inner mitochondrial membrane)

• electrons passed through protein carriers → energy released → used to make ATP

• final electron acceptor is O2, which forms water

• O2 is essential because it is highly electronegative, making it effective at pulling electrons down the ETC to release energy

Cellular respiration definition and where it happens in

definition: converts chemical energy in food molecules into chemical energy in ATP

where it happens: mitochondria of nearly all eukaryotic cells

Stage: glycolysis

location: cytosol

function: splits glucose into 2 pyruvates

ATP yield: 2

Stage: pyruvate oxidation and citric acid cycle

location: mitochondria

function: completes glucose breakdown to CO2

ATP yield: 2

Stage: oxidative phoshorylation

location: inner mitochondrial membrane

function: uses electrons from NADH and FADH2 to make ATP via ETC and chemiosmosis

ATP yield: about 28

electron carriers

NADH and FADH2 deliver electrons to the ETC

final electron acceptor

O2 which reduces to H2O

glycolysis

splitting sugar, in cytosol, starts with 1 glucose (6 carbons), ends with 2 pyruvate (3 carbons each) involves 9 enzyme catalyzed reactions. 2NAD+ → 2NADH, net gain of 2 ATP via substrate level phosphorylation

fermentation

enables ATP production without O2. 2 ATP per glucose. Glucose → pyruvate. Reduces NAD+ → NADH

Problems with fermentation

NAD+ must be regenerated without the electron transport chain

solutions to problems in fermentation

fermentation recycles NADH→ NAD+ by converting pyruvates into other products

Lactic acid fermentation

muscle cells and certain bacteria

converts pyruvate → lactate regenerates NAD+

cheese yogurt soy

lactate is not the cause of muscle soreness, inflammation from microtrauma is more likely

alcohol fermentation

yeasts and some bacteria

converts pyruvate → CO2 and ethanol

regenerates NAD+

CO2 causes bread to rise and bubbles in beer and champagne

ethanol is toxic to yeast; they die when it reaches around 14%

pyruvate is metabolic fork

leads to fermentation/ aerobic respiration depending on O2 availability

glycolysis evolutionary significance

universal; found in nearly all organisms, anerobic, simple; happens in cytoplasm, predates atmospheric O2

Citric Acid Cycle- Pyruate Oxidation

each glucose → 2 pyruvate → 2 A=acetyl CoA

Steps per pyruvate.

• Decarboxylation- pyruvate loses 1 carbon → Co2

• Redox reaction- remaining 2 carbon fragments oxidized → NAD+ reduced to NADH

• formation of acetyl CoA- coenzyme A binds to the 2-carbon fragment

Per glucose

• 2 CO2 released

• 2 NADH produced

• 2 acetyl CoA formed

Citric Acid Cycle (Krebs Cycle)

each acetyl CoA enters the cycle once. Since glucose yields 2 acetyl CoA, the cycle runs twice per glucose

Per acetyl CoA

• 2 CO2, 1 ATP, 3 NADH, 1 FADH2

Double it for each glucose

For glycolysis, pyruvate oxidation and citric acid cycle: 

6 CO2

4 ATP

10 NADH

2 FADH2

per glucose at substate level

ETC- Oxidative phosphorylation- the ATP jackpot

electrons from NADH and FADH2 are passed down a series of protein complexes, O2 is the final O2 acceptor, forming H2O, energy from electrons flow pumps protons into the intermembrane space

chemiosmosis- Oxidative Phosphorylation- the ATP jackpot

H+ flows back through ATP synthase, driving the phosphorylation of ADP→ ATP, this process produces around 28 ATP per glucose

NO O2 MEANS FERMENTATION CHEMIOSMOSIS NEEDS O2

Chloroplasts: Solar energy to chemical energy

function: organelles in plants and Alge that perform photosynthesis. Convert light energy → chemical energy stored in sugar

Structure: outer and inner membrane with intermembrane space, stroma is a thick fluid inside the inner membrane with enzymes, ribosomes and chloroplast DNA. Thylakoids are interconnected sacs in the stroma, stacked in granum, inner compartment is the thylakoid space.

Photosynthesis site: thylakoid membrane contains chlorophyll molecules that trap solar energy. Act as the chloroplasts “solar power pack”

Photosynthesis powers most life on earth

energy source: Solar energy, chloroplasts capture sunlight convert → energy

Photosynthesis: CO2+H2O+light energy→ C6H12O6+O2

role of photoautotrophs

producers of biosphere, provide food, O2 and raw materials, support consumers, clothing (cotton), housing (wood), need light, CO2, H2O to make food

Photosynthesis occurs in chloroplast in plant cells

Location: all green parts of plants, mainly leaves

Chlorophyll: pigment that gives plants their green color, absorb light energy

Leaf structure and gas exchange: Mesophyll is the interior leaf tissue with lots of chloroplasts, stomata are pores for gas exchange CO2 enter and O2 exists, veins transport water from roots and sugars → other parts

Photosynthesis is a redox process: Photosynthesis vs cellular respiration

Photosynthesis: H2O is oxidized to O2, CO2 is reduced to sugar, electrons gain energy as they move from H2O → Co2, endergonic

Cellular respiration: Glucose is Oxidized to CO2, O2 is reduced to H2O, electrons loose energy as they move to O2, exergonic

Stage 1 Light Reactions (thylakoid membrane)

Light + H2O → O2 + ATP +ADPH

water is split → releases electrons and O2

Light energy excites electrons → transferred from NADP+ to NADPH

ATP is generated from ADP+Pi

Stage 2 Clavin Cycle (stroma) (light independent reactions)

CO2+ATP+NADPH → Sugar(G3P)

Carbon fixation: CO2 incorporated → organic compounds 

molecules reduced to form sugars

powered by ATP+NADPH from light reactions

doesn’t require light but depends on the light reactions

Photosystem capture solar energy

Energy transformation: light energy excites electrons in pigment molecules → electrons jump to higher energy levels, become unstable, releases energy by heat/light

Photosystems in chloroplasts: thylakoid membrane, light harvesting complexes: pigments bond to proteins that absorb light and transmit energy, reaction center complex: contains special chlorophyll A and a primary electron acceptor

PS2- functions first

PS1- functions 2nd, works together to convert light energy → chemical energy (ATP+NADPH)

2 Photosystems +ETC= ATP+NADPH

electron flow

1. photon excites electron in PS2→ primary electron acceptor

2. electron goes down ETC → release energy→ ATP produced

3. electron reaches PS1→ 2nd photon excites it → captured again

4. electron is used to reduce NADP+→ NADPH

Water splitting

• enzyme splits H2O→ 2 electrons + 2 H* + O atom

• O atoms combine → O2 (released via stomata)

• electrons replace lost in PS2

ATP Produced via chemiosmosis

• ETC pumps H+ into thylakoid space

• H+ gradient across the membrane

• H+ flows back through ATP synthase → ADP+Pi→ ATP

• Photophosphorylation

Visualizing the light reactions

Thylakoid membrane components: PS2, ECT, PS1, TP synthase

electrons and energy flow- light energy → excites electrons → passed from H2O → NADP energy from electrons → pumps H* → makes gradient H* flows through ATP synthase → ATP produced

The Calvin Cycle: Reducing CO2→ Sugar

CO2+ATP+NADPH→ G3P +3Carbon Sugar+Sucrose+Organics

1. Carbon fixation: enzyme rubisco attaches to CO2 to RuBP(5 carbon sugar), forms unstable 6 carbon → splits into 2 3 carbon molecules

2. Reduction: ATP+NADPH reduce 3 carbon molecules→ G3P

3. Release: for every 3 CO2 fixed→ 1 G3P exits the cycle

4. Regeneration: remaining G3P molecules rearranged → regenerate RuBP(requires ATP)

Energy cost: to make 1 G3P, uses 9 ATP+6NADPH. Glucose is highly reduced → requires significant energy and electrons to synthesize

Chromosomes

coiled DNA with proteins

Chromatin

when not dividing DNA and protein

nuclear envelope

double membrane, controls material flow in/out of nucleus, contains protein lined pores that regulate molecular traffic and connect the endoplasmic reticulum

An individual rabbit

a. can only have one allele for the FUZY gene.

b. has two alleles for the FUZY gene.

c. can have more than two alleles for the FUZY gene.

b. has two alleles for the FUZY gene.

The two alleles an individual rabbit has for the FUZY gene

a. are always the same.

b. are always different.

c. can be either the same or different.

c. can be either the same or different

Within a population of rabbits, can there be more than two different alleles for the FUZY gene?

No

Yes

Yes

Expression of the human gene NCR produces a protein that’s important for controlling cell division. A mutation in the NCR gene that increases the activity of the NCR protein has been linked to various types of cancer. Therefore, it’s reasonable to predict that the NCR protein __________ cell division.

promotes

inhibits

promotes

A diploid cell has twenty total chromosomes (pieces of DNA). Therefore, the cell has _____ pairs of homologous chromosomes prior to DNA replication, and _____ pairs of homologous chromosomes after DNA replication.

ten; twenty

twenty; twenty

ten; ten

twenty; forty

ten; ten

Homologous chromosomes _____________ genes; sister chromatids _____________ genes.

a. can have the same or different; always have the same

b. can have the same or different; can have the same or different

c. always have the same; can have the same or different

d. always have the same; always have the same

d. always have the same; always have the same

Homologous chromosomes _____________ alleles for a gene; sister chromatids _____________ alleles for a gene.

a. can have different; can have different

b. always have the same; can have different

c. can have different; always have the same

d. always have the same; always have the same

c. can have different; always have the same

In a human lung cell, a substitution mutation occurs in a gene on one chromosome; the other homologous chromosome is not affected by the mutation. This results in a lung cell with one mutated copy of the gene and one non-mutated copy of the gene. What will be found in the daughter cells when this cell divides by mitosis?

Hint - Think about the chromosomes present in a diploid cell and what you know about the process and products of mitosis.

a. both daughter cells will have two mutated copies of the gene

b. both daughter cells will have one mutated and one non-mutated copy of the gene

c. one daughter cell will have two mutated copies of the gene, and the other daughter cell will have two non-mutated copies of the gene

d. one daughter cell will have one mutated copy and one non-mutated copy of the gene, and the other daughter cell will have two non-mutated copies of the gene

b. both daughter cells will have one mutated and one non-mutated copy of the gene

The image below shows a pair of homologous chromosomes following DNA replication. Letters indicate individual pieces of DNA.

What letter pairs represent non-sister chromatids?

A and C

A and D

B and C

B and D

All of the above

All of the above

Non-sister chromatids

a. always have the same genes and the same alleles for each gene.

b. can have different genes.

c. always have the same genes, but can have the same or different alleles for each gene.

c. always have the same genes, but can have the same or different alleles for each gene.

Which of the following, if any, correctly describes a difference between prokaryotic and eukaryotic cells/organisms?

a. All prokaryotic cells are haploid; all eukaryotic cells are diploid.

b. Prokaryotic cells only divide by mitosis; eukaryotic cells only divide by meiosis.

c. Prokaryotes only reproduce asexually; eukaryotes only reproduce via sexual reproduction.

d. None of the above

d. None of the above

A diploid cell has twelve pairs of homologous chromosomes. How many individual chromosomes (pieces of DNA) will be copied during DNA replication?

six

twelve

twenty-four

forty-eight

twenty-four

Select ALL statements that correctly describe BOTH prokaryotic division and mitosis.

a. Nuclear envelope (membrane) breaks down.

b. Each copy of a chromosome generated by DNA replication is distributed to opposite ends of a dividing cell.

c. Produces two genetically identical daughter cells.

d. DNA is replicated once prior to division.

b. Each copy of a chromosome generated by DNA replication is distributed to opposite ends of a dividing cell.

c. Produces two genetically identical daughter cells.

d. DNA is replicated once prior to division.

Compare the purposes of cell division in prokaryotes and eukaryotes.

In Prokaryotes there is one circular chromosome and are not wound around proteins, there are no organelles, and there are ONLY single-celled organisms.

In Eukaryotes there are multiple linear chromosomes that are wrapped around proteins, the chromosomes are in the nucleus, and there are both single-celled and multiple celled organisms.